From af7bcfffa4e7390025ee87b4f11f78369401908d Mon Sep 17 00:00:00 2001 From: CI Date: Wed, 30 Apr 2025 07:01:27 +0000 Subject: [PATCH] Build branch main with version main (c733de2) Build pipeline: viash-hub.biobox.main-lltcw Source commit: https://github.com/viash-hub/biobox/commit/c733de2e4cc21eccb241060f82bce0b332f79d81 Source message: Bump viash to 0.9.4 (#175) * Bump viash to 0.9.4 * Add CHANGELOG entry * Add PR number --- CHANGELOG.md | 2 + _viash.yaml | 2 +- .../agat_convert_bed2gff/.config.vsh.yaml | 8 +- .../agat_convert_bed2gff/agat_convert_bed2gff | 6 +- .../agat_convert_embl2gff/.config.vsh.yaml | 8 +- .../agat_convert_embl2gff | 6 +- .../agat_convert_genscan2gff/.config.vsh.yaml | 8 +- .../agat_convert_genscan2gff | 6 +- .../agat_convert_mfannot2gff/.config.vsh.yaml | 8 +- .../agat_convert_mfannot2gff | 6 +- .../agat_convert_sp_gff2gtf/.config.vsh.yaml | 8 +- .../agat_convert_sp_gff2gtf | 6 +- .../agat_convert_sp_gff2tsv/.config.vsh.yaml | 8 +- .../agat_convert_sp_gff2tsv | 6 +- .../agat_convert_sp_gxf2gxf/.config.vsh.yaml | 8 +- .../agat_convert_sp_gxf2gxf | 6 +- .../agat/agat_sp_add_introns/.config.vsh.yaml | 8 +- .../agat_sp_add_introns/agat_sp_add_introns | 6 +- .../.config.vsh.yaml | 8 +- .../agat_sp_filter_feature_from_kill_list | 6 +- .../.config.vsh.yaml | 8 +- .../agat_sp_merge_annotations | 6 +- .../agat/agat_sp_statistics/.config.vsh.yaml | 8 +- .../agat_sp_statistics/agat_sp_statistics | 6 +- .../agat/agat_sq_stat_basic/.config.vsh.yaml | 8 +- .../agat_sq_stat_basic/agat_sq_stat_basic | 6 +- target/executable/arriba/.config.vsh.yaml | 8 +- target/executable/arriba/arriba | 6 +- .../executable/bases2fastq/.config.vsh.yaml | 8 +- target/executable/bases2fastq/bases2fastq | 6 +- .../bbmap/bbmap_bbsplit/.config.vsh.yaml | 8 +- .../bbmap/bbmap_bbsplit/bbmap_bbsplit | 6 +- .../bcftools_annotate/.config.vsh.yaml | 8 +- .../bcftools_annotate/bcftools_annotate | 6 +- .../bcftools/bcftools_concat/.config.vsh.yaml | 8 +- .../bcftools/bcftools_concat/bcftools_concat | 6 +- .../bcftools/bcftools_norm/.config.vsh.yaml | 8 +- .../bcftools/bcftools_norm/bcftools_norm | 6 +- .../bcftools/bcftools_sort/.config.vsh.yaml | 8 +- .../bcftools/bcftools_sort/bcftools_sort | 6 +- .../bcftools/bcftools_stats/.config.vsh.yaml | 8 +- .../bcftools/bcftools_stats/bcftools_stats | 6 +- .../executable/bcl_convert/.config.vsh.yaml | 8 +- target/executable/bcl_convert/bcl_convert | 6 +- .../.config.vsh.yaml | 8 +- .../bd_rhapsody_make_reference | 6 +- .../.config.vsh.yaml | 8 +- .../bd_rhapsody_sequence_analysis | 6 +- .../bedtools_bamtobed/.config.vsh.yaml | 8 +- .../bedtools_bamtobed/bedtools_bamtobed | 6 +- .../bedtools_bamtofastq/.config.vsh.yaml | 8 +- .../bedtools_bamtofastq/bedtools_bamtofastq | 6 +- .../bedtools_bed12tobed6/.config.vsh.yaml | 8 +- .../bedtools_bed12tobed6/bedtools_bed12tobed6 | 6 +- .../bedtools_bedtobam/.config.vsh.yaml | 8 +- .../bedtools_bedtobam/bedtools_bedtobam | 6 +- .../bedtools_genomecov/.config.vsh.yaml | 8 +- .../bedtools_genomecov/bedtools_genomecov | 6 +- .../bedtools_getfasta/.config.vsh.yaml | 8 +- .../bedtools_getfasta/bedtools_getfasta | 6 +- .../bedtools_groupby/.config.vsh.yaml | 8 +- .../bedtools_groupby/bedtools_groupby | 6 +- .../bedtools_intersect/.config.vsh.yaml | 8 +- .../bedtools_intersect/bedtools_intersect | 6 +- .../bedtools/bedtools_links/.config.vsh.yaml | 8 +- .../bedtools/bedtools_links/bedtools_links | 6 +- .../bedtools/bedtools_merge/.config.vsh.yaml | 8 +- .../bedtools/bedtools_merge/bedtools_merge | 6 +- .../bedtools/bedtools_sort/.config.vsh.yaml | 8 +- .../bedtools/bedtools_sort/bedtools_sort | 6 +- .../busco_download_datasets/.config.vsh.yaml | 8 +- .../busco_download_datasets | 6 +- .../busco_list_datasets/.config.vsh.yaml | 8 +- .../busco_list_datasets/busco_list_datasets | 6 +- .../busco/busco_run/.config.vsh.yaml | 8 +- target/executable/busco/busco_run/busco_run | 6 +- .../cellranger_mkref/.config.vsh.yaml | 8 +- .../cellranger_mkref/cellranger_mkref | 6 +- target/executable/cutadapt/.config.vsh.yaml | 8 +- target/executable/cutadapt/cutadapt | 6 +- target/executable/falco/.config.vsh.yaml | 8 +- target/executable/falco/falco | 6 +- target/executable/fastp/.config.vsh.yaml | 8 +- target/executable/fastp/fastp | 6 +- target/executable/fastqc/.config.vsh.yaml | 8 +- target/executable/fastqc/fastqc | 6 +- .../executable/featurecounts/.config.vsh.yaml | 8 +- target/executable/featurecounts/featurecounts | 6 +- .../executable/fq_subsample/.config.vsh.yaml | 8 +- target/executable/fq_subsample/fq_subsample | 6 +- target/executable/gffread/.config.vsh.yaml | 8 +- target/executable/gffread/gffread | 6 +- .../kallisto/kallisto_index/.config.vsh.yaml | 8 +- .../kallisto/kallisto_index/kallisto_index | 6 +- .../kallisto/kallisto_quant/.config.vsh.yaml | 8 +- .../kallisto/kallisto_quant/kallisto_quant | 6 +- .../lofreq/lofreq_call/.config.vsh.yaml | 8 +- .../executable/lofreq/lofreq_call/lofreq_call | 6 +- .../lofreq/lofreq_indelqual/.config.vsh.yaml | 8 +- .../lofreq/lofreq_indelqual/lofreq_indelqual | 6 +- target/executable/multiqc/.config.vsh.yaml | 8 +- target/executable/multiqc/multiqc | 6 +- target/executable/nanoplot/.config.vsh.yaml | 8 +- target/executable/nanoplot/nanoplot | 6 +- target/executable/pear/.config.vsh.yaml | 8 +- target/executable/pear/pear | 6 +- .../qualimap/qualimap_rnaseq/.config.vsh.yaml | 8 +- .../qualimap/qualimap_rnaseq/qualimap_rnaseq | 6 +- .../.config.vsh.yaml | 8 +- .../rsem_calculate_expression | 6 +- .../rsem_prepare_reference/.config.vsh.yaml | 8 +- .../rsem_prepare_reference | 6 +- .../rseqc/rseqc_bamstat/.config.vsh.yaml | 8 +- .../rseqc/rseqc_bamstat/rseqc_bamstat | 6 +- .../rseqc_inferexperiment/.config.vsh.yaml | 8 +- .../rseqc_inferexperiment | 6 +- .../rseqc_inner_distance/.config.vsh.yaml | 8 +- .../rseqc_inner_distance/rseqc_inner_distance | 6 +- .../salmon/salmon_index/.config.vsh.yaml | 8 +- .../salmon/salmon_index/salmon_index | 6 +- .../salmon/salmon_quant/.config.vsh.yaml | 8 +- .../salmon/salmon_quant/salmon_quant | 6 +- .../samtools_collate/.config.vsh.yaml | 8 +- .../samtools_collate/samtools_collate | 6 +- .../samtools/samtools_faidx/.config.vsh.yaml | 8 +- .../samtools/samtools_faidx/samtools_faidx | 6 +- .../samtools/samtools_fasta/.config.vsh.yaml | 8 +- .../samtools/samtools_fasta/samtools_fasta | 6 +- .../samtools/samtools_fastq/.config.vsh.yaml | 8 +- .../samtools/samtools_fastq/samtools_fastq | 6 +- .../samtools_flagstat/.config.vsh.yaml | 8 +- .../samtools_flagstat/samtools_flagstat | 6 +- .../samtools_idxstats/.config.vsh.yaml | 8 +- .../samtools_idxstats/samtools_idxstats | 6 +- .../samtools/samtools_index/.config.vsh.yaml | 8 +- .../samtools/samtools_index/samtools_index | 6 +- .../samtools/samtools_sort/.config.vsh.yaml | 8 +- .../samtools/samtools_sort/samtools_sort | 6 +- .../samtools/samtools_stats/.config.vsh.yaml | 8 +- .../samtools/samtools_stats/samtools_stats | 6 +- .../samtools/samtools_view/.config.vsh.yaml | 8 +- .../samtools/samtools_view/samtools_view | 6 +- .../seqtk/seqtk_sample/.config.vsh.yaml | 8 +- .../seqtk/seqtk_sample/seqtk_sample | 6 +- .../seqtk/seqtk_subseq/.config.vsh.yaml | 8 +- .../seqtk/seqtk_subseq/seqtk_subseq | 6 +- target/executable/sgdemux/.config.vsh.yaml | 8 +- target/executable/sgdemux/sgdemux | 6 +- target/executable/snpeff/.config.vsh.yaml | 8 +- target/executable/snpeff/snpeff | 6 +- target/executable/sortmerna/.config.vsh.yaml | 8 +- target/executable/sortmerna/sortmerna | 6 +- .../star/star_align_reads/.config.vsh.yaml | 8 +- .../star/star_align_reads/star_align_reads | 6 +- .../star_genome_generate/.config.vsh.yaml | 8 +- .../star_genome_generate/star_genome_generate | 6 +- target/executable/trimgalore/.config.vsh.yaml | 8 +- target/executable/trimgalore/trimgalore | 6 +- .../umi_tools_dedup/.config.vsh.yaml | 8 +- .../umi_tools/umi_tools_dedup/umi_tools_dedup | 6 +- .../umi_tools_extract/.config.vsh.yaml | 8 +- .../umi_tools_extract/umi_tools_extract | 6 +- .../umi_tools_prepareforrsem/.config.vsh.yaml | 8 +- .../umi_tools_prepareforrsem | 6 +- .../agat_convert_bed2gff/.config.vsh.yaml | 8 +- .../agat/agat_convert_bed2gff/main.nf | 98 ++++++++++------- .../agat_convert_embl2gff/.config.vsh.yaml | 8 +- .../agat/agat_convert_embl2gff/main.nf | 98 ++++++++++------- .../agat_convert_genscan2gff/.config.vsh.yaml | 8 +- .../agat/agat_convert_genscan2gff/main.nf | 98 ++++++++++------- .../agat_convert_mfannot2gff/.config.vsh.yaml | 8 +- .../agat/agat_convert_mfannot2gff/main.nf | 98 ++++++++++------- .../agat_convert_sp_gff2gtf/.config.vsh.yaml | 8 +- .../agat/agat_convert_sp_gff2gtf/main.nf | 98 ++++++++++------- .../agat_convert_sp_gff2tsv/.config.vsh.yaml | 8 +- .../agat/agat_convert_sp_gff2tsv/main.nf | 98 ++++++++++------- .../agat_convert_sp_gxf2gxf/.config.vsh.yaml | 8 +- .../agat/agat_convert_sp_gxf2gxf/main.nf | 98 ++++++++++------- .../agat/agat_sp_add_introns/.config.vsh.yaml | 8 +- .../nextflow/agat/agat_sp_add_introns/main.nf | 98 ++++++++++------- .../.config.vsh.yaml | 8 +- .../main.nf | 98 ++++++++++------- .../nextflow_schema.json | 6 +- .../.config.vsh.yaml | 8 +- .../agat/agat_sp_merge_annotations/main.nf | 98 ++++++++++------- .../agat/agat_sp_statistics/.config.vsh.yaml | 8 +- .../nextflow/agat/agat_sp_statistics/main.nf | 98 ++++++++++------- .../agat/agat_sq_stat_basic/.config.vsh.yaml | 8 +- .../nextflow/agat/agat_sq_stat_basic/main.nf | 98 ++++++++++------- target/nextflow/arriba/.config.vsh.yaml | 8 +- target/nextflow/arriba/main.nf | 98 ++++++++++------- target/nextflow/bases2fastq/.config.vsh.yaml | 8 +- target/nextflow/bases2fastq/main.nf | 98 ++++++++++------- .../nextflow/bases2fastq/nextflow_schema.json | 18 ++-- .../bbmap/bbmap_bbsplit/.config.vsh.yaml | 8 +- target/nextflow/bbmap/bbmap_bbsplit/main.nf | 98 ++++++++++------- .../bbmap/bbmap_bbsplit/nextflow_schema.json | 6 +- .../bcftools_annotate/.config.vsh.yaml | 8 +- .../bcftools/bcftools_annotate/main.nf | 98 ++++++++++------- .../bcftools_annotate/nextflow_schema.json | 6 +- .../bcftools/bcftools_concat/.config.vsh.yaml | 8 +- .../nextflow/bcftools/bcftools_concat/main.nf | 98 ++++++++++------- .../bcftools_concat/nextflow_schema.json | 6 +- .../bcftools/bcftools_norm/.config.vsh.yaml | 8 +- .../nextflow/bcftools/bcftools_norm/main.nf | 98 ++++++++++------- .../bcftools_norm/nextflow_schema.json | 6 +- .../bcftools/bcftools_sort/.config.vsh.yaml | 8 +- .../nextflow/bcftools/bcftools_sort/main.nf | 98 ++++++++++------- .../bcftools_sort/nextflow_schema.json | 6 +- .../bcftools/bcftools_stats/.config.vsh.yaml | 8 +- .../nextflow/bcftools/bcftools_stats/main.nf | 98 ++++++++++------- .../bcftools_stats/nextflow_schema.json | 6 +- target/nextflow/bcl_convert/.config.vsh.yaml | 8 +- target/nextflow/bcl_convert/main.nf | 98 ++++++++++------- .../nextflow/bcl_convert/nextflow_schema.json | 18 ++-- .../.config.vsh.yaml | 8 +- .../bd_rhapsody_make_reference/main.nf | 100 ++++++++++-------- .../.config.vsh.yaml | 8 +- .../bd_rhapsody_sequence_analysis/main.nf | 100 ++++++++++-------- .../nextflow_schema.json | 6 +- .../bedtools_bamtobed/.config.vsh.yaml | 8 +- .../bedtools/bedtools_bamtobed/main.nf | 98 ++++++++++------- .../bedtools_bamtobed/nextflow_schema.json | 6 +- .../bedtools_bamtofastq/.config.vsh.yaml | 8 +- .../bedtools/bedtools_bamtofastq/main.nf | 98 ++++++++++------- .../bedtools_bamtofastq/nextflow_schema.json | 12 +-- .../bedtools_bed12tobed6/.config.vsh.yaml | 8 +- .../bedtools/bedtools_bed12tobed6/main.nf | 98 ++++++++++------- .../bedtools_bed12tobed6/nextflow_schema.json | 6 +- .../bedtools_bedtobam/.config.vsh.yaml | 8 +- .../bedtools/bedtools_bedtobam/main.nf | 98 ++++++++++------- .../bedtools_bedtobam/nextflow_schema.json | 6 +- .../bedtools_genomecov/.config.vsh.yaml | 8 +- .../bedtools/bedtools_genomecov/main.nf | 98 ++++++++++------- .../bedtools_getfasta/.config.vsh.yaml | 8 +- .../bedtools/bedtools_getfasta/main.nf | 98 ++++++++++------- .../bedtools_getfasta/nextflow_schema.json | 6 +- .../bedtools_groupby/.config.vsh.yaml | 8 +- .../bedtools/bedtools_groupby/main.nf | 98 ++++++++++------- .../bedtools_intersect/.config.vsh.yaml | 8 +- .../bedtools/bedtools_intersect/main.nf | 98 ++++++++++------- .../bedtools/bedtools_links/.config.vsh.yaml | 8 +- .../nextflow/bedtools/bedtools_links/main.nf | 98 ++++++++++------- .../bedtools_links/nextflow_schema.json | 6 +- .../bedtools/bedtools_merge/.config.vsh.yaml | 8 +- .../nextflow/bedtools/bedtools_merge/main.nf | 98 ++++++++++------- .../bedtools_merge/nextflow_schema.json | 6 +- .../bedtools/bedtools_sort/.config.vsh.yaml | 8 +- .../nextflow/bedtools/bedtools_sort/main.nf | 98 ++++++++++------- .../bedtools_sort/nextflow_schema.json | 6 +- .../busco_download_datasets/.config.vsh.yaml | 8 +- .../busco/busco_download_datasets/main.nf | 98 ++++++++++------- .../nextflow_schema.json | 6 +- .../busco_list_datasets/.config.vsh.yaml | 8 +- .../busco/busco_list_datasets/main.nf | 98 ++++++++++------- .../busco_list_datasets/nextflow_schema.json | 6 +- .../nextflow/busco/busco_run/.config.vsh.yaml | 8 +- target/nextflow/busco/busco_run/main.nf | 98 ++++++++++------- .../busco/busco_run/nextflow_schema.json | 6 +- .../cellranger_mkref/.config.vsh.yaml | 8 +- .../cellranger/cellranger_mkref/main.nf | 98 ++++++++++------- .../cellranger_mkref/nextflow_schema.json | 6 +- target/nextflow/cutadapt/.config.vsh.yaml | 8 +- target/nextflow/cutadapt/main.nf | 98 ++++++++++------- target/nextflow/falco/.config.vsh.yaml | 8 +- target/nextflow/falco/main.nf | 98 ++++++++++------- target/nextflow/falco/nextflow_schema.json | 24 ++--- target/nextflow/fastp/.config.vsh.yaml | 8 +- target/nextflow/fastp/main.nf | 98 ++++++++++------- target/nextflow/fastp/nextflow_schema.json | 6 +- target/nextflow/fastqc/.config.vsh.yaml | 8 +- target/nextflow/fastqc/main.nf | 98 ++++++++++------- .../nextflow/featurecounts/.config.vsh.yaml | 8 +- target/nextflow/featurecounts/main.nf | 98 ++++++++++------- .../featurecounts/nextflow_schema.json | 6 +- target/nextflow/fq_subsample/.config.vsh.yaml | 8 +- target/nextflow/fq_subsample/main.nf | 98 ++++++++++------- .../fq_subsample/nextflow_schema.json | 12 +-- target/nextflow/gffread/.config.vsh.yaml | 8 +- target/nextflow/gffread/main.nf | 98 ++++++++++------- .../kallisto/kallisto_index/.config.vsh.yaml | 8 +- .../nextflow/kallisto/kallisto_index/main.nf | 98 ++++++++++------- .../kallisto_index/nextflow_schema.json | 6 +- .../kallisto/kallisto_quant/.config.vsh.yaml | 8 +- .../nextflow/kallisto/kallisto_quant/main.nf | 98 ++++++++++------- .../kallisto_quant/nextflow_schema.json | 12 +-- .../lofreq/lofreq_call/.config.vsh.yaml | 8 +- target/nextflow/lofreq/lofreq_call/main.nf | 98 ++++++++++------- .../lofreq/lofreq_indelqual/.config.vsh.yaml | 8 +- .../nextflow/lofreq/lofreq_indelqual/main.nf | 98 ++++++++++------- target/nextflow/multiqc/.config.vsh.yaml | 8 +- target/nextflow/multiqc/main.nf | 98 ++++++++++------- target/nextflow/multiqc/nextflow_schema.json | 12 +-- target/nextflow/nanoplot/.config.vsh.yaml | 8 +- target/nextflow/nanoplot/main.nf | 98 ++++++++++------- target/nextflow/nanoplot/nextflow_schema.json | 6 +- target/nextflow/pear/.config.vsh.yaml | 8 +- target/nextflow/pear/main.nf | 98 ++++++++++------- target/nextflow/pear/nextflow_schema.json | 24 ++--- .../qualimap/qualimap_rnaseq/.config.vsh.yaml | 8 +- .../nextflow/qualimap/qualimap_rnaseq/main.nf | 98 ++++++++++------- .../qualimap_rnaseq/nextflow_schema.json | 6 +- .../.config.vsh.yaml | 8 +- .../rsem/rsem_calculate_expression/main.nf | 98 ++++++++++------- .../rsem_prepare_reference/.config.vsh.yaml | 8 +- .../rsem/rsem_prepare_reference/main.nf | 98 ++++++++++------- .../nextflow_schema.json | 6 +- .../rseqc/rseqc_bamstat/.config.vsh.yaml | 8 +- target/nextflow/rseqc/rseqc_bamstat/main.nf | 98 ++++++++++------- .../rseqc/rseqc_bamstat/nextflow_schema.json | 6 +- .../rseqc_inferexperiment/.config.vsh.yaml | 8 +- .../rseqc/rseqc_inferexperiment/main.nf | 98 ++++++++++------- .../rseqc_inner_distance/.config.vsh.yaml | 8 +- .../rseqc/rseqc_inner_distance/main.nf | 98 ++++++++++------- .../rseqc_inner_distance/nextflow_schema.json | 30 +++--- .../salmon/salmon_index/.config.vsh.yaml | 8 +- target/nextflow/salmon/salmon_index/main.nf | 98 ++++++++++------- .../salmon/salmon_index/nextflow_schema.json | 6 +- .../salmon/salmon_quant/.config.vsh.yaml | 8 +- target/nextflow/salmon/salmon_quant/main.nf | 98 ++++++++++------- .../salmon/salmon_quant/nextflow_schema.json | 12 +-- .../samtools_collate/.config.vsh.yaml | 8 +- .../samtools/samtools_collate/main.nf | 98 ++++++++++------- .../samtools_collate/nextflow_schema.json | 6 +- .../samtools/samtools_faidx/.config.vsh.yaml | 8 +- .../nextflow/samtools/samtools_faidx/main.nf | 98 ++++++++++------- .../samtools/samtools_fasta/.config.vsh.yaml | 8 +- .../nextflow/samtools/samtools_fasta/main.nf | 98 ++++++++++------- .../samtools_fasta/nextflow_schema.json | 30 +++--- .../samtools/samtools_fastq/.config.vsh.yaml | 8 +- .../nextflow/samtools/samtools_fastq/main.nf | 98 ++++++++++------- .../samtools_fastq/nextflow_schema.json | 30 +++--- .../samtools_flagstat/.config.vsh.yaml | 8 +- .../samtools/samtools_flagstat/main.nf | 98 ++++++++++------- .../samtools_idxstats/.config.vsh.yaml | 8 +- .../samtools/samtools_idxstats/main.nf | 98 ++++++++++------- .../samtools/samtools_index/.config.vsh.yaml | 8 +- .../nextflow/samtools/samtools_index/main.nf | 98 ++++++++++------- .../samtools/samtools_sort/.config.vsh.yaml | 8 +- .../nextflow/samtools/samtools_sort/main.nf | 98 ++++++++++------- .../samtools/samtools_stats/.config.vsh.yaml | 8 +- .../nextflow/samtools/samtools_stats/main.nf | 98 ++++++++++------- .../samtools/samtools_view/.config.vsh.yaml | 8 +- .../nextflow/samtools/samtools_view/main.nf | 98 ++++++++++------- .../seqtk/seqtk_sample/.config.vsh.yaml | 8 +- target/nextflow/seqtk/seqtk_sample/main.nf | 98 ++++++++++------- .../seqtk/seqtk_sample/nextflow_schema.json | 6 +- .../seqtk/seqtk_subseq/.config.vsh.yaml | 8 +- target/nextflow/seqtk/seqtk_subseq/main.nf | 98 ++++++++++------- .../seqtk/seqtk_subseq/nextflow_schema.json | 6 +- target/nextflow/sgdemux/.config.vsh.yaml | 8 +- target/nextflow/sgdemux/main.nf | 98 ++++++++++------- target/nextflow/sgdemux/nextflow_schema.json | 6 +- target/nextflow/snpeff/.config.vsh.yaml | 8 +- target/nextflow/snpeff/main.nf | 98 ++++++++++------- target/nextflow/snpeff/nextflow_schema.json | 12 +-- target/nextflow/sortmerna/.config.vsh.yaml | 8 +- target/nextflow/sortmerna/main.nf | 98 ++++++++++------- .../nextflow/sortmerna/nextflow_schema.json | 12 +-- .../star/star_align_reads/.config.vsh.yaml | 8 +- target/nextflow/star/star_align_reads/main.nf | 100 ++++++++++-------- .../star_genome_generate/.config.vsh.yaml | 8 +- .../star/star_genome_generate/main.nf | 98 ++++++++++------- .../star_genome_generate/nextflow_schema.json | 6 +- target/nextflow/trimgalore/.config.vsh.yaml | 8 +- target/nextflow/trimgalore/main.nf | 98 ++++++++++------- .../nextflow/trimgalore/nextflow_schema.json | 6 +- .../umi_tools_dedup/.config.vsh.yaml | 8 +- .../umi_tools/umi_tools_dedup/main.nf | 98 ++++++++++------- .../umi_tools_dedup/nextflow_schema.json | 6 +- .../umi_tools_extract/.config.vsh.yaml | 8 +- .../umi_tools/umi_tools_extract/main.nf | 98 ++++++++++------- .../umi_tools_extract/nextflow_schema.json | 30 +++--- .../umi_tools_prepareforrsem/.config.vsh.yaml | 8 +- .../umi_tools_prepareforrsem/main.nf | 98 ++++++++++------- .../nextflow_schema.json | 12 +-- 376 files changed, 5766 insertions(+), 4468 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c91ab764..6bcd4cba 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,8 @@ * Replace the deprecated use of the meta variable `functionality_name` by just `name` (PR #174). +* Bump viash to `0.9.4` (PR #175). + # biobox 0.3.0 ## NEW FUNCTIONALITY diff --git a/_viash.yaml b/_viash.yaml index 2fec1f37..dd8e733a 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -7,7 +7,7 @@ links: issue_tracker: https://github.com/viash-hub/biobox/issues repository: https://github.com/viash-hub/biobox -viash_version: 0.9.2 +viash_version: 0.9.4 config_mods: | .requirements.commands := ['ps'] diff --git a/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml b/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml index 4007a6d6..285a9d9a 100644 --- a/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml @@ -237,16 +237,16 @@ build_info: engine: "docker|native" output: "target/executable/agat/agat_convert_bed2gff" executable: "target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff b/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff index aa0e9f00..9ecbf8d2 100755 --- a/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff +++ b/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff @@ -2,7 +2,7 @@ # agat_convert_bed2gff main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_bed2gff" -LABEL org.opencontainers.image.created="2025-04-22T08:55:22Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:47Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml b/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml index d4a09725..8ecb896e 100644 --- a/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml @@ -227,16 +227,16 @@ build_info: engine: "docker|native" output: "target/executable/agat/agat_convert_embl2gff" executable: "target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff b/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff index 0b5025ee..24b1fbc8 100755 --- a/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff +++ b/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff @@ -2,7 +2,7 @@ # agat_convert_embl2gff main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_embl2gff" -LABEL org.opencontainers.image.created="2025-04-22T08:55:23Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:48Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/agat/agat_convert_genscan2gff/.config.vsh.yaml b/target/executable/agat/agat_convert_genscan2gff/.config.vsh.yaml index e1f3014c..9f14aef8 100644 --- a/target/executable/agat/agat_convert_genscan2gff/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_genscan2gff/.config.vsh.yaml @@ -232,16 +232,16 @@ build_info: engine: "docker|native" output: "target/executable/agat/agat_convert_genscan2gff" executable: "target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff b/target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff index 2a047c7f..0ab7b058 100755 --- a/target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff +++ b/target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff @@ -2,7 +2,7 @@ # agat_convert_genscan2gff main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_genscan2gff" -LABEL org.opencontainers.image.created="2025-04-22T08:55:22Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:47Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/agat/agat_convert_mfannot2gff/.config.vsh.yaml b/target/executable/agat/agat_convert_mfannot2gff/.config.vsh.yaml index 26cca4a0..302ca5ee 100644 --- a/target/executable/agat/agat_convert_mfannot2gff/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_mfannot2gff/.config.vsh.yaml @@ -188,16 +188,16 @@ build_info: engine: "docker|native" output: "target/executable/agat/agat_convert_mfannot2gff" executable: "target/executable/agat/agat_convert_mfannot2gff/agat_convert_mfannot2gff" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/agat/agat_convert_mfannot2gff/agat_convert_mfannot2gff b/target/executable/agat/agat_convert_mfannot2gff/agat_convert_mfannot2gff index cf92d3e2..e103d8d1 100755 --- a/target/executable/agat/agat_convert_mfannot2gff/agat_convert_mfannot2gff +++ b/target/executable/agat/agat_convert_mfannot2gff/agat_convert_mfannot2gff @@ -2,7 +2,7 @@ # agat_convert_mfannot2gff main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_mfannot2gff" -LABEL org.opencontainers.image.created="2025-04-22T08:55:23Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:47Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml b/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml index 234b0f36..b4d434a7 100644 --- a/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml @@ -230,16 +230,16 @@ build_info: engine: "docker|native" output: "target/executable/agat/agat_convert_sp_gff2gtf" executable: "target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf b/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf index b149c2b1..9021dcdf 100755 --- a/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf +++ b/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf @@ -2,7 +2,7 @@ # agat_convert_sp_gff2gtf main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gff2gtf" -LABEL org.opencontainers.image.created="2025-04-22T08:55:21Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:46Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml b/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml index c221a85b..b2ff2516 100644 --- a/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml @@ -190,16 +190,16 @@ build_info: engine: "docker|native" output: "target/executable/agat/agat_convert_sp_gff2tsv" executable: "target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv b/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv index c7198955..10563312 100755 --- a/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv +++ b/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv @@ -2,7 +2,7 @@ # agat_convert_sp_gff2tsv main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gff2tsv" -LABEL org.opencontainers.image.created="2025-04-22T08:55:22Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:46Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml b/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml index eb10f4cd..76011b72 100644 --- a/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml @@ -197,16 +197,16 @@ build_info: engine: "docker|native" output: "target/executable/agat/agat_convert_sp_gxf2gxf" executable: "target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf b/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf index 9f1f8bf2..9e6d23c4 100755 --- a/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf +++ b/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf @@ -2,7 +2,7 @@ # agat_convert_sp_gxf2gxf main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gxf2gxf" -LABEL org.opencontainers.image.created="2025-04-22T08:55:24Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:48Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/agat/agat_sp_add_introns/.config.vsh.yaml b/target/executable/agat/agat_sp_add_introns/.config.vsh.yaml index f946317b..69469311 100644 --- a/target/executable/agat/agat_sp_add_introns/.config.vsh.yaml +++ b/target/executable/agat/agat_sp_add_introns/.config.vsh.yaml @@ -188,16 +188,16 @@ build_info: engine: "docker|native" output: "target/executable/agat/agat_sp_add_introns" executable: "target/executable/agat/agat_sp_add_introns/agat_sp_add_introns" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/agat/agat_sp_add_introns/agat_sp_add_introns b/target/executable/agat/agat_sp_add_introns/agat_sp_add_introns index 0ef2268a..59e169c3 100755 --- a/target/executable/agat/agat_sp_add_introns/agat_sp_add_introns +++ b/target/executable/agat/agat_sp_add_introns/agat_sp_add_introns @@ -2,7 +2,7 @@ # agat_sp_add_introns main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_sp_add_introns" -LABEL org.opencontainers.image.created="2025-04-22T08:55:21Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:46Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml b/target/executable/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml index 0c32cb66..5fb3affb 100644 --- a/target/executable/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml +++ b/target/executable/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml @@ -238,16 +238,16 @@ build_info: engine: "docker|native" output: "target/executable/agat/agat_sp_filter_feature_from_kill_list" executable: "target/executable/agat/agat_sp_filter_feature_from_kill_list/agat_sp_filter_feature_from_kill_list" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/agat/agat_sp_filter_feature_from_kill_list/agat_sp_filter_feature_from_kill_list b/target/executable/agat/agat_sp_filter_feature_from_kill_list/agat_sp_filter_feature_from_kill_list index e8b73a4c..3d281f48 100755 --- a/target/executable/agat/agat_sp_filter_feature_from_kill_list/agat_sp_filter_feature_from_kill_list +++ b/target/executable/agat/agat_sp_filter_feature_from_kill_list/agat_sp_filter_feature_from_kill_list @@ -2,7 +2,7 @@ # agat_sp_filter_feature_from_kill_list main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_sp_filter_feature_from_kill_list" -LABEL org.opencontainers.image.created="2025-04-22T08:55:22Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:47Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/agat/agat_sp_merge_annotations/.config.vsh.yaml b/target/executable/agat/agat_sp_merge_annotations/.config.vsh.yaml index 246e6fef..946b8dec 100644 --- a/target/executable/agat/agat_sp_merge_annotations/.config.vsh.yaml +++ b/target/executable/agat/agat_sp_merge_annotations/.config.vsh.yaml @@ -186,16 +186,16 @@ build_info: engine: "docker|native" output: "target/executable/agat/agat_sp_merge_annotations" executable: "target/executable/agat/agat_sp_merge_annotations/agat_sp_merge_annotations" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/agat/agat_sp_merge_annotations/agat_sp_merge_annotations b/target/executable/agat/agat_sp_merge_annotations/agat_sp_merge_annotations index a4181acf..36cf0051 100755 --- a/target/executable/agat/agat_sp_merge_annotations/agat_sp_merge_annotations +++ b/target/executable/agat/agat_sp_merge_annotations/agat_sp_merge_annotations @@ -2,7 +2,7 @@ # agat_sp_merge_annotations main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_sp_merge_annotations" -LABEL org.opencontainers.image.created="2025-04-22T08:55:23Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:48Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/agat/agat_sp_statistics/.config.vsh.yaml b/target/executable/agat/agat_sp_statistics/.config.vsh.yaml index bed7284f..d549f5b3 100644 --- a/target/executable/agat/agat_sp_statistics/.config.vsh.yaml +++ b/target/executable/agat/agat_sp_statistics/.config.vsh.yaml @@ -233,16 +233,16 @@ build_info: engine: "docker|native" output: "target/executable/agat/agat_sp_statistics" executable: "target/executable/agat/agat_sp_statistics/agat_sp_statistics" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/agat/agat_sp_statistics/agat_sp_statistics b/target/executable/agat/agat_sp_statistics/agat_sp_statistics index 30fc9004..a875dc25 100755 --- a/target/executable/agat/agat_sp_statistics/agat_sp_statistics +++ b/target/executable/agat/agat_sp_statistics/agat_sp_statistics @@ -2,7 +2,7 @@ # agat_sp_statistics main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -452,9 +452,9 @@ RUN agat --version | sed 's/.*v\.//; s/\s.*//' | sed 's/^/AGAT: /' > /var/softwa LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_sp_statistics" -LABEL org.opencontainers.image.created="2025-04-22T08:55:23Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:48Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/agat/agat_sq_stat_basic/.config.vsh.yaml b/target/executable/agat/agat_sq_stat_basic/.config.vsh.yaml index 08ede155..6aa98a8e 100644 --- a/target/executable/agat/agat_sq_stat_basic/.config.vsh.yaml +++ b/target/executable/agat/agat_sq_stat_basic/.config.vsh.yaml @@ -229,16 +229,16 @@ build_info: engine: "docker|native" output: "target/executable/agat/agat_sq_stat_basic" executable: "target/executable/agat/agat_sq_stat_basic/agat_sq_stat_basic" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/agat/agat_sq_stat_basic/agat_sq_stat_basic b/target/executable/agat/agat_sq_stat_basic/agat_sq_stat_basic index 83fcd21c..601d5813 100755 --- a/target/executable/agat/agat_sq_stat_basic/agat_sq_stat_basic +++ b/target/executable/agat/agat_sq_stat_basic/agat_sq_stat_basic @@ -2,7 +2,7 @@ # agat_sq_stat_basic main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_sq_stat_basic" -LABEL org.opencontainers.image.created="2025-04-22T08:55:21Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:46Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/arriba/.config.vsh.yaml b/target/executable/arriba/.config.vsh.yaml index 5aedf8ef..2a756193 100644 --- a/target/executable/arriba/.config.vsh.yaml +++ b/target/executable/arriba/.config.vsh.yaml @@ -708,16 +708,16 @@ build_info: engine: "docker|native" output: "target/executable/arriba" executable: "target/executable/arriba/arriba" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/arriba/arriba b/target/executable/arriba/arriba index e1c39f13..d472f969 100755 --- a/target/executable/arriba/arriba +++ b/target/executable/arriba/arriba @@ -2,7 +2,7 @@ # arriba main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -452,9 +452,9 @@ RUN arriba -h | grep 'Version:' 2>&1 | sed 's/Version:\s\(.*\)/arriba: "\1"/' > LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component arriba" -LABEL org.opencontainers.image.created="2025-04-22T08:55:25Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:49Z" LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bases2fastq/.config.vsh.yaml b/target/executable/bases2fastq/.config.vsh.yaml index d9e33b79..e9ad29f1 100644 --- a/target/executable/bases2fastq/.config.vsh.yaml +++ b/target/executable/bases2fastq/.config.vsh.yaml @@ -396,16 +396,16 @@ build_info: engine: "docker|native" output: "target/executable/bases2fastq" executable: "target/executable/bases2fastq/bases2fastq" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/bases2fastq/bases2fastq b/target/executable/bases2fastq/bases2fastq index 2108ab57..c82a2207 100755 --- a/target/executable/bases2fastq/bases2fastq +++ b/target/executable/bases2fastq/bases2fastq @@ -2,7 +2,7 @@ # bases2fastq main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -456,9 +456,9 @@ RUN echo "bases2fastq: $(bases2fastq --version | cut -d' ' -f3)" > /var/software LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component bases2fastq" -LABEL org.opencontainers.image.created="2025-04-22T08:55:21Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:46Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bbmap/bbmap_bbsplit/.config.vsh.yaml b/target/executable/bbmap/bbmap_bbsplit/.config.vsh.yaml index a9fd7d02..5502e483 100644 --- a/target/executable/bbmap/bbmap_bbsplit/.config.vsh.yaml +++ b/target/executable/bbmap/bbmap_bbsplit/.config.vsh.yaml @@ -370,16 +370,16 @@ build_info: engine: "docker|native" output: "target/executable/bbmap/bbmap_bbsplit" executable: "target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit b/target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit index 4b90993d..15ba4b38 100755 --- a/target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit +++ b/target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit @@ -2,7 +2,7 @@ # bbmap_bbsplit main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -454,9 +454,9 @@ cp -r bbmap/* /usr/local/bin RUN bbsplit.sh --version 2>&1 | awk '/BBMap version/{print "BBMAP:", $NF}' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component bbmap bbmap_bbsplit" -LABEL org.opencontainers.image.created="2025-04-22T08:55:18Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:43Z" LABEL org.opencontainers.image.source="https://github.com/BioInfoTools/BBMap/blob/master/sh/bbsplit.sh" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml b/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml index 44168493..3e6f4df9 100644 --- a/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml +++ b/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml @@ -471,16 +471,16 @@ build_info: engine: "docker|native" output: "target/executable/bcftools/bcftools_annotate" executable: "target/executable/bcftools/bcftools_annotate/bcftools_annotate" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/bcftools/bcftools_annotate/bcftools_annotate b/target/executable/bcftools/bcftools_annotate/bcftools_annotate index e4f79d15..181fa287 100755 --- a/target/executable/bcftools/bcftools_annotate/bcftools_annotate +++ b/target/executable/bcftools/bcftools_annotate/bcftools_annotate @@ -2,7 +2,7 @@ # bcftools_annotate main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -456,9 +456,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_annotate" -LABEL org.opencontainers.image.created="2025-04-22T08:55:17Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:43Z" LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bcftools/bcftools_concat/.config.vsh.yaml b/target/executable/bcftools/bcftools_concat/.config.vsh.yaml index f76abd47..5890d16d 100644 --- a/target/executable/bcftools/bcftools_concat/.config.vsh.yaml +++ b/target/executable/bcftools/bcftools_concat/.config.vsh.yaml @@ -337,16 +337,16 @@ build_info: engine: "docker|native" output: "target/executable/bcftools/bcftools_concat" executable: "target/executable/bcftools/bcftools_concat/bcftools_concat" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/bcftools/bcftools_concat/bcftools_concat b/target/executable/bcftools/bcftools_concat/bcftools_concat index 51960234..3c6417d2 100755 --- a/target/executable/bcftools/bcftools_concat/bcftools_concat +++ b/target/executable/bcftools/bcftools_concat/bcftools_concat @@ -2,7 +2,7 @@ # bcftools_concat main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -456,9 +456,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_concat" -LABEL org.opencontainers.image.created="2025-04-22T08:55:17Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:42Z" LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bcftools/bcftools_norm/.config.vsh.yaml b/target/executable/bcftools/bcftools_norm/.config.vsh.yaml index 2754aac0..3c9b2d37 100644 --- a/target/executable/bcftools/bcftools_norm/.config.vsh.yaml +++ b/target/executable/bcftools/bcftools_norm/.config.vsh.yaml @@ -418,16 +418,16 @@ build_info: engine: "docker|native" output: "target/executable/bcftools/bcftools_norm" executable: "target/executable/bcftools/bcftools_norm/bcftools_norm" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/bcftools/bcftools_norm/bcftools_norm b/target/executable/bcftools/bcftools_norm/bcftools_norm index 90903608..9d0ddc0b 100755 --- a/target/executable/bcftools/bcftools_norm/bcftools_norm +++ b/target/executable/bcftools/bcftools_norm/bcftools_norm @@ -2,7 +2,7 @@ # bcftools_norm main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -456,9 +456,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_norm" -LABEL org.opencontainers.image.created="2025-04-22T08:55:16Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:42Z" LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bcftools/bcftools_sort/.config.vsh.yaml b/target/executable/bcftools/bcftools_sort/.config.vsh.yaml index 7591f9e6..c67a1bff 100644 --- a/target/executable/bcftools/bcftools_sort/.config.vsh.yaml +++ b/target/executable/bcftools/bcftools_sort/.config.vsh.yaml @@ -187,16 +187,16 @@ build_info: engine: "docker|native" output: "target/executable/bcftools/bcftools_sort" executable: "target/executable/bcftools/bcftools_sort/bcftools_sort" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/bcftools/bcftools_sort/bcftools_sort b/target/executable/bcftools/bcftools_sort/bcftools_sort index 181741cb..eeeb4a61 100755 --- a/target/executable/bcftools/bcftools_sort/bcftools_sort +++ b/target/executable/bcftools/bcftools_sort/bcftools_sort @@ -2,7 +2,7 @@ # bcftools_sort main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -456,9 +456,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_sort" -LABEL org.opencontainers.image.created="2025-04-22T08:55:17Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:42Z" LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bcftools/bcftools_stats/.config.vsh.yaml b/target/executable/bcftools/bcftools_stats/.config.vsh.yaml index 403eb72e..25d8e625 100644 --- a/target/executable/bcftools/bcftools_stats/.config.vsh.yaml +++ b/target/executable/bcftools/bcftools_stats/.config.vsh.yaml @@ -460,16 +460,16 @@ build_info: engine: "docker|native" output: "target/executable/bcftools/bcftools_stats" executable: "target/executable/bcftools/bcftools_stats/bcftools_stats" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/bcftools/bcftools_stats/bcftools_stats b/target/executable/bcftools/bcftools_stats/bcftools_stats index 03c4d1c7..5156e3e0 100755 --- a/target/executable/bcftools/bcftools_stats/bcftools_stats +++ b/target/executable/bcftools/bcftools_stats/bcftools_stats @@ -2,7 +2,7 @@ # bcftools_stats main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -456,9 +456,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_stats" -LABEL org.opencontainers.image.created="2025-04-22T08:55:16Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:42Z" LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bcl_convert/.config.vsh.yaml b/target/executable/bcl_convert/.config.vsh.yaml index a8928f61..0d22bdbf 100644 --- a/target/executable/bcl_convert/.config.vsh.yaml +++ b/target/executable/bcl_convert/.config.vsh.yaml @@ -430,16 +430,16 @@ build_info: engine: "docker|native" output: "target/executable/bcl_convert" executable: "target/executable/bcl_convert/bcl_convert" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/bcl_convert/bcl_convert b/target/executable/bcl_convert/bcl_convert index fc0019be..0cd49bef 100755 --- a/target/executable/bcl_convert/bcl_convert +++ b/target/executable/bcl_convert/bcl_convert @@ -2,7 +2,7 @@ # bcl_convert main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -462,9 +462,9 @@ RUN echo "bcl-convert: \"$(bcl-convert -V 2>&1 >/dev/null | sed -n '/Version/ s/ LABEL org.opencontainers.image.authors="Toni Verbeiren, Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component bcl_convert" -LABEL org.opencontainers.image.created="2025-04-22T08:55:18Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:44Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml index 23eb8fdf..8f23832f 100644 --- a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml +++ b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml @@ -276,16 +276,16 @@ build_info: engine: "docker|native" output: "target/executable/bd_rhapsody/bd_rhapsody_make_reference" executable: "target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference index 7176b966..1c98e7b2 100755 --- a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference +++ b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference @@ -2,7 +2,7 @@ # bd_rhapsody_make_reference main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -465,9 +465,9 @@ RUN VERSION=$(ls -v /var/bd_rhapsody_cwl | grep '^v' | sed 's#v##' | tail -1) RUN echo "bdgenomics/rhapsody: \"$VERSION\"" > /var/software_versions.txt LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Weiwei Schultz" LABEL org.opencontainers.image.description="Companion container for running component bd_rhapsody bd_rhapsody_make_reference" -LABEL org.opencontainers.image.created="2025-04-22T08:55:19Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:44Z" LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1/Extra_Utilities/" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml b/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml index f6e22673..02788fcb 100644 --- a/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml +++ b/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml @@ -1117,16 +1117,16 @@ build_info: engine: "docker|native" output: "target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis" executable: "target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis b/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis index 7996e399..c8b22d26 100755 --- a/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis +++ b/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis @@ -2,7 +2,7 @@ # bd_rhapsody_sequence_analysis main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -465,9 +465,9 @@ RUN VERSION=$(ls -v /var/bd_rhapsody_cwl | grep '^v' | sed 's#v##' | tail -1) RUN echo "bdgenomics/rhapsody: \"$VERSION\"" > /var/software_versions.txt LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Weiwei Schultz" LABEL org.opencontainers.image.description="Companion container for running component bd_rhapsody bd_rhapsody_sequence_analysis" -LABEL org.opencontainers.image.created="2025-04-22T08:55:19Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:44Z" LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_bamtobed/.config.vsh.yaml b/target/executable/bedtools/bedtools_bamtobed/.config.vsh.yaml index 5e250d11..3d86a568 100644 --- a/target/executable/bedtools/bedtools_bamtobed/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_bamtobed/.config.vsh.yaml @@ -237,16 +237,16 @@ build_info: engine: "docker|native" output: "target/executable/bedtools/bedtools_bamtobed" executable: "target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed b/target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed index f84d25cb..e4f4617e 100755 --- a/target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed +++ b/target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed @@ -2,7 +2,7 @@ # bedtools_bamtobed main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -456,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bamtobed" -LABEL org.opencontainers.image.created="2025-04-22T08:55:22Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:46Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml b/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml index 1d69b68e..6064b44f 100644 --- a/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml @@ -189,16 +189,16 @@ build_info: engine: "docker|native" output: "target/executable/bedtools/bedtools_bamtofastq" executable: "target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq b/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq index cdc8096c..df5a9a26 100755 --- a/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq +++ b/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq @@ -2,7 +2,7 @@ # bedtools_bamtofastq main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -456,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bamtofastq" -LABEL org.opencontainers.image.created="2025-04-22T08:55:24Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:49Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml b/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml index 33734882..1efe24b3 100644 --- a/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml @@ -178,16 +178,16 @@ build_info: engine: "docker|native" output: "target/executable/bedtools/bedtools_bed12tobed6" executable: "target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6 b/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6 index 48086234..fda2e5f9 100755 --- a/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6 +++ b/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6 @@ -2,7 +2,7 @@ # bedtools_bed12tobed6 main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -456,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bed12tobed6" -LABEL org.opencontainers.image.created="2025-04-22T08:55:24Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:49Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml b/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml index 7de6d5da..9730eed5 100644 --- a/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml @@ -216,16 +216,16 @@ build_info: engine: "docker|native" output: "target/executable/bedtools/bedtools_bedtobam" executable: "target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam b/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam index 9955c9e0..993667d4 100755 --- a/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam +++ b/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam @@ -2,7 +2,7 @@ # bedtools_bedtobam main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -456,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bedtobam" -LABEL org.opencontainers.image.created="2025-04-22T08:55:24Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:49Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml b/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml index 38d03d01..b1babd14 100644 --- a/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml @@ -339,16 +339,16 @@ build_info: engine: "docker|native" output: "target/executable/bedtools/bedtools_genomecov" executable: "target/executable/bedtools/bedtools_genomecov/bedtools_genomecov" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov b/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov index c043ab6d..a85ee1ab 100755 --- a/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov +++ b/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov @@ -2,7 +2,7 @@ # bedtools_genomecov main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -456,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_genomecov" -LABEL org.opencontainers.image.created="2025-04-22T08:55:22Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:47Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml b/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml index cc614960..61c7599b 100644 --- a/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml @@ -234,16 +234,16 @@ build_info: engine: "docker|native" output: "target/executable/bedtools/bedtools_getfasta" executable: "target/executable/bedtools/bedtools_getfasta/bedtools_getfasta" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta index d6b30911..c806404e 100755 --- a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta +++ b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta @@ -2,7 +2,7 @@ # bedtools_getfasta main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -456,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_getfasta" -LABEL org.opencontainers.image.created="2025-04-22T08:55:22Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:47Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml b/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml index a97732ac..36cad95c 100644 --- a/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml @@ -275,16 +275,16 @@ build_info: engine: "docker|native" output: "target/executable/bedtools/bedtools_groupby" executable: "target/executable/bedtools/bedtools_groupby/bedtools_groupby" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/bedtools/bedtools_groupby/bedtools_groupby b/target/executable/bedtools/bedtools_groupby/bedtools_groupby index e1fde84c..4a5f9583 100755 --- a/target/executable/bedtools/bedtools_groupby/bedtools_groupby +++ b/target/executable/bedtools/bedtools_groupby/bedtools_groupby @@ -2,7 +2,7 @@ # bedtools_groupby main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -456,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_groupby" -LABEL org.opencontainers.image.created="2025-04-22T08:55:23Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:47Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml b/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml index 2f323f17..43f3a8be 100644 --- a/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml @@ -412,16 +412,16 @@ build_info: engine: "docker|native" output: "target/executable/bedtools/bedtools_intersect" executable: "target/executable/bedtools/bedtools_intersect/bedtools_intersect" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/bedtools/bedtools_intersect/bedtools_intersect b/target/executable/bedtools/bedtools_intersect/bedtools_intersect index 68f7c1d4..27a6d565 100755 --- a/target/executable/bedtools/bedtools_intersect/bedtools_intersect +++ b/target/executable/bedtools/bedtools_intersect/bedtools_intersect @@ -2,7 +2,7 @@ # bedtools_intersect main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -456,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_intersect" -LABEL org.opencontainers.image.created="2025-04-22T08:55:23Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:48Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_links/.config.vsh.yaml b/target/executable/bedtools/bedtools_links/.config.vsh.yaml index 742c0cf8..7d429074 100644 --- a/target/executable/bedtools/bedtools_links/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_links/.config.vsh.yaml @@ -212,16 +212,16 @@ build_info: engine: "docker|native" output: "target/executable/bedtools/bedtools_links" executable: "target/executable/bedtools/bedtools_links/bedtools_links" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/bedtools/bedtools_links/bedtools_links b/target/executable/bedtools/bedtools_links/bedtools_links index 004e6190..37b18592 100755 --- a/target/executable/bedtools/bedtools_links/bedtools_links +++ b/target/executable/bedtools/bedtools_links/bedtools_links @@ -2,7 +2,7 @@ # bedtools_links main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -456,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_links" -LABEL org.opencontainers.image.created="2025-04-22T08:55:24Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:48Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_merge/.config.vsh.yaml b/target/executable/bedtools/bedtools_merge/.config.vsh.yaml index 8baf1870..ff705a5a 100644 --- a/target/executable/bedtools/bedtools_merge/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_merge/.config.vsh.yaml @@ -281,16 +281,16 @@ build_info: engine: "docker|native" output: "target/executable/bedtools/bedtools_merge" executable: "target/executable/bedtools/bedtools_merge/bedtools_merge" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/bedtools/bedtools_merge/bedtools_merge b/target/executable/bedtools/bedtools_merge/bedtools_merge index 10a0c4b5..a4fea9fa 100755 --- a/target/executable/bedtools/bedtools_merge/bedtools_merge +++ b/target/executable/bedtools/bedtools_merge/bedtools_merge @@ -2,7 +2,7 @@ # bedtools_merge main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -456,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_merge" -LABEL org.opencontainers.image.created="2025-04-22T08:55:23Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:48Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_sort/.config.vsh.yaml b/target/executable/bedtools/bedtools_sort/.config.vsh.yaml index 8d4ca88d..f2f69e1f 100644 --- a/target/executable/bedtools/bedtools_sort/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_sort/.config.vsh.yaml @@ -224,16 +224,16 @@ build_info: engine: "docker|native" output: "target/executable/bedtools/bedtools_sort" executable: "target/executable/bedtools/bedtools_sort/bedtools_sort" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/bedtools/bedtools_sort/bedtools_sort b/target/executable/bedtools/bedtools_sort/bedtools_sort index 875da0d9..1b34f0d5 100755 --- a/target/executable/bedtools/bedtools_sort/bedtools_sort +++ b/target/executable/bedtools/bedtools_sort/bedtools_sort @@ -2,7 +2,7 @@ # bedtools_sort main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -456,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_sort" -LABEL org.opencontainers.image.created="2025-04-22T08:55:23Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:47Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/busco/busco_download_datasets/.config.vsh.yaml b/target/executable/busco/busco_download_datasets/.config.vsh.yaml index fd72cd12..0d9acfc0 100644 --- a/target/executable/busco/busco_download_datasets/.config.vsh.yaml +++ b/target/executable/busco/busco_download_datasets/.config.vsh.yaml @@ -160,16 +160,16 @@ build_info: engine: "docker|native" output: "target/executable/busco/busco_download_datasets" executable: "target/executable/busco/busco_download_datasets/busco_download_datasets" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/busco/busco_download_datasets/busco_download_datasets b/target/executable/busco/busco_download_datasets/busco_download_datasets index d0ff1e77..b14d2a5e 100755 --- a/target/executable/busco/busco_download_datasets/busco_download_datasets +++ b/target/executable/busco/busco_download_datasets/busco_download_datasets @@ -2,7 +2,7 @@ # busco_download_datasets main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -452,9 +452,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component busco busco_download_datasets" -LABEL org.opencontainers.image.created="2025-04-22T08:55:20Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:45Z" LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/busco/busco_list_datasets/.config.vsh.yaml b/target/executable/busco/busco_list_datasets/.config.vsh.yaml index 80471222..65e820b2 100644 --- a/target/executable/busco/busco_list_datasets/.config.vsh.yaml +++ b/target/executable/busco/busco_list_datasets/.config.vsh.yaml @@ -147,16 +147,16 @@ build_info: engine: "docker|native" output: "target/executable/busco/busco_list_datasets" executable: "target/executable/busco/busco_list_datasets/busco_list_datasets" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/busco/busco_list_datasets/busco_list_datasets b/target/executable/busco/busco_list_datasets/busco_list_datasets index e7efd61d..2288e247 100755 --- a/target/executable/busco/busco_list_datasets/busco_list_datasets +++ b/target/executable/busco/busco_list_datasets/busco_list_datasets @@ -2,7 +2,7 @@ # busco_list_datasets main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -452,9 +452,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component busco busco_list_datasets" -LABEL org.opencontainers.image.created="2025-04-22T08:55:19Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:45Z" LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/busco/busco_run/.config.vsh.yaml b/target/executable/busco/busco_run/.config.vsh.yaml index 5cfde4de..50b4c9ff 100644 --- a/target/executable/busco/busco_run/.config.vsh.yaml +++ b/target/executable/busco/busco_run/.config.vsh.yaml @@ -425,16 +425,16 @@ build_info: engine: "docker|native" output: "target/executable/busco/busco_run" executable: "target/executable/busco/busco_run/busco_run" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/busco/busco_run/busco_run b/target/executable/busco/busco_run/busco_run index 6c33fa93..390a1a07 100755 --- a/target/executable/busco/busco_run/busco_run +++ b/target/executable/busco/busco_run/busco_run @@ -2,7 +2,7 @@ # busco_run main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -452,9 +452,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component busco busco_run" -LABEL org.opencontainers.image.created="2025-04-22T08:55:20Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:45Z" LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/cellranger/cellranger_mkref/.config.vsh.yaml b/target/executable/cellranger/cellranger_mkref/.config.vsh.yaml index 8b83ace4..bd2eb4fa 100644 --- a/target/executable/cellranger/cellranger_mkref/.config.vsh.yaml +++ b/target/executable/cellranger/cellranger_mkref/.config.vsh.yaml @@ -197,16 +197,16 @@ build_info: engine: "docker|native" output: "target/executable/cellranger/cellranger_mkref" executable: "target/executable/cellranger/cellranger_mkref/cellranger_mkref" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/cellranger/cellranger_mkref/cellranger_mkref b/target/executable/cellranger/cellranger_mkref/cellranger_mkref index 3ab5ccd1..c894b919 100755 --- a/target/executable/cellranger/cellranger_mkref/cellranger_mkref +++ b/target/executable/cellranger/cellranger_mkref/cellranger_mkref @@ -2,7 +2,7 @@ # cellranger_mkref main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -454,9 +454,9 @@ RUN apt-get update && \ LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component cellranger cellranger_mkref" -LABEL org.opencontainers.image.created="2025-04-22T08:55:24Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:49Z" LABEL org.opencontainers.image.source="https://github.com/10XGenomics/cellranger/blob/main/lib/python/cellranger/reference_builder.py" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/cutadapt/.config.vsh.yaml b/target/executable/cutadapt/.config.vsh.yaml index 701636ac..78d3dd99 100644 --- a/target/executable/cutadapt/.config.vsh.yaml +++ b/target/executable/cutadapt/.config.vsh.yaml @@ -742,16 +742,16 @@ build_info: engine: "docker|native" output: "target/executable/cutadapt" executable: "target/executable/cutadapt/cutadapt" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/cutadapt/cutadapt b/target/executable/cutadapt/cutadapt index 9ed31da7..89608262 100755 --- a/target/executable/cutadapt/cutadapt +++ b/target/executable/cutadapt/cutadapt @@ -2,7 +2,7 @@ # cutadapt main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -455,9 +455,9 @@ RUN cutadapt --version | sed 's/\(.*\)/cutadapt: "\1"/' > /var/software_versions LABEL org.opencontainers.image.authors="Toni Verbeiren" LABEL org.opencontainers.image.description="Companion container for running component cutadapt" -LABEL org.opencontainers.image.created="2025-04-22T08:55:21Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:46Z" LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/falco/.config.vsh.yaml b/target/executable/falco/.config.vsh.yaml index b2b4ee24..72f17909 100644 --- a/target/executable/falco/.config.vsh.yaml +++ b/target/executable/falco/.config.vsh.yaml @@ -319,16 +319,16 @@ build_info: engine: "docker|native" output: "target/executable/falco" executable: "target/executable/falco/falco" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/falco/falco b/target/executable/falco/falco index 46840b82..921a19f9 100755 --- a/target/executable/falco/falco +++ b/target/executable/falco/falco @@ -2,7 +2,7 @@ # falco main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -464,9 +464,9 @@ RUN echo "falco: \"$(falco -v | sed -n 's/^falco //p')\"" > /var/software_versio LABEL org.opencontainers.image.authors="Toni Verbeiren" LABEL org.opencontainers.image.description="Companion container for running component falco" -LABEL org.opencontainers.image.created="2025-04-22T08:55:26Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:51Z" LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/fastp/.config.vsh.yaml b/target/executable/fastp/.config.vsh.yaml index 524404ce..098453c2 100644 --- a/target/executable/fastp/.config.vsh.yaml +++ b/target/executable/fastp/.config.vsh.yaml @@ -1085,16 +1085,16 @@ build_info: engine: "docker|native" output: "target/executable/fastp" executable: "target/executable/fastp/fastp" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/fastp/fastp b/target/executable/fastp/fastp index ab09a6e4..6efd6fe0 100755 --- a/target/executable/fastp/fastp +++ b/target/executable/fastp/fastp @@ -2,7 +2,7 @@ # fastp main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -452,9 +452,9 @@ RUN fastp --version 2>&1 | sed 's# #: "#;s#$#"#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component fastp" -LABEL org.opencontainers.image.created="2025-04-22T08:55:18Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:43Z" LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/fastqc/.config.vsh.yaml b/target/executable/fastqc/.config.vsh.yaml index c5f5b44f..96532761 100644 --- a/target/executable/fastqc/.config.vsh.yaml +++ b/target/executable/fastqc/.config.vsh.yaml @@ -342,16 +342,16 @@ build_info: engine: "docker|native" output: "target/executable/fastqc" executable: "target/executable/fastqc/fastqc" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/fastqc/fastqc b/target/executable/fastqc/fastqc index 8d7adf63..390e853d 100755 --- a/target/executable/fastqc/fastqc +++ b/target/executable/fastqc/fastqc @@ -2,7 +2,7 @@ # fastqc main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -452,9 +452,9 @@ RUN echo "fastqc: $(fastqc --version | sed -n 's/^FastQC //p')" > /var/software_ LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component fastqc" -LABEL org.opencontainers.image.created="2025-04-22T08:55:27Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:51Z" LABEL org.opencontainers.image.source="https://github.com/s-andrews/FastQC" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/featurecounts/.config.vsh.yaml b/target/executable/featurecounts/.config.vsh.yaml index e9009f37..cb3de751 100644 --- a/target/executable/featurecounts/.config.vsh.yaml +++ b/target/executable/featurecounts/.config.vsh.yaml @@ -647,16 +647,16 @@ build_info: engine: "docker|native" output: "target/executable/featurecounts" executable: "target/executable/featurecounts/featurecounts" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/featurecounts/featurecounts b/target/executable/featurecounts/featurecounts index b77db0b6..2de1d59f 100755 --- a/target/executable/featurecounts/featurecounts +++ b/target/executable/featurecounts/featurecounts @@ -2,7 +2,7 @@ # featurecounts main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -452,9 +452,9 @@ RUN featureCounts -v 2>&1 | sed 's/featureCounts v\([0-9.]*\)/featureCounts: \1/ LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa" LABEL org.opencontainers.image.description="Companion container for running component featurecounts" -LABEL org.opencontainers.image.created="2025-04-22T08:55:21Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:46Z" LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/fq_subsample/.config.vsh.yaml b/target/executable/fq_subsample/.config.vsh.yaml index 6eaf8169..cc82f288 100644 --- a/target/executable/fq_subsample/.config.vsh.yaml +++ b/target/executable/fq_subsample/.config.vsh.yaml @@ -192,16 +192,16 @@ build_info: engine: "docker|native" output: "target/executable/fq_subsample" executable: "target/executable/fq_subsample/fq_subsample" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/fq_subsample/fq_subsample b/target/executable/fq_subsample/fq_subsample index 9d4414ec..2e416fac 100755 --- a/target/executable/fq_subsample/fq_subsample +++ b/target/executable/fq_subsample/fq_subsample @@ -2,7 +2,7 @@ # fq_subsample main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -453,9 +453,9 @@ mv target/release/fq /usr/local/bin/ && \ cd / && rm -rf /fq LABEL org.opencontainers.image.description="Companion container for running component fq_subsample" -LABEL org.opencontainers.image.created="2025-04-22T08:55:26Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:51Z" LABEL org.opencontainers.image.source="https://github.com/stjude-rust-labs/fq" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/gffread/.config.vsh.yaml b/target/executable/gffread/.config.vsh.yaml index d748fb61..14d466f9 100644 --- a/target/executable/gffread/.config.vsh.yaml +++ b/target/executable/gffread/.config.vsh.yaml @@ -687,16 +687,16 @@ build_info: engine: "docker|native" output: "target/executable/gffread" executable: "target/executable/gffread/gffread" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/gffread/gffread b/target/executable/gffread/gffread index d4f0eec0..2bd5ff95 100755 --- a/target/executable/gffread/gffread +++ b/target/executable/gffread/gffread @@ -2,7 +2,7 @@ # gffread main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -452,9 +452,9 @@ RUN echo "gffread: \"$(gffread --version 2>&1)\"" > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component gffread" -LABEL org.opencontainers.image.created="2025-04-22T08:55:18Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:44Z" LABEL org.opencontainers.image.source="https://github.com/gpertea/gffread" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/kallisto/kallisto_index/.config.vsh.yaml b/target/executable/kallisto/kallisto_index/.config.vsh.yaml index 628ecaca..ca368f08 100644 --- a/target/executable/kallisto/kallisto_index/.config.vsh.yaml +++ b/target/executable/kallisto/kallisto_index/.config.vsh.yaml @@ -220,16 +220,16 @@ build_info: engine: "docker|native" output: "target/executable/kallisto/kallisto_index" executable: "target/executable/kallisto/kallisto_index/kallisto_index" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/kallisto/kallisto_index/kallisto_index b/target/executable/kallisto/kallisto_index/kallisto_index index 7828dbf6..e1ed98f7 100755 --- a/target/executable/kallisto/kallisto_index/kallisto_index +++ b/target/executable/kallisto/kallisto_index/kallisto_index @@ -2,7 +2,7 @@ # kallisto_index main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -452,9 +452,9 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \ mv kallisto/kallisto /usr/local/bin/ LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_index" -LABEL org.opencontainers.image.created="2025-04-22T08:55:25Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:50Z" LABEL org.opencontainers.image.source="https://github.com/pachterlab/kallisto" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml index 4fec901a..924cb7ac 100644 --- a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml +++ b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml @@ -248,16 +248,16 @@ build_info: engine: "docker|native" output: "target/executable/kallisto/kallisto_quant" executable: "target/executable/kallisto/kallisto_quant/kallisto_quant" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/kallisto/kallisto_quant/kallisto_quant b/target/executable/kallisto/kallisto_quant/kallisto_quant index 95ae1568..abf7c70f 100755 --- a/target/executable/kallisto/kallisto_quant/kallisto_quant +++ b/target/executable/kallisto/kallisto_quant/kallisto_quant @@ -2,7 +2,7 @@ # kallisto_quant main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -454,9 +454,9 @@ mv kallisto/kallisto /usr/local/bin/ RUN echo "kallisto: $(kallisto version | sed 's/kallisto, version //')" > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_quant" -LABEL org.opencontainers.image.created="2025-04-22T08:55:25Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:50Z" LABEL org.opencontainers.image.source="https://github.com/pachterlab/kallisto" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/lofreq/lofreq_call/.config.vsh.yaml b/target/executable/lofreq/lofreq_call/.config.vsh.yaml index 72583f2a..aafcd5e4 100644 --- a/target/executable/lofreq/lofreq_call/.config.vsh.yaml +++ b/target/executable/lofreq/lofreq_call/.config.vsh.yaml @@ -509,16 +509,16 @@ build_info: engine: "docker|native" output: "target/executable/lofreq/lofreq_call" executable: "target/executable/lofreq/lofreq_call/lofreq_call" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/lofreq/lofreq_call/lofreq_call b/target/executable/lofreq/lofreq_call/lofreq_call index 2b8ac95a..06fbd319 100755 --- a/target/executable/lofreq/lofreq_call/lofreq_call +++ b/target/executable/lofreq/lofreq_call/lofreq_call @@ -2,7 +2,7 @@ # lofreq_call main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -453,9 +453,9 @@ echo "lofreq: $version" > /var/software_versions.txt LABEL org.opencontainers.image.authors="Kai Waldrant" LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_call" -LABEL org.opencontainers.image.created="2025-04-22T08:55:20Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:45Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml b/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml index a6569b30..918ec59c 100644 --- a/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml +++ b/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml @@ -217,16 +217,16 @@ build_info: engine: "docker|native" output: "target/executable/lofreq/lofreq_indelqual" executable: "target/executable/lofreq/lofreq_indelqual/lofreq_indelqual" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual b/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual index eb161372..4a59f6f2 100755 --- a/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual +++ b/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual @@ -2,7 +2,7 @@ # lofreq_indelqual main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -453,9 +453,9 @@ echo "lofreq: $version" > /var/software_versions.txt LABEL org.opencontainers.image.authors="Kai Waldrant" LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_indelqual" -LABEL org.opencontainers.image.created="2025-04-22T08:55:19Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:45Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/multiqc/.config.vsh.yaml b/target/executable/multiqc/.config.vsh.yaml index 37323166..ddb1d0c2 100644 --- a/target/executable/multiqc/.config.vsh.yaml +++ b/target/executable/multiqc/.config.vsh.yaml @@ -458,16 +458,16 @@ build_info: engine: "docker|native" output: "target/executable/multiqc" executable: "target/executable/multiqc/multiqc" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/multiqc/multiqc b/target/executable/multiqc/multiqc index 7f234991..7603c505 100755 --- a/target/executable/multiqc/multiqc +++ b/target/executable/multiqc/multiqc @@ -2,7 +2,7 @@ # multiqc main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -452,9 +452,9 @@ RUN multiqc --version | sed 's/multiqc, version\s\(.*\)/multiqc: "\1"/' > /var/s LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component multiqc" -LABEL org.opencontainers.image.created="2025-04-22T08:55:26Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:51Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/nanoplot/.config.vsh.yaml b/target/executable/nanoplot/.config.vsh.yaml index 8d4d2aae..2e2ec349 100644 --- a/target/executable/nanoplot/.config.vsh.yaml +++ b/target/executable/nanoplot/.config.vsh.yaml @@ -494,16 +494,16 @@ build_info: engine: "docker|native" output: "target/executable/nanoplot" executable: "target/executable/nanoplot/nanoplot" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/nanoplot/nanoplot b/target/executable/nanoplot/nanoplot index f94d6676..a5dedd29 100755 --- a/target/executable/nanoplot/nanoplot +++ b/target/executable/nanoplot/nanoplot @@ -2,7 +2,7 @@ # nanoplot main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -449,9 +449,9 @@ RUN version=$(NanoPlot --version) && \ echo "$version" > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component nanoplot" -LABEL org.opencontainers.image.created="2025-04-22T08:55:24Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:49Z" LABEL org.opencontainers.image.source="https://github.com/wdecoster/NanoPlot" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/pear/.config.vsh.yaml b/target/executable/pear/.config.vsh.yaml index ca174843..3c886cfd 100644 --- a/target/executable/pear/.config.vsh.yaml +++ b/target/executable/pear/.config.vsh.yaml @@ -400,16 +400,16 @@ build_info: engine: "docker|native" output: "target/executable/pear" executable: "target/executable/pear/pear" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/pear/pear b/target/executable/pear/pear index 2684fe5d..7d266ecb 100755 --- a/target/executable/pear/pear +++ b/target/executable/pear/pear @@ -2,7 +2,7 @@ # pear main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -453,9 +453,9 @@ echo "pear: $version" > /var/software_versions.txt LABEL org.opencontainers.image.authors="Kai Waldrant" LABEL org.opencontainers.image.description="Companion container for running component pear" -LABEL org.opencontainers.image.created="2025-04-22T08:55:26Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:51Z" LABEL org.opencontainers.image.source="https://github.com/tseemann/PEAR" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml b/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml index 40b4bc9d..8e185550 100644 --- a/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml +++ b/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml @@ -266,16 +266,16 @@ build_info: engine: "docker|native" output: "target/executable/qualimap/qualimap_rnaseq" executable: "target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq b/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq index add3545e..91c2b0d5 100755 --- a/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq +++ b/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq @@ -2,7 +2,7 @@ # qualimap_rnaseq main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -452,9 +452,9 @@ RUN echo QualiMap: $(qualimap 2>&1 | grep QualiMap | sed 's/^.*QualiMap//') > /v LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component qualimap qualimap_rnaseq" -LABEL org.opencontainers.image.created="2025-04-22T08:55:20Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:45Z" LABEL org.opencontainers.image.source="https://bitbucket.org/kokonech/qualimap/commits/branch/master" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml b/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml index b65eaf50..a1468f94 100644 --- a/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml +++ b/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml @@ -854,16 +854,16 @@ build_info: engine: "docker|native" output: "target/executable/rsem/rsem_calculate_expression" executable: "target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression b/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression index 1a83a42e..42b3f78c 100755 --- a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression +++ b/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression @@ -2,7 +2,7 @@ # rsem_calculate_expression main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -470,9 +470,9 @@ echo "bowtie: `bowtie --version | grep -oP 'bowtie-align-s version \K\d+\.\d+\.\ echo "HISAT2: `hisat2 --version | grep -oP 'hisat2-align-s version \K\d+\.\d+\.\d+'`" >> /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_calculate_expression" -LABEL org.opencontainers.image.created="2025-04-22T08:55:20Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:45Z" LABEL org.opencontainers.image.source="https://github.com/deweylab/RSEM" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml b/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml index 35c097de..8a19cd31 100644 --- a/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml +++ b/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml @@ -418,16 +418,16 @@ build_info: engine: "docker|native" output: "target/executable/rsem/rsem_prepare_reference" executable: "target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference b/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference index 6bd20f27..59e7d070 100755 --- a/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference +++ b/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference @@ -2,7 +2,7 @@ # rsem_prepare_reference main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -494,9 +494,9 @@ echo "HISAT2: `hisat2 --version | grep -oP 'hisat2-align-s version \K\d+\.\d+\.\ LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa" LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_prepare_reference" -LABEL org.opencontainers.image.created="2025-04-22T08:55:20Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:45Z" LABEL org.opencontainers.image.source="https://github.com/deweylab/RSEM" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml b/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml index 9befbf70..d36b057a 100644 --- a/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml @@ -177,16 +177,16 @@ build_info: engine: "docker|native" output: "target/executable/rseqc/rseqc_bamstat" executable: "target/executable/rseqc/rseqc_bamstat/rseqc_bamstat" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat b/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat index 02991afe..eec648da 100755 --- a/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat +++ b/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat @@ -2,7 +2,7 @@ # rseqc_bamstat main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -455,9 +455,9 @@ RUN echo "RSeQC bam_stat.py: $(bam_stat.py --version | cut -d' ' -f2-)" > /var/s LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_bamstat" -LABEL org.opencontainers.image.created="2025-04-22T08:55:26Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:51Z" LABEL org.opencontainers.image.source="https://github.com/MonashBioinformaticsPlatform/RSeQC" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml b/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml index 2aac972a..e2da321e 100644 --- a/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml @@ -203,16 +203,16 @@ build_info: engine: "docker|native" output: "target/executable/rseqc/rseqc_inferexperiment" executable: "target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment b/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment index 369c525a..05245665 100755 --- a/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment +++ b/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment @@ -2,7 +2,7 @@ # rseqc_inferexperiment main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -455,9 +455,9 @@ RUN echo "RSeQC - infer_experiment.py: $(infer_experiment.py --version | cut -d' LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_inferexperiment" -LABEL org.opencontainers.image.created="2025-04-22T08:55:25Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:50Z" LABEL org.opencontainers.image.source="https://github.com/MonashBioinformaticsPlatform/RSeQC" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_inner_distance/.config.vsh.yaml b/target/executable/rseqc/rseqc_inner_distance/.config.vsh.yaml index a8be0ae3..f78a12d9 100644 --- a/target/executable/rseqc/rseqc_inner_distance/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_inner_distance/.config.vsh.yaml @@ -296,16 +296,16 @@ build_info: engine: "docker|native" output: "target/executable/rseqc/rseqc_inner_distance" executable: "target/executable/rseqc/rseqc_inner_distance/rseqc_inner_distance" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/rseqc/rseqc_inner_distance/rseqc_inner_distance b/target/executable/rseqc/rseqc_inner_distance/rseqc_inner_distance index 314820dc..bda7c379 100755 --- a/target/executable/rseqc/rseqc_inner_distance/rseqc_inner_distance +++ b/target/executable/rseqc/rseqc_inner_distance/rseqc_inner_distance @@ -2,7 +2,7 @@ # rseqc_inner_distance main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -459,9 +459,9 @@ RUN echo "RSeQC - inner_distance.py: $(inner_distance.py --version | cut -d' ' - LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_inner_distance" -LABEL org.opencontainers.image.created="2025-04-22T08:55:26Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:50Z" LABEL org.opencontainers.image.source="https://github.com/MonashBioinformaticsPlatform/RSeQC" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/salmon/salmon_index/.config.vsh.yaml b/target/executable/salmon/salmon_index/.config.vsh.yaml index b572329e..39e29877 100644 --- a/target/executable/salmon/salmon_index/.config.vsh.yaml +++ b/target/executable/salmon/salmon_index/.config.vsh.yaml @@ -279,16 +279,16 @@ build_info: engine: "docker|native" output: "target/executable/salmon/salmon_index" executable: "target/executable/salmon/salmon_index/salmon_index" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/salmon/salmon_index/salmon_index b/target/executable/salmon/salmon_index/salmon_index index 186a8571..b6f64f8e 100755 --- a/target/executable/salmon/salmon_index/salmon_index +++ b/target/executable/salmon/salmon_index/salmon_index @@ -2,7 +2,7 @@ # salmon_index main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -452,9 +452,9 @@ RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/softwar LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa" LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_index" -LABEL org.opencontainers.image.created="2025-04-22T08:55:16Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:41Z" LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/salmon/salmon_quant/.config.vsh.yaml b/target/executable/salmon/salmon_quant/.config.vsh.yaml index 938e9919..5572dd1e 100644 --- a/target/executable/salmon/salmon_quant/.config.vsh.yaml +++ b/target/executable/salmon/salmon_quant/.config.vsh.yaml @@ -1175,16 +1175,16 @@ build_info: engine: "docker|native" output: "target/executable/salmon/salmon_quant" executable: "target/executable/salmon/salmon_quant/salmon_quant" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/salmon/salmon_quant/salmon_quant b/target/executable/salmon/salmon_quant/salmon_quant index a80dbefb..f1ea3426 100755 --- a/target/executable/salmon/salmon_quant/salmon_quant +++ b/target/executable/salmon/salmon_quant/salmon_quant @@ -2,7 +2,7 @@ # salmon_quant main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -452,9 +452,9 @@ RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/softwar LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa" LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_quant" -LABEL org.opencontainers.image.created="2025-04-22T08:55:16Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:41Z" LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_collate/.config.vsh.yaml b/target/executable/samtools/samtools_collate/.config.vsh.yaml index 956261e7..5b8115d6 100644 --- a/target/executable/samtools/samtools_collate/.config.vsh.yaml +++ b/target/executable/samtools/samtools_collate/.config.vsh.yaml @@ -266,16 +266,16 @@ build_info: engine: "docker|native" output: "target/executable/samtools/samtools_collate" executable: "target/executable/samtools/samtools_collate/samtools_collate" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/samtools/samtools_collate/samtools_collate b/target/executable/samtools/samtools_collate/samtools_collate index 2cd383f8..7664822a 100755 --- a/target/executable/samtools/samtools_collate/samtools_collate +++ b/target/executable/samtools/samtools_collate/samtools_collate @@ -2,7 +2,7 @@ # samtools_collate main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -453,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_collate" -LABEL org.opencontainers.image.created="2025-04-22T08:55:15Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:41Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_faidx/.config.vsh.yaml b/target/executable/samtools/samtools_faidx/.config.vsh.yaml index 4a995abb..d048b604 100644 --- a/target/executable/samtools/samtools_faidx/.config.vsh.yaml +++ b/target/executable/samtools/samtools_faidx/.config.vsh.yaml @@ -245,16 +245,16 @@ build_info: engine: "docker|native" output: "target/executable/samtools/samtools_faidx" executable: "target/executable/samtools/samtools_faidx/samtools_faidx" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/samtools/samtools_faidx/samtools_faidx b/target/executable/samtools/samtools_faidx/samtools_faidx index 53a9a601..7c8e11b3 100755 --- a/target/executable/samtools/samtools_faidx/samtools_faidx +++ b/target/executable/samtools/samtools_faidx/samtools_faidx @@ -2,7 +2,7 @@ # samtools_faidx main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -453,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_faidx" -LABEL org.opencontainers.image.created="2025-04-22T08:55:18Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:43Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_fasta/.config.vsh.yaml b/target/executable/samtools/samtools_fasta/.config.vsh.yaml index ba62b81e..a888410c 100644 --- a/target/executable/samtools/samtools_fasta/.config.vsh.yaml +++ b/target/executable/samtools/samtools_fasta/.config.vsh.yaml @@ -435,16 +435,16 @@ build_info: engine: "docker|native" output: "target/executable/samtools/samtools_fasta" executable: "target/executable/samtools/samtools_fasta/samtools_fasta" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/samtools/samtools_fasta/samtools_fasta b/target/executable/samtools/samtools_fasta/samtools_fasta index 709bdefc..db972d8f 100755 --- a/target/executable/samtools/samtools_fasta/samtools_fasta +++ b/target/executable/samtools/samtools_fasta/samtools_fasta @@ -2,7 +2,7 @@ # samtools_fasta main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -453,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_fasta" -LABEL org.opencontainers.image.created="2025-04-22T08:55:17Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:42Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_fastq/.config.vsh.yaml b/target/executable/samtools/samtools_fastq/.config.vsh.yaml index 6e165d9c..baac9030 100644 --- a/target/executable/samtools/samtools_fastq/.config.vsh.yaml +++ b/target/executable/samtools/samtools_fastq/.config.vsh.yaml @@ -435,16 +435,16 @@ build_info: engine: "docker|native" output: "target/executable/samtools/samtools_fastq" executable: "target/executable/samtools/samtools_fastq/samtools_fastq" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/samtools/samtools_fastq/samtools_fastq b/target/executable/samtools/samtools_fastq/samtools_fastq index 8da794b9..f4b32d3f 100755 --- a/target/executable/samtools/samtools_fastq/samtools_fastq +++ b/target/executable/samtools/samtools_fastq/samtools_fastq @@ -2,7 +2,7 @@ # samtools_fastq main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -453,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_fastq" -LABEL org.opencontainers.image.created="2025-04-22T08:55:16Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:42Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_flagstat/.config.vsh.yaml b/target/executable/samtools/samtools_flagstat/.config.vsh.yaml index 0282f153..674aed2b 100644 --- a/target/executable/samtools/samtools_flagstat/.config.vsh.yaml +++ b/target/executable/samtools/samtools_flagstat/.config.vsh.yaml @@ -175,16 +175,16 @@ build_info: engine: "docker|native" output: "target/executable/samtools/samtools_flagstat" executable: "target/executable/samtools/samtools_flagstat/samtools_flagstat" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/samtools/samtools_flagstat/samtools_flagstat b/target/executable/samtools/samtools_flagstat/samtools_flagstat index aa17e94b..e98c3632 100755 --- a/target/executable/samtools/samtools_flagstat/samtools_flagstat +++ b/target/executable/samtools/samtools_flagstat/samtools_flagstat @@ -2,7 +2,7 @@ # samtools_flagstat main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -453,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_flagstat" -LABEL org.opencontainers.image.created="2025-04-22T08:55:16Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:41Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_idxstats/.config.vsh.yaml b/target/executable/samtools/samtools_idxstats/.config.vsh.yaml index 9f663675..a94e130c 100644 --- a/target/executable/samtools/samtools_idxstats/.config.vsh.yaml +++ b/target/executable/samtools/samtools_idxstats/.config.vsh.yaml @@ -185,16 +185,16 @@ build_info: engine: "docker|native" output: "target/executable/samtools/samtools_idxstats" executable: "target/executable/samtools/samtools_idxstats/samtools_idxstats" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/samtools/samtools_idxstats/samtools_idxstats b/target/executable/samtools/samtools_idxstats/samtools_idxstats index ab94e17f..b4239ee6 100755 --- a/target/executable/samtools/samtools_idxstats/samtools_idxstats +++ b/target/executable/samtools/samtools_idxstats/samtools_idxstats @@ -2,7 +2,7 @@ # samtools_idxstats main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -453,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_idxstats" -LABEL org.opencontainers.image.created="2025-04-22T08:55:16Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:41Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_index/.config.vsh.yaml b/target/executable/samtools/samtools_index/.config.vsh.yaml index 9d693ff7..407843ba 100644 --- a/target/executable/samtools/samtools_index/.config.vsh.yaml +++ b/target/executable/samtools/samtools_index/.config.vsh.yaml @@ -191,16 +191,16 @@ build_info: engine: "docker|native" output: "target/executable/samtools/samtools_index" executable: "target/executable/samtools/samtools_index/samtools_index" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/samtools/samtools_index/samtools_index b/target/executable/samtools/samtools_index/samtools_index index 44f6abba..8ab5083b 100755 --- a/target/executable/samtools/samtools_index/samtools_index +++ b/target/executable/samtools/samtools_index/samtools_index @@ -2,7 +2,7 @@ # samtools_index main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -453,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_index" -LABEL org.opencontainers.image.created="2025-04-22T08:55:17Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:42Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_sort/.config.vsh.yaml b/target/executable/samtools/samtools_sort/.config.vsh.yaml index cc887d6e..0f79e57a 100644 --- a/target/executable/samtools/samtools_sort/.config.vsh.yaml +++ b/target/executable/samtools/samtools_sort/.config.vsh.yaml @@ -334,16 +334,16 @@ build_info: engine: "docker|native" output: "target/executable/samtools/samtools_sort" executable: "target/executable/samtools/samtools_sort/samtools_sort" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/samtools/samtools_sort/samtools_sort b/target/executable/samtools/samtools_sort/samtools_sort index 84bfb42b..59f5e4e7 100755 --- a/target/executable/samtools/samtools_sort/samtools_sort +++ b/target/executable/samtools/samtools_sort/samtools_sort @@ -2,7 +2,7 @@ # samtools_sort main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -453,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_sort" -LABEL org.opencontainers.image.created="2025-04-22T08:55:18Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:43Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_stats/.config.vsh.yaml b/target/executable/samtools/samtools_stats/.config.vsh.yaml index 6c2e00d0..4e068e6b 100644 --- a/target/executable/samtools/samtools_stats/.config.vsh.yaml +++ b/target/executable/samtools/samtools_stats/.config.vsh.yaml @@ -403,16 +403,16 @@ build_info: engine: "docker|native" output: "target/executable/samtools/samtools_stats" executable: "target/executable/samtools/samtools_stats/samtools_stats" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/samtools/samtools_stats/samtools_stats b/target/executable/samtools/samtools_stats/samtools_stats index 71675ecf..f56a2279 100755 --- a/target/executable/samtools/samtools_stats/samtools_stats +++ b/target/executable/samtools/samtools_stats/samtools_stats @@ -2,7 +2,7 @@ # samtools_stats main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -453,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_stats" -LABEL org.opencontainers.image.created="2025-04-22T08:55:17Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:43Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_view/.config.vsh.yaml b/target/executable/samtools/samtools_view/.config.vsh.yaml index e192dc8d..eeea1f0e 100644 --- a/target/executable/samtools/samtools_view/.config.vsh.yaml +++ b/target/executable/samtools/samtools_view/.config.vsh.yaml @@ -667,16 +667,16 @@ build_info: engine: "docker|native" output: "target/executable/samtools/samtools_view" executable: "target/executable/samtools/samtools_view/samtools_view" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/samtools/samtools_view/samtools_view b/target/executable/samtools/samtools_view/samtools_view index 9f3c9aae..4e733006 100755 --- a/target/executable/samtools/samtools_view/samtools_view +++ b/target/executable/samtools/samtools_view/samtools_view @@ -2,7 +2,7 @@ # samtools_view main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -453,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_view" -LABEL org.opencontainers.image.created="2025-04-22T08:55:17Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:42Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/seqtk/seqtk_sample/.config.vsh.yaml b/target/executable/seqtk/seqtk_sample/.config.vsh.yaml index 8f5a9681..a354330d 100644 --- a/target/executable/seqtk/seqtk_sample/.config.vsh.yaml +++ b/target/executable/seqtk/seqtk_sample/.config.vsh.yaml @@ -175,16 +175,16 @@ build_info: engine: "docker|native" output: "target/executable/seqtk/seqtk_sample" executable: "target/executable/seqtk/seqtk_sample/seqtk_sample" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/seqtk/seqtk_sample/seqtk_sample b/target/executable/seqtk/seqtk_sample/seqtk_sample index c8da53b5..15ebfe2d 100755 --- a/target/executable/seqtk/seqtk_sample/seqtk_sample +++ b/target/executable/seqtk/seqtk_sample/seqtk_sample @@ -2,7 +2,7 @@ # seqtk_sample main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -450,9 +450,9 @@ FROM quay.io/biocontainers/seqtk:1.4--he4a0461_2 ENTRYPOINT [] LABEL org.opencontainers.image.authors="Jakub Majercik" LABEL org.opencontainers.image.description="Companion container for running component seqtk seqtk_sample" -LABEL org.opencontainers.image.created="2025-04-22T08:55:25Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:49Z" LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml b/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml index 97ec8216..0004da54 100644 --- a/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml +++ b/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml @@ -198,16 +198,16 @@ build_info: engine: "docker|native" output: "target/executable/seqtk/seqtk_subseq" executable: "target/executable/seqtk/seqtk_subseq/seqtk_subseq" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/seqtk/seqtk_subseq/seqtk_subseq b/target/executable/seqtk/seqtk_subseq/seqtk_subseq index 5b0a92d7..05d40d3a 100755 --- a/target/executable/seqtk/seqtk_subseq/seqtk_subseq +++ b/target/executable/seqtk/seqtk_subseq/seqtk_subseq @@ -2,7 +2,7 @@ # seqtk_subseq main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -452,9 +452,9 @@ RUN echo $(echo $(seqtk 2>&1) | sed -n 's/.*\(Version: [^ ]*\).*/\1/p') > /var/s LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component seqtk seqtk_subseq" -LABEL org.opencontainers.image.created="2025-04-22T08:55:25Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:50Z" LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/sgdemux/.config.vsh.yaml b/target/executable/sgdemux/.config.vsh.yaml index 0b240246..60ad8757 100644 --- a/target/executable/sgdemux/.config.vsh.yaml +++ b/target/executable/sgdemux/.config.vsh.yaml @@ -431,16 +431,16 @@ build_info: engine: "docker|native" output: "target/executable/sgdemux" executable: "target/executable/sgdemux/sgdemux" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/sgdemux/sgdemux b/target/executable/sgdemux/sgdemux index a5b7bbe8..4320a3c6 100755 --- a/target/executable/sgdemux/sgdemux +++ b/target/executable/sgdemux/sgdemux @@ -2,7 +2,7 @@ # sgdemux main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -457,9 +457,9 @@ echo "sgdemux: $(sgdemux --version | cut -d' ' -f2)" > /var/software_versions.tx LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component sgdemux" -LABEL org.opencontainers.image.created="2025-04-22T08:55:15Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:41Z" LABEL org.opencontainers.image.source="https://github.com/Singular-Genomics/singular-demux" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/snpeff/.config.vsh.yaml b/target/executable/snpeff/.config.vsh.yaml index d60937f7..9f6ffc73 100644 --- a/target/executable/snpeff/.config.vsh.yaml +++ b/target/executable/snpeff/.config.vsh.yaml @@ -630,16 +630,16 @@ build_info: engine: "docker|native" output: "target/executable/snpeff" executable: "target/executable/snpeff/snpeff" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/snpeff/snpeff b/target/executable/snpeff/snpeff index e326dd7d..3d7d5625 100755 --- a/target/executable/snpeff/snpeff +++ b/target/executable/snpeff/snpeff @@ -2,7 +2,7 @@ # snpeff main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -450,9 +450,9 @@ version_trimmed=$(echo "$version" | awk '{print $1, $2}') && \ echo "$version_trimmed" > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component snpeff" -LABEL org.opencontainers.image.created="2025-04-22T08:55:19Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:44Z" LABEL org.opencontainers.image.source="https://github.com/pcingola/SnpEff" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/sortmerna/.config.vsh.yaml b/target/executable/sortmerna/.config.vsh.yaml index 886d0773..25ef6a83 100644 --- a/target/executable/sortmerna/.config.vsh.yaml +++ b/target/executable/sortmerna/.config.vsh.yaml @@ -596,16 +596,16 @@ build_info: engine: "docker|native" output: "target/executable/sortmerna" executable: "target/executable/sortmerna/sortmerna" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/sortmerna/sortmerna b/target/executable/sortmerna/sortmerna index 0f52d9f6..04df72b0 100755 --- a/target/executable/sortmerna/sortmerna +++ b/target/executable/sortmerna/sortmerna @@ -2,7 +2,7 @@ # sortmerna main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -448,9 +448,9 @@ ENTRYPOINT [] RUN echo SortMeRNA: `sortmerna --version | sed -n 's/.*version \([0-9]\+\.[0-9]\+\.[0-9]\+\).*/\1/p'` LABEL org.opencontainers.image.description="Companion container for running component sortmerna" -LABEL org.opencontainers.image.created="2025-04-22T08:55:27Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:51Z" LABEL org.opencontainers.image.source="https://github.com/sortmerna/sortmerna" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/star/star_align_reads/.config.vsh.yaml b/target/executable/star/star_align_reads/.config.vsh.yaml index 7d14c4f9..f8b69d40 100644 --- a/target/executable/star/star_align_reads/.config.vsh.yaml +++ b/target/executable/star/star_align_reads/.config.vsh.yaml @@ -2665,16 +2665,16 @@ build_info: engine: "docker|native" output: "target/executable/star/star_align_reads" executable: "target/executable/star/star_align_reads/star_align_reads" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/star/star_align_reads/star_align_reads b/target/executable/star/star_align_reads/star_align_reads index fd353bee..7a91617b 100755 --- a/target/executable/star/star_align_reads/star_align_reads +++ b/target/executable/star/star_align_reads/star_align_reads @@ -2,7 +2,7 @@ # star_align_reads main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -475,9 +475,9 @@ RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component star star_align_reads" -LABEL org.opencontainers.image.created="2025-04-22T08:55:26Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:50Z" LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/star/star_genome_generate/.config.vsh.yaml b/target/executable/star/star_genome_generate/.config.vsh.yaml index ce3f14f3..81ed9207 100644 --- a/target/executable/star/star_genome_generate/.config.vsh.yaml +++ b/target/executable/star/star_genome_generate/.config.vsh.yaml @@ -335,16 +335,16 @@ build_info: engine: "docker|native" output: "target/executable/star/star_genome_generate" executable: "target/executable/star/star_genome_generate/star_genome_generate" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/star/star_genome_generate/star_genome_generate b/target/executable/star/star_genome_generate/star_genome_generate index 2d6a0784..e88a61a6 100755 --- a/target/executable/star/star_genome_generate/star_genome_generate +++ b/target/executable/star/star_genome_generate/star_genome_generate @@ -2,7 +2,7 @@ # star_genome_generate main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -467,9 +467,9 @@ RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa" LABEL org.opencontainers.image.description="Companion container for running component star star_genome_generate" -LABEL org.opencontainers.image.created="2025-04-22T08:55:25Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:50Z" LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/trimgalore/.config.vsh.yaml b/target/executable/trimgalore/.config.vsh.yaml index 3764de7c..4c18428c 100644 --- a/target/executable/trimgalore/.config.vsh.yaml +++ b/target/executable/trimgalore/.config.vsh.yaml @@ -772,16 +772,16 @@ build_info: engine: "docker|native" output: "target/executable/trimgalore" executable: "target/executable/trimgalore/trimgalore" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/trimgalore/trimgalore b/target/executable/trimgalore/trimgalore index 73cea6ec..60057b1e 100755 --- a/target/executable/trimgalore/trimgalore +++ b/target/executable/trimgalore/trimgalore @@ -2,7 +2,7 @@ # trimgalore main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -452,9 +452,9 @@ RUN echo "TrimGalore: `trim_galore --version | sed -n 's/.*version\s\+\([0-9]\+\ LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa" LABEL org.opencontainers.image.description="Companion container for running component trimgalore" -LABEL org.opencontainers.image.created="2025-04-22T08:55:26Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:50Z" LABEL org.opencontainers.image.source="https://github.com/FelixKrueger/TrimGalore" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml b/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml index 2c10a622..f0748ceb 100644 --- a/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml +++ b/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml @@ -613,16 +613,16 @@ build_info: engine: "docker|native" output: "target/executable/umi_tools/umi_tools_dedup" executable: "target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup b/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup index 7abcf0b4..42afc17a 100755 --- a/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup +++ b/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup @@ -2,7 +2,7 @@ # umi_tools_dedup main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -452,9 +452,9 @@ RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_dedup" -LABEL org.opencontainers.image.created="2025-04-22T08:55:18Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:43Z" LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml b/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml index 2d775853..440ff121 100644 --- a/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml +++ b/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml @@ -436,16 +436,16 @@ build_info: engine: "docker|native" output: "target/executable/umi_tools/umi_tools_extract" executable: "target/executable/umi_tools/umi_tools_extract/umi_tools_extract" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/umi_tools/umi_tools_extract/umi_tools_extract b/target/executable/umi_tools/umi_tools_extract/umi_tools_extract index f7c51a86..8a68b75d 100755 --- a/target/executable/umi_tools/umi_tools_extract/umi_tools_extract +++ b/target/executable/umi_tools/umi_tools_extract/umi_tools_extract @@ -2,7 +2,7 @@ # umi_tools_extract main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -448,9 +448,9 @@ ENTRYPOINT [] RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_extract" -LABEL org.opencontainers.image.created="2025-04-22T08:55:18Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:44Z" LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml b/target/executable/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml index 95f1a23e..67db6650 100644 --- a/target/executable/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml +++ b/target/executable/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml @@ -258,16 +258,16 @@ build_info: engine: "docker|native" output: "target/executable/umi_tools/umi_tools_prepareforrsem" executable: "target/executable/umi_tools/umi_tools_prepareforrsem/umi_tools_prepareforrsem" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/executable/umi_tools/umi_tools_prepareforrsem/umi_tools_prepareforrsem b/target/executable/umi_tools/umi_tools_prepareforrsem/umi_tools_prepareforrsem index 6ef936b7..af2a6c03 100755 --- a/target/executable/umi_tools/umi_tools_prepareforrsem/umi_tools_prepareforrsem +++ b/target/executable/umi_tools/umi_tools_prepareforrsem/umi_tools_prepareforrsem @@ -2,7 +2,7 @@ # umi_tools_prepareforrsem main # -# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data # Intuitive. # @@ -448,9 +448,9 @@ ENTRYPOINT [] RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_prepareforrsem" -LABEL org.opencontainers.image.created="2025-04-22T08:55:19Z" +LABEL org.opencontainers.image.created="2025-04-29T10:54:44Z" LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools" -LABEL org.opencontainers.image.revision="1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" +LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml b/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml index bc017af4..1e4b90cf 100644 --- a/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml @@ -237,16 +237,16 @@ build_info: engine: "docker|native" output: "target/nextflow/agat/agat_convert_bed2gff" executable: "target/nextflow/agat/agat_convert_bed2gff/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/agat/agat_convert_bed2gff/main.nf b/target/nextflow/agat/agat_convert_bed2gff/main.nf index b59c7a91..72ad27d5 100644 --- a/target/nextflow/agat/agat_convert_bed2gff/main.nf +++ b/target/nextflow/agat/agat_convert_bed2gff/main.nf @@ -1,6 +1,6 @@ // agat_convert_bed2gff main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3326,16 +3321,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_bed2gff", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3749,7 +3744,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3763,6 +3758,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml b/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml index 80014e29..992dedd7 100644 --- a/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml @@ -227,16 +227,16 @@ build_info: engine: "docker|native" output: "target/nextflow/agat/agat_convert_embl2gff" executable: "target/nextflow/agat/agat_convert_embl2gff/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/agat/agat_convert_embl2gff/main.nf b/target/nextflow/agat/agat_convert_embl2gff/main.nf index 8d61767d..042bf731 100644 --- a/target/nextflow/agat/agat_convert_embl2gff/main.nf +++ b/target/nextflow/agat/agat_convert_embl2gff/main.nf @@ -1,6 +1,6 @@ // agat_convert_embl2gff main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3319,16 +3314,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_embl2gff", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3745,7 +3740,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3759,6 +3754,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/agat/agat_convert_genscan2gff/.config.vsh.yaml b/target/nextflow/agat/agat_convert_genscan2gff/.config.vsh.yaml index 20159f97..ed200dfa 100644 --- a/target/nextflow/agat/agat_convert_genscan2gff/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_genscan2gff/.config.vsh.yaml @@ -232,16 +232,16 @@ build_info: engine: "docker|native" output: "target/nextflow/agat/agat_convert_genscan2gff" executable: "target/nextflow/agat/agat_convert_genscan2gff/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/agat/agat_convert_genscan2gff/main.nf b/target/nextflow/agat/agat_convert_genscan2gff/main.nf index ebe88be3..4e07c956 100644 --- a/target/nextflow/agat/agat_convert_genscan2gff/main.nf +++ b/target/nextflow/agat/agat_convert_genscan2gff/main.nf @@ -1,6 +1,6 @@ // agat_convert_genscan2gff main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3321,16 +3316,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_genscan2gff", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3745,7 +3740,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3759,6 +3754,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/agat/agat_convert_mfannot2gff/.config.vsh.yaml b/target/nextflow/agat/agat_convert_mfannot2gff/.config.vsh.yaml index 9a4c89cd..30b38611 100644 --- a/target/nextflow/agat/agat_convert_mfannot2gff/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_mfannot2gff/.config.vsh.yaml @@ -188,16 +188,16 @@ build_info: engine: "docker|native" output: "target/nextflow/agat/agat_convert_mfannot2gff" executable: "target/nextflow/agat/agat_convert_mfannot2gff/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/agat/agat_convert_mfannot2gff/main.nf b/target/nextflow/agat/agat_convert_mfannot2gff/main.nf index 5fe6a313..d588b428 100644 --- a/target/nextflow/agat/agat_convert_mfannot2gff/main.nf +++ b/target/nextflow/agat/agat_convert_mfannot2gff/main.nf @@ -1,6 +1,6 @@ // agat_convert_mfannot2gff main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3281,16 +3276,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_mfannot2gff", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3691,7 +3686,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3705,6 +3700,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml b/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml index 55dc2027..690a3788 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml @@ -230,16 +230,16 @@ build_info: engine: "docker|native" output: "target/nextflow/agat/agat_convert_sp_gff2gtf" executable: "target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf b/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf index e11855e3..5a41f0a1 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf +++ b/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf @@ -1,6 +1,6 @@ // agat_convert_sp_gff2gtf main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3302,16 +3297,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_sp_gff2gtf", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3712,7 +3707,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3726,6 +3721,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml b/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml index 0945ec22..9d508212 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml @@ -190,16 +190,16 @@ build_info: engine: "docker|native" output: "target/nextflow/agat/agat_convert_sp_gff2tsv" executable: "target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf b/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf index 3db811c6..0d3cd8dd 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf +++ b/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf @@ -1,6 +1,6 @@ // agat_convert_sp_gff2tsv main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3280,16 +3275,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_sp_gff2tsv", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3688,7 +3683,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3702,6 +3697,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml b/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml index 9a1aa44b..66e83395 100644 --- a/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml @@ -197,16 +197,16 @@ build_info: engine: "docker|native" output: "target/nextflow/agat/agat_convert_sp_gxf2gxf" executable: "target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf b/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf index 49071185..68e9e99d 100644 --- a/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf +++ b/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf @@ -1,6 +1,6 @@ // agat_convert_sp_gxf2gxf main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3280,16 +3275,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_sp_gxf2gxf", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3688,7 +3683,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3702,6 +3697,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/agat/agat_sp_add_introns/.config.vsh.yaml b/target/nextflow/agat/agat_sp_add_introns/.config.vsh.yaml index 1c72984c..48e9b710 100644 --- a/target/nextflow/agat/agat_sp_add_introns/.config.vsh.yaml +++ b/target/nextflow/agat/agat_sp_add_introns/.config.vsh.yaml @@ -188,16 +188,16 @@ build_info: engine: "docker|native" output: "target/nextflow/agat/agat_sp_add_introns" executable: "target/nextflow/agat/agat_sp_add_introns/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/agat/agat_sp_add_introns/main.nf b/target/nextflow/agat/agat_sp_add_introns/main.nf index a2b72985..e17689aa 100644 --- a/target/nextflow/agat/agat_sp_add_introns/main.nf +++ b/target/nextflow/agat/agat_sp_add_introns/main.nf @@ -1,6 +1,6 @@ // agat_sp_add_introns main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3283,16 +3278,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/agat/agat_sp_add_introns", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3693,7 +3688,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3707,6 +3702,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml b/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml index 2c54c321..5962bd01 100644 --- a/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml +++ b/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml @@ -238,16 +238,16 @@ build_info: engine: "docker|native" output: "target/nextflow/agat/agat_sp_filter_feature_from_kill_list" executable: "target/nextflow/agat/agat_sp_filter_feature_from_kill_list/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/main.nf b/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/main.nf index ae81dee9..849d289a 100644 --- a/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/main.nf +++ b/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/main.nf @@ -1,6 +1,6 @@ // agat_sp_filter_feature_from_kill_list main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3330,16 +3325,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/agat/agat_sp_filter_feature_from_kill_list", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3755,7 +3750,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3769,6 +3764,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/nextflow_schema.json b/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/nextflow_schema.json index 7a25e872..035d050c 100644 --- a/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/nextflow_schema.json +++ b/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/nextflow_schema.json @@ -47,10 +47,10 @@ "output": { "type": "string", - "description": "Type: `file`, required, default: `$id.$key.output.output`. Path to the output GFF file that contains filtered features", - "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Path to the output GFF file that contains filtered features. \n" + "description": "Type: `file`, required, default: `$id.$key.output`. Path to the output GFF file that contains filtered features", + "help_text": "Type: `file`, required, default: `$id.$key.output`. Path to the output GFF file that contains filtered features. \n" , - "default":"$id.$key.output.output" + "default":"$id.$key.output" } diff --git a/target/nextflow/agat/agat_sp_merge_annotations/.config.vsh.yaml b/target/nextflow/agat/agat_sp_merge_annotations/.config.vsh.yaml index b50baf03..726ee9a0 100644 --- a/target/nextflow/agat/agat_sp_merge_annotations/.config.vsh.yaml +++ b/target/nextflow/agat/agat_sp_merge_annotations/.config.vsh.yaml @@ -186,16 +186,16 @@ build_info: engine: "docker|native" output: "target/nextflow/agat/agat_sp_merge_annotations" executable: "target/nextflow/agat/agat_sp_merge_annotations/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/agat/agat_sp_merge_annotations/main.nf b/target/nextflow/agat/agat_sp_merge_annotations/main.nf index 54522334..df88b802 100644 --- a/target/nextflow/agat/agat_sp_merge_annotations/main.nf +++ b/target/nextflow/agat/agat_sp_merge_annotations/main.nf @@ -1,6 +1,6 @@ // agat_sp_merge_annotations main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3280,16 +3275,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/agat/agat_sp_merge_annotations", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3698,7 +3693,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3712,6 +3707,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/agat/agat_sp_statistics/.config.vsh.yaml b/target/nextflow/agat/agat_sp_statistics/.config.vsh.yaml index d55e0cc2..49ea49e7 100644 --- a/target/nextflow/agat/agat_sp_statistics/.config.vsh.yaml +++ b/target/nextflow/agat/agat_sp_statistics/.config.vsh.yaml @@ -233,16 +233,16 @@ build_info: engine: "docker|native" output: "target/nextflow/agat/agat_sp_statistics" executable: "target/nextflow/agat/agat_sp_statistics/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/agat/agat_sp_statistics/main.nf b/target/nextflow/agat/agat_sp_statistics/main.nf index 619b9b59..8bc858b1 100644 --- a/target/nextflow/agat/agat_sp_statistics/main.nf +++ b/target/nextflow/agat/agat_sp_statistics/main.nf @@ -1,6 +1,6 @@ // agat_sp_statistics main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3330,16 +3325,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/agat/agat_sp_statistics", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3757,7 +3752,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3771,6 +3766,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/agat/agat_sq_stat_basic/.config.vsh.yaml b/target/nextflow/agat/agat_sq_stat_basic/.config.vsh.yaml index ef520044..9d0744a1 100644 --- a/target/nextflow/agat/agat_sq_stat_basic/.config.vsh.yaml +++ b/target/nextflow/agat/agat_sq_stat_basic/.config.vsh.yaml @@ -229,16 +229,16 @@ build_info: engine: "docker|native" output: "target/nextflow/agat/agat_sq_stat_basic" executable: "target/nextflow/agat/agat_sq_stat_basic/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/agat/agat_sq_stat_basic/main.nf b/target/nextflow/agat/agat_sq_stat_basic/main.nf index 098e47cc..d532a593 100644 --- a/target/nextflow/agat/agat_sq_stat_basic/main.nf +++ b/target/nextflow/agat/agat_sq_stat_basic/main.nf @@ -1,6 +1,6 @@ // agat_sq_stat_basic main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3316,16 +3311,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/agat/agat_sq_stat_basic", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3749,7 +3744,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3763,6 +3758,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/arriba/.config.vsh.yaml b/target/nextflow/arriba/.config.vsh.yaml index bb4f058d..9ac0c7bd 100644 --- a/target/nextflow/arriba/.config.vsh.yaml +++ b/target/nextflow/arriba/.config.vsh.yaml @@ -708,16 +708,16 @@ build_info: engine: "docker|native" output: "target/nextflow/arriba" executable: "target/nextflow/arriba/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/arriba/main.nf b/target/nextflow/arriba/main.nf index 1b661888..3aee78c4 100644 --- a/target/nextflow/arriba/main.nf +++ b/target/nextflow/arriba/main.nf @@ -1,6 +1,6 @@ // arriba main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3826,16 +3821,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/arriba", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -4313,7 +4308,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -4327,6 +4322,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/bases2fastq/.config.vsh.yaml b/target/nextflow/bases2fastq/.config.vsh.yaml index 4f1dfd73..46d24803 100644 --- a/target/nextflow/bases2fastq/.config.vsh.yaml +++ b/target/nextflow/bases2fastq/.config.vsh.yaml @@ -396,16 +396,16 @@ build_info: engine: "docker|native" output: "target/nextflow/bases2fastq" executable: "target/nextflow/bases2fastq/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/bases2fastq/main.nf b/target/nextflow/bases2fastq/main.nf index 270bdca4..483695cd 100644 --- a/target/nextflow/bases2fastq/main.nf +++ b/target/nextflow/bases2fastq/main.nf @@ -1,6 +1,6 @@ // bases2fastq main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3518,16 +3513,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/bases2fastq", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -4051,7 +4046,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -4065,6 +4060,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/bases2fastq/nextflow_schema.json b/target/nextflow/bases2fastq/nextflow_schema.json index 2342a391..d59d797b 100644 --- a/target/nextflow/bases2fastq/nextflow_schema.json +++ b/target/nextflow/bases2fastq/nextflow_schema.json @@ -310,10 +310,10 @@ "output_directory": { "type": "string", - "description": "Type: `file`, required, default: `$id.$key.output_directory.output_directory`, example: `fastq_dir`. Location to save output fastqs", - "help_text": "Type: `file`, required, default: `$id.$key.output_directory.output_directory`, example: `fastq_dir`. Location to save output fastqs" + "description": "Type: `file`, required, default: `$id.$key.output_directory`, example: `fastq_dir`. Location to save output fastqs", + "help_text": "Type: `file`, required, default: `$id.$key.output_directory`, example: `fastq_dir`. Location to save output fastqs" , - "default":"$id.$key.output_directory.output_directory" + "default":"$id.$key.output_directory" } @@ -321,10 +321,10 @@ "report": { "type": "string", - "description": "Type: `file`, default: `$id.$key.report.report`. Output location for the HTML report", - "help_text": "Type: `file`, default: `$id.$key.report.report`. Output location for the HTML report" + "description": "Type: `file`, default: `$id.$key.report`. Output location for the HTML report", + "help_text": "Type: `file`, default: `$id.$key.report`. Output location for the HTML report" , - "default":"$id.$key.report.report" + "default":"$id.$key.report" } @@ -332,10 +332,10 @@ "logs": { "type": "string", - "description": "Type: `file`, default: `$id.$key.logs.logs`, example: `logs_dir`. Directory containing log files", - "help_text": "Type: `file`, default: `$id.$key.logs.logs`, example: `logs_dir`. Directory containing log files" + "description": "Type: `file`, default: `$id.$key.logs`, example: `logs_dir`. Directory containing log files", + "help_text": "Type: `file`, default: `$id.$key.logs`, example: `logs_dir`. Directory containing log files" , - "default":"$id.$key.logs.logs" + "default":"$id.$key.logs" } diff --git a/target/nextflow/bbmap/bbmap_bbsplit/.config.vsh.yaml b/target/nextflow/bbmap/bbmap_bbsplit/.config.vsh.yaml index a79d365d..f5a07929 100644 --- a/target/nextflow/bbmap/bbmap_bbsplit/.config.vsh.yaml +++ b/target/nextflow/bbmap/bbmap_bbsplit/.config.vsh.yaml @@ -370,16 +370,16 @@ build_info: engine: "docker|native" output: "target/nextflow/bbmap/bbmap_bbsplit" executable: "target/nextflow/bbmap/bbmap_bbsplit/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/bbmap/bbmap_bbsplit/main.nf b/target/nextflow/bbmap/bbmap_bbsplit/main.nf index 492fb03b..2593b202 100644 --- a/target/nextflow/bbmap/bbmap_bbsplit/main.nf +++ b/target/nextflow/bbmap/bbmap_bbsplit/main.nf @@ -1,6 +1,6 @@ // bbmap_bbsplit main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -82,64 +82,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -151,10 +143,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3454,16 +3449,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/bbmap/bbmap_bbsplit", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3964,7 +3959,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3978,6 +3973,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/bbmap/bbmap_bbsplit/nextflow_schema.json b/target/nextflow/bbmap/bbmap_bbsplit/nextflow_schema.json index e33875e7..7b8b1edd 100644 --- a/target/nextflow/bbmap/bbmap_bbsplit/nextflow_schema.json +++ b/target/nextflow/bbmap/bbmap_bbsplit/nextflow_schema.json @@ -187,10 +187,10 @@ "index": { "type": "string", - "description": "Type: `file`, default: `$id.$key.index.index`, example: `BBSplit_index`. Location to write the index", - "help_text": "Type: `file`, default: `$id.$key.index.index`, example: `BBSplit_index`. Location to write the index.\n" + "description": "Type: `file`, default: `$id.$key.index`, example: `BBSplit_index`. Location to write the index", + "help_text": "Type: `file`, default: `$id.$key.index`, example: `BBSplit_index`. Location to write the index.\n" , - "default":"$id.$key.index.index" + "default":"$id.$key.index" } diff --git a/target/nextflow/bcftools/bcftools_annotate/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_annotate/.config.vsh.yaml index 946e8cb5..2e3f7c05 100644 --- a/target/nextflow/bcftools/bcftools_annotate/.config.vsh.yaml +++ b/target/nextflow/bcftools/bcftools_annotate/.config.vsh.yaml @@ -471,16 +471,16 @@ build_info: engine: "docker|native" output: "target/nextflow/bcftools/bcftools_annotate" executable: "target/nextflow/bcftools/bcftools_annotate/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/bcftools/bcftools_annotate/main.nf b/target/nextflow/bcftools/bcftools_annotate/main.nf index b5718410..284d8d08 100644 --- a/target/nextflow/bcftools/bcftools_annotate/main.nf +++ b/target/nextflow/bcftools/bcftools_annotate/main.nf @@ -1,6 +1,6 @@ // bcftools_annotate main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3569,16 +3564,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/bcftools/bcftools_annotate", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -4046,7 +4041,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -4060,6 +4055,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/bcftools/bcftools_annotate/nextflow_schema.json b/target/nextflow/bcftools/bcftools_annotate/nextflow_schema.json index c61fa726..c2a06bda 100644 --- a/target/nextflow/bcftools/bcftools_annotate/nextflow_schema.json +++ b/target/nextflow/bcftools/bcftools_annotate/nextflow_schema.json @@ -37,10 +37,10 @@ "output": { "type": "string", - "description": "Type: `file`, required, default: `$id.$key.output.output`. Output annotated file", - "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Output annotated file." + "description": "Type: `file`, required, default: `$id.$key.output`. Output annotated file", + "help_text": "Type: `file`, required, default: `$id.$key.output`. Output annotated file." , - "default":"$id.$key.output.output" + "default":"$id.$key.output" } diff --git a/target/nextflow/bcftools/bcftools_concat/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_concat/.config.vsh.yaml index ab75dbd4..bd72d046 100644 --- a/target/nextflow/bcftools/bcftools_concat/.config.vsh.yaml +++ b/target/nextflow/bcftools/bcftools_concat/.config.vsh.yaml @@ -337,16 +337,16 @@ build_info: engine: "docker|native" output: "target/nextflow/bcftools/bcftools_concat" executable: "target/nextflow/bcftools/bcftools_concat/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/bcftools/bcftools_concat/main.nf b/target/nextflow/bcftools/bcftools_concat/main.nf index 453ca0a2..167efb40 100644 --- a/target/nextflow/bcftools/bcftools_concat/main.nf +++ b/target/nextflow/bcftools/bcftools_concat/main.nf @@ -1,6 +1,6 @@ // bcftools_concat main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3441,16 +3436,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/bcftools/bcftools_concat", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3908,7 +3903,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3922,6 +3917,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/bcftools/bcftools_concat/nextflow_schema.json b/target/nextflow/bcftools/bcftools_concat/nextflow_schema.json index 5c7ba654..5889e67f 100644 --- a/target/nextflow/bcftools/bcftools_concat/nextflow_schema.json +++ b/target/nextflow/bcftools/bcftools_concat/nextflow_schema.json @@ -47,10 +47,10 @@ "output": { "type": "string", - "description": "Type: `file`, required, default: `$id.$key.output.output`. Output concatenated VCF/BCF file", - "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Output concatenated VCF/BCF file." + "description": "Type: `file`, required, default: `$id.$key.output`. Output concatenated VCF/BCF file", + "help_text": "Type: `file`, required, default: `$id.$key.output`. Output concatenated VCF/BCF file." , - "default":"$id.$key.output.output" + "default":"$id.$key.output" } diff --git a/target/nextflow/bcftools/bcftools_norm/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_norm/.config.vsh.yaml index a6988489..9d3af5c8 100644 --- a/target/nextflow/bcftools/bcftools_norm/.config.vsh.yaml +++ b/target/nextflow/bcftools/bcftools_norm/.config.vsh.yaml @@ -418,16 +418,16 @@ build_info: engine: "docker|native" output: "target/nextflow/bcftools/bcftools_norm" executable: "target/nextflow/bcftools/bcftools_norm/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/bcftools/bcftools_norm/main.nf b/target/nextflow/bcftools/bcftools_norm/main.nf index 18d54bdc..2f1c37ae 100644 --- a/target/nextflow/bcftools/bcftools_norm/main.nf +++ b/target/nextflow/bcftools/bcftools_norm/main.nf @@ -1,6 +1,6 @@ // bcftools_norm main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3534,16 +3529,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/bcftools/bcftools_norm", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -4001,7 +3996,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -4015,6 +4010,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/bcftools/bcftools_norm/nextflow_schema.json b/target/nextflow/bcftools/bcftools_norm/nextflow_schema.json index 26c453b5..7f18c71d 100644 --- a/target/nextflow/bcftools/bcftools_norm/nextflow_schema.json +++ b/target/nextflow/bcftools/bcftools_norm/nextflow_schema.json @@ -37,10 +37,10 @@ "output": { "type": "string", - "description": "Type: `file`, required, default: `$id.$key.output.output`. Output normalized VCF/BCF file", - "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Output normalized VCF/BCF file." + "description": "Type: `file`, required, default: `$id.$key.output`. Output normalized VCF/BCF file", + "help_text": "Type: `file`, required, default: `$id.$key.output`. Output normalized VCF/BCF file." , - "default":"$id.$key.output.output" + "default":"$id.$key.output" } diff --git a/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml index 48a663e6..a0d422a7 100644 --- a/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml +++ b/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml @@ -187,16 +187,16 @@ build_info: engine: "docker|native" output: "target/nextflow/bcftools/bcftools_sort" executable: "target/nextflow/bcftools/bcftools_sort/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/bcftools/bcftools_sort/main.nf b/target/nextflow/bcftools/bcftools_sort/main.nf index 9b1a39e1..a9c36975 100644 --- a/target/nextflow/bcftools/bcftools_sort/main.nf +++ b/target/nextflow/bcftools/bcftools_sort/main.nf @@ -1,6 +1,6 @@ // bcftools_sort main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3282,16 +3277,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/bcftools/bcftools_sort", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3696,7 +3691,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3710,6 +3705,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/bcftools/bcftools_sort/nextflow_schema.json b/target/nextflow/bcftools/bcftools_sort/nextflow_schema.json index 8f06643a..46f051fd 100644 --- a/target/nextflow/bcftools/bcftools_sort/nextflow_schema.json +++ b/target/nextflow/bcftools/bcftools_sort/nextflow_schema.json @@ -37,10 +37,10 @@ "output": { "type": "string", - "description": "Type: `file`, required, default: `$id.$key.output.output`. Output sorted VCF/BCF file", - "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Output sorted VCF/BCF file." + "description": "Type: `file`, required, default: `$id.$key.output`. Output sorted VCF/BCF file", + "help_text": "Type: `file`, required, default: `$id.$key.output`. Output sorted VCF/BCF file." , - "default":"$id.$key.output.output" + "default":"$id.$key.output" } diff --git a/target/nextflow/bcftools/bcftools_stats/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_stats/.config.vsh.yaml index fcd5ffc1..b25d656d 100644 --- a/target/nextflow/bcftools/bcftools_stats/.config.vsh.yaml +++ b/target/nextflow/bcftools/bcftools_stats/.config.vsh.yaml @@ -460,16 +460,16 @@ build_info: engine: "docker|native" output: "target/nextflow/bcftools/bcftools_stats" executable: "target/nextflow/bcftools/bcftools_stats/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/bcftools/bcftools_stats/main.nf b/target/nextflow/bcftools/bcftools_stats/main.nf index 229374a6..1feccf3e 100644 --- a/target/nextflow/bcftools/bcftools_stats/main.nf +++ b/target/nextflow/bcftools/bcftools_stats/main.nf @@ -1,6 +1,6 @@ // bcftools_stats main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3571,16 +3566,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/bcftools/bcftools_stats", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -4046,7 +4041,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -4060,6 +4055,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/bcftools/bcftools_stats/nextflow_schema.json b/target/nextflow/bcftools/bcftools_stats/nextflow_schema.json index 88ee92a7..168dea65 100644 --- a/target/nextflow/bcftools/bcftools_stats/nextflow_schema.json +++ b/target/nextflow/bcftools/bcftools_stats/nextflow_schema.json @@ -37,10 +37,10 @@ "output": { "type": "string", - "description": "Type: `file`, required, default: `$id.$key.output.output`. Output txt statistics file", - "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Output txt statistics file." + "description": "Type: `file`, required, default: `$id.$key.output`. Output txt statistics file", + "help_text": "Type: `file`, required, default: `$id.$key.output`. Output txt statistics file." , - "default":"$id.$key.output.output" + "default":"$id.$key.output" } diff --git a/target/nextflow/bcl_convert/.config.vsh.yaml b/target/nextflow/bcl_convert/.config.vsh.yaml index 17e783af..f68787b3 100644 --- a/target/nextflow/bcl_convert/.config.vsh.yaml +++ b/target/nextflow/bcl_convert/.config.vsh.yaml @@ -430,16 +430,16 @@ build_info: engine: "docker|native" output: "target/nextflow/bcl_convert" executable: "target/nextflow/bcl_convert/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/bcl_convert/main.nf b/target/nextflow/bcl_convert/main.nf index 4cc815f3..3cdcd436 100644 --- a/target/nextflow/bcl_convert/main.nf +++ b/target/nextflow/bcl_convert/main.nf @@ -1,6 +1,6 @@ // bcl_convert main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -86,64 +86,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -155,10 +147,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3575,16 +3570,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/bcl_convert", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -4041,7 +4036,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -4055,6 +4050,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/bcl_convert/nextflow_schema.json b/target/nextflow/bcl_convert/nextflow_schema.json index 9a5f8f8d..9927d09d 100644 --- a/target/nextflow/bcl_convert/nextflow_schema.json +++ b/target/nextflow/bcl_convert/nextflow_schema.json @@ -237,10 +237,10 @@ "output_directory": { "type": "string", - "description": "Type: `file`, required, default: `$id.$key.output_directory.output_directory`, example: `fastq_dir`. Output directory containig fastq files", - "help_text": "Type: `file`, required, default: `$id.$key.output_directory.output_directory`, example: `fastq_dir`. Output directory containig fastq files" + "description": "Type: `file`, required, default: `$id.$key.output_directory`, example: `fastq_dir`. Output directory containig fastq files", + "help_text": "Type: `file`, required, default: `$id.$key.output_directory`, example: `fastq_dir`. Output directory containig fastq files" , - "default":"$id.$key.output_directory.output_directory" + "default":"$id.$key.output_directory" } @@ -268,10 +268,10 @@ "reports": { "type": "string", - "description": "Type: `file`, default: `$id.$key.reports.reports`, example: `reports_dir`. Reports directory", - "help_text": "Type: `file`, default: `$id.$key.reports.reports`, example: `reports_dir`. Reports directory" + "description": "Type: `file`, default: `$id.$key.reports`, example: `reports_dir`. Reports directory", + "help_text": "Type: `file`, default: `$id.$key.reports`, example: `reports_dir`. Reports directory" , - "default":"$id.$key.reports.reports" + "default":"$id.$key.reports" } @@ -279,10 +279,10 @@ "logs": { "type": "string", - "description": "Type: `file`, default: `$id.$key.logs.logs`, example: `logs_dir`. Reports directory", - "help_text": "Type: `file`, default: `$id.$key.logs.logs`, example: `logs_dir`. Reports directory" + "description": "Type: `file`, default: `$id.$key.logs`, example: `logs_dir`. Reports directory", + "help_text": "Type: `file`, default: `$id.$key.logs`, example: `logs_dir`. Reports directory" , - "default":"$id.$key.logs.logs" + "default":"$id.$key.logs" } diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml index b2eaa853..60341575 100644 --- a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml +++ b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml @@ -276,16 +276,16 @@ build_info: engine: "docker|native" output: "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference" executable: "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf index ac136fb4..a47c6562 100644 --- a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf +++ b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf @@ -1,6 +1,6 @@ // bd_rhapsody_make_reference main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -86,64 +86,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -155,10 +147,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3380,16 +3375,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3420,7 +3415,7 @@ meta = [ // inner workflow hook def innerWorkflowFactory(args) { def rawScript = '''set -e -tempscript=".viash_script.sh" +tempscript=".viash_script.py" cat > "$tempscript" << VIASHMAIN import os import re @@ -3935,7 +3930,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3949,6 +3944,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml b/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml index b3d2b251..30893fb1 100644 --- a/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml +++ b/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml @@ -1117,16 +1117,16 @@ build_info: engine: "docker|native" output: "target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis" executable: "target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/main.nf b/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/main.nf index f94ab90b..5ffa18a4 100644 --- a/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/main.nf +++ b/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/main.nf @@ -1,6 +1,6 @@ // bd_rhapsody_sequence_analysis main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -86,64 +86,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -155,10 +147,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -4427,16 +4422,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -4467,7 +4462,7 @@ meta = [ // inner workflow hook def innerWorkflowFactory(args) { def rawScript = '''set -e -tempscript=".viash_script.sh" +tempscript=".viash_script.py" cat > "$tempscript" << VIASHMAIN import os import re @@ -5102,7 +5097,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -5116,6 +5111,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/nextflow_schema.json b/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/nextflow_schema.json index 8d89d724..cbff45df 100644 --- a/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/nextflow_schema.json +++ b/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/nextflow_schema.json @@ -47,10 +47,10 @@ "output_dir": { "type": "string", - "description": "Type: `file`, required, default: `$id.$key.output_dir.output_dir`, example: `output_dir`. The unprocessed output directory containing all the outputs from the pipeline", - "help_text": "Type: `file`, required, default: `$id.$key.output_dir.output_dir`, example: `output_dir`. The unprocessed output directory containing all the outputs from the pipeline." + "description": "Type: `file`, required, default: `$id.$key.output_dir`, example: `output_dir`. The unprocessed output directory containing all the outputs from the pipeline", + "help_text": "Type: `file`, required, default: `$id.$key.output_dir`, example: `output_dir`. The unprocessed output directory containing all the outputs from the pipeline." , - "default":"$id.$key.output_dir.output_dir" + "default":"$id.$key.output_dir" } diff --git a/target/nextflow/bedtools/bedtools_bamtobed/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bamtobed/.config.vsh.yaml index d8698435..d0a485a5 100644 --- a/target/nextflow/bedtools/bedtools_bamtobed/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_bamtobed/.config.vsh.yaml @@ -237,16 +237,16 @@ build_info: engine: "docker|native" output: "target/nextflow/bedtools/bedtools_bamtobed" executable: "target/nextflow/bedtools/bedtools_bamtobed/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/bedtools/bedtools_bamtobed/main.nf b/target/nextflow/bedtools/bedtools_bamtobed/main.nf index 41f51668..9affb821 100644 --- a/target/nextflow/bedtools/bedtools_bamtobed/main.nf +++ b/target/nextflow/bedtools/bedtools_bamtobed/main.nf @@ -1,6 +1,6 @@ // bedtools_bamtobed main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3335,16 +3330,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_bamtobed", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3780,7 +3775,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3794,6 +3789,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/bedtools/bedtools_bamtobed/nextflow_schema.json b/target/nextflow/bedtools/bedtools_bamtobed/nextflow_schema.json index 0c6b2711..4d266fca 100644 --- a/target/nextflow/bedtools/bedtools_bamtobed/nextflow_schema.json +++ b/target/nextflow/bedtools/bedtools_bamtobed/nextflow_schema.json @@ -37,10 +37,10 @@ "output": { "type": "string", - "description": "Type: `file`, required, default: `$id.$key.output.output`. Output BED file", - "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Output BED file." + "description": "Type: `file`, required, default: `$id.$key.output`. Output BED file", + "help_text": "Type: `file`, required, default: `$id.$key.output`. Output BED file." , - "default":"$id.$key.output.output" + "default":"$id.$key.output" } diff --git a/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml index 075e83f1..3a8d548e 100644 --- a/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml @@ -189,16 +189,16 @@ build_info: engine: "docker|native" output: "target/nextflow/bedtools/bedtools_bamtofastq" executable: "target/nextflow/bedtools/bedtools_bamtofastq/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/bedtools/bedtools_bamtofastq/main.nf b/target/nextflow/bedtools/bedtools_bamtofastq/main.nf index f716fabb..e0e6964c 100644 --- a/target/nextflow/bedtools/bedtools_bamtofastq/main.nf +++ b/target/nextflow/bedtools/bedtools_bamtofastq/main.nf @@ -1,6 +1,6 @@ // bedtools_bamtofastq main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3284,16 +3279,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_bamtofastq", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3702,7 +3697,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3716,6 +3711,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/bedtools/bedtools_bamtofastq/nextflow_schema.json b/target/nextflow/bedtools/bedtools_bamtofastq/nextflow_schema.json index a246cb01..b88a7bd4 100644 --- a/target/nextflow/bedtools/bedtools_bamtofastq/nextflow_schema.json +++ b/target/nextflow/bedtools/bedtools_bamtofastq/nextflow_schema.json @@ -37,10 +37,10 @@ "fastq": { "type": "string", - "description": "Type: `file`, required, default: `$id.$key.fastq.fastq`. Output FASTQ file", - "help_text": "Type: `file`, required, default: `$id.$key.fastq.fastq`. Output FASTQ file." + "description": "Type: `file`, required, default: `$id.$key.fastq`. Output FASTQ file", + "help_text": "Type: `file`, required, default: `$id.$key.fastq`. Output FASTQ file." , - "default":"$id.$key.fastq.fastq" + "default":"$id.$key.fastq" } @@ -48,10 +48,10 @@ "fastq2": { "type": "string", - "description": "Type: `file`, default: `$id.$key.fastq2.fastq2`. FASTQ for second end", - "help_text": "Type: `file`, default: `$id.$key.fastq2.fastq2`. FASTQ for second end. Used if BAM contains paired-end data.\nBAM should be sorted by query name is creating paired FASTQ.\n" + "description": "Type: `file`, default: `$id.$key.fastq2`. FASTQ for second end", + "help_text": "Type: `file`, default: `$id.$key.fastq2`. FASTQ for second end. Used if BAM contains paired-end data.\nBAM should be sorted by query name is creating paired FASTQ.\n" , - "default":"$id.$key.fastq2.fastq2" + "default":"$id.$key.fastq2" } diff --git a/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml index d5fc5b2b..35d5d79e 100644 --- a/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml @@ -178,16 +178,16 @@ build_info: engine: "docker|native" output: "target/nextflow/bedtools/bedtools_bed12tobed6" executable: "target/nextflow/bedtools/bedtools_bed12tobed6/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf b/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf index 1944e9c2..09ac500d 100644 --- a/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf +++ b/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf @@ -1,6 +1,6 @@ // bedtools_bed12tobed6 main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3269,16 +3264,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_bed12tobed6", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3683,7 +3678,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3697,6 +3692,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/bedtools/bedtools_bed12tobed6/nextflow_schema.json b/target/nextflow/bedtools/bedtools_bed12tobed6/nextflow_schema.json index e9118c0f..efbe0c2a 100644 --- a/target/nextflow/bedtools/bedtools_bed12tobed6/nextflow_schema.json +++ b/target/nextflow/bedtools/bedtools_bed12tobed6/nextflow_schema.json @@ -37,10 +37,10 @@ "output": { "type": "string", - "description": "Type: `file`, default: `$id.$key.output.output`. Output BED6 file to be written", - "help_text": "Type: `file`, default: `$id.$key.output.output`. Output BED6 file to be written." + "description": "Type: `file`, default: `$id.$key.output`. Output BED6 file to be written", + "help_text": "Type: `file`, default: `$id.$key.output`. Output BED6 file to be written." , - "default":"$id.$key.output.output" + "default":"$id.$key.output" } diff --git a/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml index d14ea9a2..177ed8c3 100644 --- a/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml @@ -216,16 +216,16 @@ build_info: engine: "docker|native" output: "target/nextflow/bedtools/bedtools_bedtobam" executable: "target/nextflow/bedtools/bedtools_bedtobam/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/bedtools/bedtools_bedtobam/main.nf b/target/nextflow/bedtools/bedtools_bedtobam/main.nf index 1603cc7c..39f2f510 100644 --- a/target/nextflow/bedtools/bedtools_bedtobam/main.nf +++ b/target/nextflow/bedtools/bedtools_bedtobam/main.nf @@ -1,6 +1,6 @@ // bedtools_bedtobam main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3317,16 +3312,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_bedtobam", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3738,7 +3733,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3752,6 +3747,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/bedtools/bedtools_bedtobam/nextflow_schema.json b/target/nextflow/bedtools/bedtools_bedtobam/nextflow_schema.json index fc7e6364..a3ee084c 100644 --- a/target/nextflow/bedtools/bedtools_bedtobam/nextflow_schema.json +++ b/target/nextflow/bedtools/bedtools_bedtobam/nextflow_schema.json @@ -47,10 +47,10 @@ "output": { "type": "string", - "description": "Type: `file`, default: `$id.$key.output.output`. Output BAM file to be written", - "help_text": "Type: `file`, default: `$id.$key.output.output`. Output BAM file to be written." + "description": "Type: `file`, default: `$id.$key.output`. Output BAM file to be written", + "help_text": "Type: `file`, default: `$id.$key.output`. Output BAM file to be written." , - "default":"$id.$key.output.output" + "default":"$id.$key.output" } diff --git a/target/nextflow/bedtools/bedtools_genomecov/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_genomecov/.config.vsh.yaml index 8bc1f55c..8062d5b5 100644 --- a/target/nextflow/bedtools/bedtools_genomecov/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_genomecov/.config.vsh.yaml @@ -339,16 +339,16 @@ build_info: engine: "docker|native" output: "target/nextflow/bedtools/bedtools_genomecov" executable: "target/nextflow/bedtools/bedtools_genomecov/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/bedtools/bedtools_genomecov/main.nf b/target/nextflow/bedtools/bedtools_genomecov/main.nf index e7bba2b2..c64dca24 100644 --- a/target/nextflow/bedtools/bedtools_genomecov/main.nf +++ b/target/nextflow/bedtools/bedtools_genomecov/main.nf @@ -1,6 +1,6 @@ // bedtools_genomecov main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3441,16 +3436,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_genomecov", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3912,7 +3907,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3926,6 +3921,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml index d355abf8..6ebf53be 100644 --- a/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml @@ -234,16 +234,16 @@ build_info: engine: "docker|native" output: "target/nextflow/bedtools/bedtools_getfasta" executable: "target/nextflow/bedtools/bedtools_getfasta/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/bedtools/bedtools_getfasta/main.nf b/target/nextflow/bedtools/bedtools_getfasta/main.nf index d8b28d53..e7dea91a 100644 --- a/target/nextflow/bedtools/bedtools_getfasta/main.nf +++ b/target/nextflow/bedtools/bedtools_getfasta/main.nf @@ -1,6 +1,6 @@ // bedtools_getfasta main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3320,16 +3315,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_getfasta", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3750,7 +3745,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3764,6 +3759,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/bedtools/bedtools_getfasta/nextflow_schema.json b/target/nextflow/bedtools/bedtools_getfasta/nextflow_schema.json index a543bac3..ea17c4e6 100644 --- a/target/nextflow/bedtools/bedtools_getfasta/nextflow_schema.json +++ b/target/nextflow/bedtools/bedtools_getfasta/nextflow_schema.json @@ -79,10 +79,10 @@ "output": { "type": "string", - "description": "Type: `file`, required, default: `$id.$key.output.output`. Output file where the output from the \u0027bedtools getfasta\u0027 commend will\nbe written to", - "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Output file where the output from the \u0027bedtools getfasta\u0027 commend will\nbe written to.\n" + "description": "Type: `file`, required, default: `$id.$key.output`. Output file where the output from the \u0027bedtools getfasta\u0027 commend will\nbe written to", + "help_text": "Type: `file`, required, default: `$id.$key.output`. Output file where the output from the \u0027bedtools getfasta\u0027 commend will\nbe written to.\n" , - "default":"$id.$key.output.output" + "default":"$id.$key.output" } diff --git a/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml index b4d984ca..573ddbd2 100644 --- a/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml @@ -275,16 +275,16 @@ build_info: engine: "docker|native" output: "target/nextflow/bedtools/bedtools_groupby" executable: "target/nextflow/bedtools/bedtools_groupby/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/bedtools/bedtools_groupby/main.nf b/target/nextflow/bedtools/bedtools_groupby/main.nf index 0512adc9..b16882bc 100644 --- a/target/nextflow/bedtools/bedtools_groupby/main.nf +++ b/target/nextflow/bedtools/bedtools_groupby/main.nf @@ -1,6 +1,6 @@ // bedtools_groupby main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3364,16 +3359,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_groupby", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3808,7 +3803,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3822,6 +3817,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml index a9c89fe5..89734842 100644 --- a/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml @@ -412,16 +412,16 @@ build_info: engine: "docker|native" output: "target/nextflow/bedtools/bedtools_intersect" executable: "target/nextflow/bedtools/bedtools_intersect/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/bedtools/bedtools_intersect/main.nf b/target/nextflow/bedtools/bedtools_intersect/main.nf index 4e60952d..e34bfbdd 100644 --- a/target/nextflow/bedtools/bedtools_intersect/main.nf +++ b/target/nextflow/bedtools/bedtools_intersect/main.nf @@ -1,6 +1,6 @@ // bedtools_intersect main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3516,16 +3511,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_intersect", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -4010,7 +4005,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -4024,6 +4019,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml index a073f27a..004dbf51 100644 --- a/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml @@ -212,16 +212,16 @@ build_info: engine: "docker|native" output: "target/nextflow/bedtools/bedtools_links" executable: "target/nextflow/bedtools/bedtools_links/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/bedtools/bedtools_links/main.nf b/target/nextflow/bedtools/bedtools_links/main.nf index 1164526c..a38d612f 100644 --- a/target/nextflow/bedtools/bedtools_links/main.nf +++ b/target/nextflow/bedtools/bedtools_links/main.nf @@ -1,6 +1,6 @@ // bedtools_links main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3307,16 +3302,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_links", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3722,7 +3717,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3736,6 +3731,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/bedtools/bedtools_links/nextflow_schema.json b/target/nextflow/bedtools/bedtools_links/nextflow_schema.json index 79b6d9b6..61084c87 100644 --- a/target/nextflow/bedtools/bedtools_links/nextflow_schema.json +++ b/target/nextflow/bedtools/bedtools_links/nextflow_schema.json @@ -37,10 +37,10 @@ "output": { "type": "string", - "description": "Type: `file`, default: `$id.$key.output.output`. Output HTML file to be written", - "help_text": "Type: `file`, default: `$id.$key.output.output`. Output HTML file to be written." + "description": "Type: `file`, default: `$id.$key.output`. Output HTML file to be written", + "help_text": "Type: `file`, default: `$id.$key.output`. Output HTML file to be written." , - "default":"$id.$key.output.output" + "default":"$id.$key.output" } diff --git a/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml index 87101c94..86af3e40 100644 --- a/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml @@ -281,16 +281,16 @@ build_info: engine: "docker|native" output: "target/nextflow/bedtools/bedtools_merge" executable: "target/nextflow/bedtools/bedtools_merge/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/bedtools/bedtools_merge/main.nf b/target/nextflow/bedtools/bedtools_merge/main.nf index 05e8efae..e8888b23 100644 --- a/target/nextflow/bedtools/bedtools_merge/main.nf +++ b/target/nextflow/bedtools/bedtools_merge/main.nf @@ -1,6 +1,6 @@ // bedtools_merge main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3368,16 +3363,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_merge", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3811,7 +3806,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3825,6 +3820,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/bedtools/bedtools_merge/nextflow_schema.json b/target/nextflow/bedtools/bedtools_merge/nextflow_schema.json index 77aaf1ab..1abef291 100644 --- a/target/nextflow/bedtools/bedtools_merge/nextflow_schema.json +++ b/target/nextflow/bedtools/bedtools_merge/nextflow_schema.json @@ -37,10 +37,10 @@ "output": { "type": "string", - "description": "Type: `file`, required, default: `$id.$key.output.output`. Output merged file BED to be written", - "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Output merged file BED to be written." + "description": "Type: `file`, required, default: `$id.$key.output`. Output merged file BED to be written", + "help_text": "Type: `file`, required, default: `$id.$key.output`. Output merged file BED to be written." , - "default":"$id.$key.output.output" + "default":"$id.$key.output" } diff --git a/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml index 649b326e..28662308 100644 --- a/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml @@ -224,16 +224,16 @@ build_info: engine: "docker|native" output: "target/nextflow/bedtools/bedtools_sort" executable: "target/nextflow/bedtools/bedtools_sort/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/bedtools/bedtools_sort/main.nf b/target/nextflow/bedtools/bedtools_sort/main.nf index 700a91d7..27a6dfda 100644 --- a/target/nextflow/bedtools/bedtools_sort/main.nf +++ b/target/nextflow/bedtools/bedtools_sort/main.nf @@ -1,6 +1,6 @@ // bedtools_sort main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3326,16 +3321,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_sort", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3767,7 +3762,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3781,6 +3776,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/bedtools/bedtools_sort/nextflow_schema.json b/target/nextflow/bedtools/bedtools_sort/nextflow_schema.json index 1cbf84c5..06b57afd 100644 --- a/target/nextflow/bedtools/bedtools_sort/nextflow_schema.json +++ b/target/nextflow/bedtools/bedtools_sort/nextflow_schema.json @@ -37,10 +37,10 @@ "output": { "type": "string", - "description": "Type: `file`, default: `$id.$key.output.output`. Output sorted file (bed/gff/vcf) to be written", - "help_text": "Type: `file`, default: `$id.$key.output.output`. Output sorted file (bed/gff/vcf) to be written." + "description": "Type: `file`, default: `$id.$key.output`. Output sorted file (bed/gff/vcf) to be written", + "help_text": "Type: `file`, default: `$id.$key.output`. Output sorted file (bed/gff/vcf) to be written." , - "default":"$id.$key.output.output" + "default":"$id.$key.output" } diff --git a/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml b/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml index 5dac4581..6b340030 100644 --- a/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml +++ b/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml @@ -160,16 +160,16 @@ build_info: engine: "docker|native" output: "target/nextflow/busco/busco_download_datasets" executable: "target/nextflow/busco/busco_download_datasets/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/busco/busco_download_datasets/main.nf b/target/nextflow/busco/busco_download_datasets/main.nf index a2baa26d..ef5063a6 100644 --- a/target/nextflow/busco/busco_download_datasets/main.nf +++ b/target/nextflow/busco/busco_download_datasets/main.nf @@ -1,6 +1,6 @@ // busco_download_datasets main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3245,16 +3240,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/busco/busco_download_datasets", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3657,7 +3652,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3671,6 +3666,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/busco/busco_download_datasets/nextflow_schema.json b/target/nextflow/busco/busco_download_datasets/nextflow_schema.json index 936911c2..5f010260 100644 --- a/target/nextflow/busco/busco_download_datasets/nextflow_schema.json +++ b/target/nextflow/busco/busco_download_datasets/nextflow_schema.json @@ -37,10 +37,10 @@ "download_path": { "type": "string", - "description": "Type: `file`, default: `$id.$key.download_path.download_path`, example: `busco_downloads`. Local filepath for storing BUSCO dataset downloads\n", - "help_text": "Type: `file`, default: `$id.$key.download_path.download_path`, example: `busco_downloads`. Local filepath for storing BUSCO dataset downloads\n" + "description": "Type: `file`, default: `busco_downloads`, example: `busco_downloads`. Local filepath for storing BUSCO dataset downloads\n", + "help_text": "Type: `file`, default: `busco_downloads`, example: `busco_downloads`. Local filepath for storing BUSCO dataset downloads\n" , - "default":"$id.$key.download_path.download_path" + "default":"busco_downloads" } diff --git a/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml b/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml index 33cf58e5..063c2ef8 100644 --- a/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml +++ b/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml @@ -147,16 +147,16 @@ build_info: engine: "docker|native" output: "target/nextflow/busco/busco_list_datasets" executable: "target/nextflow/busco/busco_list_datasets/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/busco/busco_list_datasets/main.nf b/target/nextflow/busco/busco_list_datasets/main.nf index 406a6027..be474549 100644 --- a/target/nextflow/busco/busco_list_datasets/main.nf +++ b/target/nextflow/busco/busco_list_datasets/main.nf @@ -1,6 +1,6 @@ // busco_list_datasets main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3231,16 +3226,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/busco/busco_list_datasets", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3634,7 +3629,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3648,6 +3643,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/busco/busco_list_datasets/nextflow_schema.json b/target/nextflow/busco/busco_list_datasets/nextflow_schema.json index ced3a09a..40c4b729 100644 --- a/target/nextflow/busco/busco_list_datasets/nextflow_schema.json +++ b/target/nextflow/busco/busco_list_datasets/nextflow_schema.json @@ -17,10 +17,10 @@ "output": { "type": "string", - "description": "Type: `file`, default: `$id.$key.output.txt`, example: `file.txt`. Output file of the available busco datasets\n", - "help_text": "Type: `file`, default: `$id.$key.output.txt`, example: `file.txt`. Output file of the available busco datasets\n" + "description": "Type: `file`, default: `busco_dataset_list.txt`, example: `file.txt`. Output file of the available busco datasets\n", + "help_text": "Type: `file`, default: `busco_dataset_list.txt`, example: `file.txt`. Output file of the available busco datasets\n" , - "default":"$id.$key.output.txt" + "default":"busco_dataset_list.txt" } diff --git a/target/nextflow/busco/busco_run/.config.vsh.yaml b/target/nextflow/busco/busco_run/.config.vsh.yaml index 52508ea6..126f98e6 100644 --- a/target/nextflow/busco/busco_run/.config.vsh.yaml +++ b/target/nextflow/busco/busco_run/.config.vsh.yaml @@ -425,16 +425,16 @@ build_info: engine: "docker|native" output: "target/nextflow/busco/busco_run" executable: "target/nextflow/busco/busco_run/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/busco/busco_run/main.nf b/target/nextflow/busco/busco_run/main.nf index 788fecc8..1a8bd3eb 100644 --- a/target/nextflow/busco/busco_run/main.nf +++ b/target/nextflow/busco/busco_run/main.nf @@ -1,6 +1,6 @@ // busco_run main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3543,16 +3538,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/busco/busco_run", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -4044,7 +4039,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -4058,6 +4053,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/busco/busco_run/nextflow_schema.json b/target/nextflow/busco/busco_run/nextflow_schema.json index ce50aeee..69e6a8e3 100644 --- a/target/nextflow/busco/busco_run/nextflow_schema.json +++ b/target/nextflow/busco/busco_run/nextflow_schema.json @@ -103,10 +103,10 @@ "output_dir": { "type": "string", - "description": "Type: `file`, default: `$id.$key.output_dir.output_dir`, example: `output_dir`. The full output directory, if so desired", - "help_text": "Type: `file`, default: `$id.$key.output_dir.output_dir`, example: `output_dir`. The full output directory, if so desired.\n" + "description": "Type: `file`, default: `$id.$key.output_dir`, example: `output_dir`. The full output directory, if so desired", + "help_text": "Type: `file`, default: `$id.$key.output_dir`, example: `output_dir`. The full output directory, if so desired.\n" , - "default":"$id.$key.output_dir.output_dir" + "default":"$id.$key.output_dir" } diff --git a/target/nextflow/cellranger/cellranger_mkref/.config.vsh.yaml b/target/nextflow/cellranger/cellranger_mkref/.config.vsh.yaml index 7e548aa8..2daad8a0 100644 --- a/target/nextflow/cellranger/cellranger_mkref/.config.vsh.yaml +++ b/target/nextflow/cellranger/cellranger_mkref/.config.vsh.yaml @@ -197,16 +197,16 @@ build_info: engine: "docker|native" output: "target/nextflow/cellranger/cellranger_mkref" executable: "target/nextflow/cellranger/cellranger_mkref/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/cellranger/cellranger_mkref/main.nf b/target/nextflow/cellranger/cellranger_mkref/main.nf index a659daf5..36ebbcba 100644 --- a/target/nextflow/cellranger/cellranger_mkref/main.nf +++ b/target/nextflow/cellranger/cellranger_mkref/main.nf @@ -1,6 +1,6 @@ // cellranger_mkref main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3293,16 +3288,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/cellranger/cellranger_mkref", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3728,7 +3723,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3742,6 +3737,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/cellranger/cellranger_mkref/nextflow_schema.json b/target/nextflow/cellranger/cellranger_mkref/nextflow_schema.json index d860ac70..c1069571 100644 --- a/target/nextflow/cellranger/cellranger_mkref/nextflow_schema.json +++ b/target/nextflow/cellranger/cellranger_mkref/nextflow_schema.json @@ -47,10 +47,10 @@ "output": { "type": "string", - "description": "Type: `file`, required, default: `$id.$key.output.output`, example: `cellranger_reference`. Output folder", - "help_text": "Type: `file`, required, default: `$id.$key.output.output`, example: `cellranger_reference`. Output folder" + "description": "Type: `file`, required, default: `$id.$key.output`, example: `cellranger_reference`. Output folder", + "help_text": "Type: `file`, required, default: `$id.$key.output`, example: `cellranger_reference`. Output folder" , - "default":"$id.$key.output.output" + "default":"$id.$key.output" } diff --git a/target/nextflow/cutadapt/.config.vsh.yaml b/target/nextflow/cutadapt/.config.vsh.yaml index 2d53cfe0..b80d1a21 100644 --- a/target/nextflow/cutadapt/.config.vsh.yaml +++ b/target/nextflow/cutadapt/.config.vsh.yaml @@ -742,16 +742,16 @@ build_info: engine: "docker|native" output: "target/nextflow/cutadapt" executable: "target/nextflow/cutadapt/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/cutadapt/main.nf b/target/nextflow/cutadapt/main.nf index 3459160e..4cae3138 100644 --- a/target/nextflow/cutadapt/main.nf +++ b/target/nextflow/cutadapt/main.nf @@ -1,6 +1,6 @@ // cutadapt main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3853,16 +3848,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/cutadapt", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -4555,7 +4550,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -4569,6 +4564,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/falco/.config.vsh.yaml b/target/nextflow/falco/.config.vsh.yaml index 22158e46..5cd6573e 100644 --- a/target/nextflow/falco/.config.vsh.yaml +++ b/target/nextflow/falco/.config.vsh.yaml @@ -319,16 +319,16 @@ build_info: engine: "docker|native" output: "target/nextflow/falco" executable: "target/nextflow/falco/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/falco/main.nf b/target/nextflow/falco/main.nf index ecfe93a3..b918c670 100644 --- a/target/nextflow/falco/main.nf +++ b/target/nextflow/falco/main.nf @@ -1,6 +1,6 @@ // falco main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3404,16 +3399,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/falco", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3839,7 +3834,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3853,6 +3848,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/falco/nextflow_schema.json b/target/nextflow/falco/nextflow_schema.json index 8d40e419..35d4cfa6 100644 --- a/target/nextflow/falco/nextflow_schema.json +++ b/target/nextflow/falco/nextflow_schema.json @@ -120,10 +120,10 @@ "outdir": { "type": "string", - "description": "Type: `file`, required, default: `$id.$key.outdir.outdir`, example: `output`. Create all output files in the specified \noutput directory", - "help_text": "Type: `file`, required, default: `$id.$key.outdir.outdir`, example: `output`. Create all output files in the specified \noutput directory. FALCO-SPECIFIC: If the \ndirectory does not exists, the program will \ncreate it.\n" + "description": "Type: `file`, required, default: `$id.$key.outdir`, example: `output`. Create all output files in the specified \noutput directory", + "help_text": "Type: `file`, required, default: `$id.$key.outdir`, example: `output`. Create all output files in the specified \noutput directory. FALCO-SPECIFIC: If the \ndirectory does not exists, the program will \ncreate it.\n" , - "default":"$id.$key.outdir.outdir" + "default":"$id.$key.outdir" } @@ -143,10 +143,10 @@ "data_filename": { "type": "string", - "description": "Type: `file`, default: `$id.$key.data_filename.data_filename`. [Falco only] Specify filename for FastQC \ndata output (TXT)", - "help_text": "Type: `file`, default: `$id.$key.data_filename.data_filename`. [Falco only] Specify filename for FastQC \ndata output (TXT). If not specified, it will \nbe called fastq_data.txt in either the input \nfile\u0027s directory or the one specified in the \n--output flag. Only available when running \nfalco with a single input.\n" + "description": "Type: `file`, default: `$id.$key.data_filename`. [Falco only] Specify filename for FastQC \ndata output (TXT)", + "help_text": "Type: `file`, default: `$id.$key.data_filename`. [Falco only] Specify filename for FastQC \ndata output (TXT). If not specified, it will \nbe called fastq_data.txt in either the input \nfile\u0027s directory or the one specified in the \n--output flag. Only available when running \nfalco with a single input.\n" , - "default":"$id.$key.data_filename.data_filename" + "default":"$id.$key.data_filename" } @@ -154,10 +154,10 @@ "report_filename": { "type": "string", - "description": "Type: `file`, default: `$id.$key.report_filename.report_filename`. [Falco only] Specify filename for FastQC \nreport output (HTML)", - "help_text": "Type: `file`, default: `$id.$key.report_filename.report_filename`. [Falco only] Specify filename for FastQC \nreport output (HTML). If not specified, it \nwill be called fastq_report.html in either \nthe input file\u0027s directory or the one \nspecified in the --output flag. Only \navailable when running falco with a single \ninput.\n" + "description": "Type: `file`, default: `$id.$key.report_filename`. [Falco only] Specify filename for FastQC \nreport output (HTML)", + "help_text": "Type: `file`, default: `$id.$key.report_filename`. [Falco only] Specify filename for FastQC \nreport output (HTML). If not specified, it \nwill be called fastq_report.html in either \nthe input file\u0027s directory or the one \nspecified in the --output flag. Only \navailable when running falco with a single \ninput.\n" , - "default":"$id.$key.report_filename.report_filename" + "default":"$id.$key.report_filename" } @@ -165,10 +165,10 @@ "summary_filename": { "type": "string", - "description": "Type: `file`, default: `$id.$key.summary_filename.summary_filename`. [Falco only] Specify filename for the short \nsummary output (TXT)", - "help_text": "Type: `file`, default: `$id.$key.summary_filename.summary_filename`. [Falco only] Specify filename for the short \nsummary output (TXT). If not specified, it \nwill be called fastq_report.html in either \nthe input file\u0027s directory or the one \nspecified in the --output flag. Only \navailable when running falco with a single \ninput.\n" + "description": "Type: `file`, default: `$id.$key.summary_filename`. [Falco only] Specify filename for the short \nsummary output (TXT)", + "help_text": "Type: `file`, default: `$id.$key.summary_filename`. [Falco only] Specify filename for the short \nsummary output (TXT). If not specified, it \nwill be called fastq_report.html in either \nthe input file\u0027s directory or the one \nspecified in the --output flag. Only \navailable when running falco with a single \ninput.\n" , - "default":"$id.$key.summary_filename.summary_filename" + "default":"$id.$key.summary_filename" } diff --git a/target/nextflow/fastp/.config.vsh.yaml b/target/nextflow/fastp/.config.vsh.yaml index 3f1229e2..95b7f316 100644 --- a/target/nextflow/fastp/.config.vsh.yaml +++ b/target/nextflow/fastp/.config.vsh.yaml @@ -1085,16 +1085,16 @@ build_info: engine: "docker|native" output: "target/nextflow/fastp" executable: "target/nextflow/fastp/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/fastp/main.nf b/target/nextflow/fastp/main.nf index a1785e1a..00d02b0e 100644 --- a/target/nextflow/fastp/main.nf +++ b/target/nextflow/fastp/main.nf @@ -1,6 +1,6 @@ // fastp main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -4257,16 +4252,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/fastp", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -4841,7 +4836,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -4855,6 +4850,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/fastp/nextflow_schema.json b/target/nextflow/fastp/nextflow_schema.json index bbc0c539..34670004 100644 --- a/target/nextflow/fastp/nextflow_schema.json +++ b/target/nextflow/fastp/nextflow_schema.json @@ -102,10 +102,10 @@ "overlapped_out": { "type": "string", - "description": "Type: `file`, default: `$id.$key.overlapped_out.overlapped_out`. For each read pair, output the overlapped region if it has no any mismatched base", - "help_text": "Type: `file`, default: `$id.$key.overlapped_out.overlapped_out`. For each read pair, output the overlapped region if it has no any mismatched base.\n" + "description": "Type: `file`, default: `$id.$key.overlapped_out`. For each read pair, output the overlapped region if it has no any mismatched base", + "help_text": "Type: `file`, default: `$id.$key.overlapped_out`. For each read pair, output the overlapped region if it has no any mismatched base.\n" , - "default":"$id.$key.overlapped_out.overlapped_out" + "default":"$id.$key.overlapped_out" } diff --git a/target/nextflow/fastqc/.config.vsh.yaml b/target/nextflow/fastqc/.config.vsh.yaml index 89c00186..047327fd 100644 --- a/target/nextflow/fastqc/.config.vsh.yaml +++ b/target/nextflow/fastqc/.config.vsh.yaml @@ -342,16 +342,16 @@ build_info: engine: "docker|native" output: "target/nextflow/fastqc" executable: "target/nextflow/fastqc/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/fastqc/main.nf b/target/nextflow/fastqc/main.nf index ad028b94..cc66f7d7 100644 --- a/target/nextflow/fastqc/main.nf +++ b/target/nextflow/fastqc/main.nf @@ -1,6 +1,6 @@ // fastqc main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3416,16 +3411,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/fastqc", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3913,7 +3908,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3927,6 +3922,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/featurecounts/.config.vsh.yaml b/target/nextflow/featurecounts/.config.vsh.yaml index c66e20f3..6b958d29 100644 --- a/target/nextflow/featurecounts/.config.vsh.yaml +++ b/target/nextflow/featurecounts/.config.vsh.yaml @@ -647,16 +647,16 @@ build_info: engine: "docker|native" output: "target/nextflow/featurecounts" executable: "target/nextflow/featurecounts/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/featurecounts/main.nf b/target/nextflow/featurecounts/main.nf index 85b61286..cdc65581 100644 --- a/target/nextflow/featurecounts/main.nf +++ b/target/nextflow/featurecounts/main.nf @@ -1,6 +1,6 @@ // featurecounts main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3783,16 +3778,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/featurecounts", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -4324,7 +4319,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -4338,6 +4333,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/featurecounts/nextflow_schema.json b/target/nextflow/featurecounts/nextflow_schema.json index 8b277f20..9276bfa3 100644 --- a/target/nextflow/featurecounts/nextflow_schema.json +++ b/target/nextflow/featurecounts/nextflow_schema.json @@ -573,10 +573,10 @@ "detailed_results": { "type": "string", - "description": "Type: `file`, default: `$id.$key.detailed_results.detailed_results`, example: `detailed_results`. Directory to save the detailed assignment results", - "help_text": "Type: `file`, default: `$id.$key.detailed_results.detailed_results`, example: `detailed_results`. Directory to save the detailed assignment results. Use `--detailed_results_format` to determine the format of the detailed results.\n" + "description": "Type: `file`, default: `$id.$key.detailed_results`, example: `detailed_results`. Directory to save the detailed assignment results", + "help_text": "Type: `file`, default: `$id.$key.detailed_results`, example: `detailed_results`. Directory to save the detailed assignment results. Use `--detailed_results_format` to determine the format of the detailed results.\n" , - "default":"$id.$key.detailed_results.detailed_results" + "default":"$id.$key.detailed_results" } diff --git a/target/nextflow/fq_subsample/.config.vsh.yaml b/target/nextflow/fq_subsample/.config.vsh.yaml index 5a4246a5..22928b5d 100644 --- a/target/nextflow/fq_subsample/.config.vsh.yaml +++ b/target/nextflow/fq_subsample/.config.vsh.yaml @@ -192,16 +192,16 @@ build_info: engine: "docker|native" output: "target/nextflow/fq_subsample" executable: "target/nextflow/fq_subsample/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/fq_subsample/main.nf b/target/nextflow/fq_subsample/main.nf index c074939e..cc6aacdd 100644 --- a/target/nextflow/fq_subsample/main.nf +++ b/target/nextflow/fq_subsample/main.nf @@ -1,6 +1,6 @@ // fq_subsample main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -82,64 +82,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -151,10 +143,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3266,16 +3261,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/fq_subsample", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3694,7 +3689,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3708,6 +3703,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/fq_subsample/nextflow_schema.json b/target/nextflow/fq_subsample/nextflow_schema.json index 511bd91d..83a6f613 100644 --- a/target/nextflow/fq_subsample/nextflow_schema.json +++ b/target/nextflow/fq_subsample/nextflow_schema.json @@ -47,10 +47,10 @@ "output_1": { "type": "string", - "description": "Type: `file`, default: `$id.$key.output_1.output_1`. Sampled read 1 fastq files", - "help_text": "Type: `file`, default: `$id.$key.output_1.output_1`. Sampled read 1 fastq files. Output will be gzipped if ends in `.gz`." + "description": "Type: `file`, default: `$id.$key.output_1`. Sampled read 1 fastq files", + "help_text": "Type: `file`, default: `$id.$key.output_1`. Sampled read 1 fastq files. Output will be gzipped if ends in `.gz`." , - "default":"$id.$key.output_1.output_1" + "default":"$id.$key.output_1" } @@ -58,10 +58,10 @@ "output_2": { "type": "string", - "description": "Type: `file`, default: `$id.$key.output_2.output_2`. Sampled read 2 fastq files", - "help_text": "Type: `file`, default: `$id.$key.output_2.output_2`. Sampled read 2 fastq files. Output will be gzipped if ends in `.gz`." + "description": "Type: `file`, default: `$id.$key.output_2`. Sampled read 2 fastq files", + "help_text": "Type: `file`, default: `$id.$key.output_2`. Sampled read 2 fastq files. Output will be gzipped if ends in `.gz`." , - "default":"$id.$key.output_2.output_2" + "default":"$id.$key.output_2" } diff --git a/target/nextflow/gffread/.config.vsh.yaml b/target/nextflow/gffread/.config.vsh.yaml index 2f899ea7..0e86d7da 100644 --- a/target/nextflow/gffread/.config.vsh.yaml +++ b/target/nextflow/gffread/.config.vsh.yaml @@ -687,16 +687,16 @@ build_info: engine: "docker|native" output: "target/nextflow/gffread" executable: "target/nextflow/gffread/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/gffread/main.nf b/target/nextflow/gffread/main.nf index 7e7d4b46..64b61619 100644 --- a/target/nextflow/gffread/main.nf +++ b/target/nextflow/gffread/main.nf @@ -1,6 +1,6 @@ // gffread main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3840,16 +3835,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/gffread", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -4427,7 +4422,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -4441,6 +4436,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml b/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml index b2d20ba9..9fed6f8c 100644 --- a/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml +++ b/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml @@ -220,16 +220,16 @@ build_info: engine: "docker|native" output: "target/nextflow/kallisto/kallisto_index" executable: "target/nextflow/kallisto/kallisto_index/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/kallisto/kallisto_index/main.nf b/target/nextflow/kallisto/kallisto_index/main.nf index c8616079..985e23ea 100644 --- a/target/nextflow/kallisto/kallisto_index/main.nf +++ b/target/nextflow/kallisto/kallisto_index/main.nf @@ -1,6 +1,6 @@ // kallisto_index main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -82,64 +82,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -151,10 +143,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3305,16 +3300,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/kallisto/kallisto_index", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3744,7 +3739,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3758,6 +3753,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/kallisto/kallisto_index/nextflow_schema.json b/target/nextflow/kallisto/kallisto_index/nextflow_schema.json index 6d0b6164..44e9e575 100644 --- a/target/nextflow/kallisto/kallisto_index/nextflow_schema.json +++ b/target/nextflow/kallisto/kallisto_index/nextflow_schema.json @@ -47,10 +47,10 @@ "index": { "type": "string", - "description": "Type: `file`, default: `$id.$key.index.index`, example: `Kallisto_index`. ", - "help_text": "Type: `file`, default: `$id.$key.index.index`, example: `Kallisto_index`. " + "description": "Type: `file`, default: `$id.$key.index`, example: `Kallisto_index`. ", + "help_text": "Type: `file`, default: `$id.$key.index`, example: `Kallisto_index`. " , - "default":"$id.$key.index.index" + "default":"$id.$key.index" } diff --git a/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml b/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml index 03d75ab3..3312ba17 100644 --- a/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml +++ b/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml @@ -248,16 +248,16 @@ build_info: engine: "docker|native" output: "target/nextflow/kallisto/kallisto_quant" executable: "target/nextflow/kallisto/kallisto_quant/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/kallisto/kallisto_quant/main.nf b/target/nextflow/kallisto/kallisto_quant/main.nf index 09a4befb..f05e9040 100644 --- a/target/nextflow/kallisto/kallisto_quant/main.nf +++ b/target/nextflow/kallisto/kallisto_quant/main.nf @@ -1,6 +1,6 @@ // kallisto_quant main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -82,64 +82,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -151,10 +143,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3339,16 +3334,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/kallisto/kallisto_quant", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3792,7 +3787,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3806,6 +3801,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/kallisto/kallisto_quant/nextflow_schema.json b/target/nextflow/kallisto/kallisto_quant/nextflow_schema.json index 40a2444f..384e1537 100644 --- a/target/nextflow/kallisto/kallisto_quant/nextflow_schema.json +++ b/target/nextflow/kallisto/kallisto_quant/nextflow_schema.json @@ -47,10 +47,10 @@ "output_dir": { "type": "string", - "description": "Type: `file`, required, default: `$id.$key.output_dir.output_dir`. Directory to write output to", - "help_text": "Type: `file`, required, default: `$id.$key.output_dir.output_dir`. Directory to write output to." + "description": "Type: `file`, required, default: `$id.$key.output_dir`. Directory to write output to", + "help_text": "Type: `file`, required, default: `$id.$key.output_dir`. Directory to write output to." , - "default":"$id.$key.output_dir.output_dir" + "default":"$id.$key.output_dir" } @@ -58,10 +58,10 @@ "log": { "type": "string", - "description": "Type: `file`, default: `$id.$key.log.log`. File containing log information from running kallisto quant", - "help_text": "Type: `file`, default: `$id.$key.log.log`. File containing log information from running kallisto quant" + "description": "Type: `file`, default: `$id.$key.log`. File containing log information from running kallisto quant", + "help_text": "Type: `file`, default: `$id.$key.log`. File containing log information from running kallisto quant" , - "default":"$id.$key.log.log" + "default":"$id.$key.log" } diff --git a/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml b/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml index d8ae68cf..20dc1dfa 100644 --- a/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml +++ b/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml @@ -509,16 +509,16 @@ build_info: engine: "docker|native" output: "target/nextflow/lofreq/lofreq_call" executable: "target/nextflow/lofreq/lofreq_call/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/lofreq/lofreq_call/main.nf b/target/nextflow/lofreq/lofreq_call/main.nf index 67a6f26a..adec26c5 100644 --- a/target/nextflow/lofreq/lofreq_call/main.nf +++ b/target/nextflow/lofreq/lofreq_call/main.nf @@ -1,6 +1,6 @@ // lofreq_call main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3648,16 +3643,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/lofreq/lofreq_call", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -4143,7 +4138,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -4157,6 +4152,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml b/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml index a9ab0f4e..4cfd2526 100644 --- a/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml +++ b/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml @@ -217,16 +217,16 @@ build_info: engine: "docker|native" output: "target/nextflow/lofreq/lofreq_indelqual" executable: "target/nextflow/lofreq/lofreq_indelqual/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/lofreq/lofreq_indelqual/main.nf b/target/nextflow/lofreq/lofreq_indelqual/main.nf index b2e78c35..2bb2fa27 100644 --- a/target/nextflow/lofreq/lofreq_indelqual/main.nf +++ b/target/nextflow/lofreq/lofreq_indelqual/main.nf @@ -1,6 +1,6 @@ // lofreq_indelqual main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3311,16 +3306,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/lofreq/lofreq_indelqual", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3730,7 +3725,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3744,6 +3739,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/multiqc/.config.vsh.yaml b/target/nextflow/multiqc/.config.vsh.yaml index b6cfcd77..02ad583b 100644 --- a/target/nextflow/multiqc/.config.vsh.yaml +++ b/target/nextflow/multiqc/.config.vsh.yaml @@ -458,16 +458,16 @@ build_info: engine: "docker|native" output: "target/nextflow/multiqc" executable: "target/nextflow/multiqc/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/multiqc/main.nf b/target/nextflow/multiqc/main.nf index a60a6714..938679b7 100644 --- a/target/nextflow/multiqc/main.nf +++ b/target/nextflow/multiqc/main.nf @@ -1,6 +1,6 @@ // multiqc main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3600,16 +3595,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/multiqc", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -4170,7 +4165,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -4184,6 +4179,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/multiqc/nextflow_schema.json b/target/nextflow/multiqc/nextflow_schema.json index 6a3bd5c6..04c0a3b7 100644 --- a/target/nextflow/multiqc/nextflow_schema.json +++ b/target/nextflow/multiqc/nextflow_schema.json @@ -48,10 +48,10 @@ "output_data": { "type": "string", - "description": "Type: `file`, default: `$id.$key.output_data.output_data`, example: `multiqc_data`. Output directory for parsed data files", - "help_text": "Type: `file`, default: `$id.$key.output_data.output_data`, example: `multiqc_data`. Output directory for parsed data files. If not provided, parsed data will not be published.\n" + "description": "Type: `file`, default: `$id.$key.output_data`, example: `multiqc_data`. Output directory for parsed data files", + "help_text": "Type: `file`, default: `$id.$key.output_data`, example: `multiqc_data`. Output directory for parsed data files. If not provided, parsed data will not be published.\n" , - "default":"$id.$key.output_data.output_data" + "default":"$id.$key.output_data" } @@ -59,10 +59,10 @@ "output_plots": { "type": "string", - "description": "Type: `file`, default: `$id.$key.output_plots.output_plots`, example: `multiqc_plots`. Output directory for generated plots", - "help_text": "Type: `file`, default: `$id.$key.output_plots.output_plots`, example: `multiqc_plots`. Output directory for generated plots. If not provided, plots will not be published.\n" + "description": "Type: `file`, default: `$id.$key.output_plots`, example: `multiqc_plots`. Output directory for generated plots", + "help_text": "Type: `file`, default: `$id.$key.output_plots`, example: `multiqc_plots`. Output directory for generated plots. If not provided, plots will not be published.\n" , - "default":"$id.$key.output_plots.output_plots" + "default":"$id.$key.output_plots" } diff --git a/target/nextflow/nanoplot/.config.vsh.yaml b/target/nextflow/nanoplot/.config.vsh.yaml index 5e615f48..650a10b6 100644 --- a/target/nextflow/nanoplot/.config.vsh.yaml +++ b/target/nextflow/nanoplot/.config.vsh.yaml @@ -494,16 +494,16 @@ build_info: engine: "docker|native" output: "target/nextflow/nanoplot" executable: "target/nextflow/nanoplot/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/nanoplot/main.nf b/target/nextflow/nanoplot/main.nf index 07ca67cf..7e7c4435 100644 --- a/target/nextflow/nanoplot/main.nf +++ b/target/nextflow/nanoplot/main.nf @@ -1,6 +1,6 @@ // nanoplot main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -82,64 +82,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -151,10 +143,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3631,16 +3626,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/nanoplot", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -4201,7 +4196,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -4215,6 +4210,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/nanoplot/nextflow_schema.json b/target/nextflow/nanoplot/nextflow_schema.json index 81c5d459..74ef439f 100644 --- a/target/nextflow/nanoplot/nextflow_schema.json +++ b/target/nextflow/nanoplot/nextflow_schema.json @@ -127,10 +127,10 @@ "outdir": { "type": "string", - "description": "Type: `file`, required, default: `$id.$key.outdir.outdir`. Specify directory in which output has to be created", - "help_text": "Type: `file`, required, default: `$id.$key.outdir.outdir`. Specify directory in which output has to be created." + "description": "Type: `file`, required, default: `$id.$key.outdir`. Specify directory in which output has to be created", + "help_text": "Type: `file`, required, default: `$id.$key.outdir`. Specify directory in which output has to be created." , - "default":"$id.$key.outdir.outdir" + "default":"$id.$key.outdir" } diff --git a/target/nextflow/pear/.config.vsh.yaml b/target/nextflow/pear/.config.vsh.yaml index 7d8a3460..d1b5c0a9 100644 --- a/target/nextflow/pear/.config.vsh.yaml +++ b/target/nextflow/pear/.config.vsh.yaml @@ -400,16 +400,16 @@ build_info: engine: "docker|native" output: "target/nextflow/pear" executable: "target/nextflow/pear/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/pear/main.nf b/target/nextflow/pear/main.nf index 6f0e67a1..5ab6c423 100644 --- a/target/nextflow/pear/main.nf +++ b/target/nextflow/pear/main.nf @@ -1,6 +1,6 @@ // pear main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3493,16 +3488,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/pear", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3973,7 +3968,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3987,6 +3982,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/pear/nextflow_schema.json b/target/nextflow/pear/nextflow_schema.json index af164e71..d5245704 100644 --- a/target/nextflow/pear/nextflow_schema.json +++ b/target/nextflow/pear/nextflow_schema.json @@ -47,10 +47,10 @@ "assembled": { "type": "string", - "description": "Type: `file`, required, default: `$id.$key.assembled.assembled`. The output file containing assembled reads", - "help_text": "Type: `file`, required, default: `$id.$key.assembled.assembled`. The output file containing assembled reads. Can be compressed with gzip." + "description": "Type: `file`, required, default: `$id.$key.assembled`. The output file containing assembled reads", + "help_text": "Type: `file`, required, default: `$id.$key.assembled`. The output file containing assembled reads. Can be compressed with gzip." , - "default":"$id.$key.assembled.assembled" + "default":"$id.$key.assembled" } @@ -58,10 +58,10 @@ "unassembled_forward": { "type": "string", - "description": "Type: `file`, required, default: `$id.$key.unassembled_forward.unassembled_forward`. The output file containing forward reads that could not be assembled", - "help_text": "Type: `file`, required, default: `$id.$key.unassembled_forward.unassembled_forward`. The output file containing forward reads that could not be assembled. Can be compressed with gzip." + "description": "Type: `file`, required, default: `$id.$key.unassembled_forward`. The output file containing forward reads that could not be assembled", + "help_text": "Type: `file`, required, default: `$id.$key.unassembled_forward`. The output file containing forward reads that could not be assembled. Can be compressed with gzip." , - "default":"$id.$key.unassembled_forward.unassembled_forward" + "default":"$id.$key.unassembled_forward" } @@ -69,10 +69,10 @@ "unassembled_reverse": { "type": "string", - "description": "Type: `file`, required, default: `$id.$key.unassembled_reverse.unassembled_reverse`. The output file containing reverse reads that could not be assembled", - "help_text": "Type: `file`, required, default: `$id.$key.unassembled_reverse.unassembled_reverse`. The output file containing reverse reads that could not be assembled. Can be compressed with gzip." + "description": "Type: `file`, required, default: `$id.$key.unassembled_reverse`. The output file containing reverse reads that could not be assembled", + "help_text": "Type: `file`, required, default: `$id.$key.unassembled_reverse`. The output file containing reverse reads that could not be assembled. Can be compressed with gzip." , - "default":"$id.$key.unassembled_reverse.unassembled_reverse" + "default":"$id.$key.unassembled_reverse" } @@ -80,10 +80,10 @@ "discarded": { "type": "string", - "description": "Type: `file`, required, default: `$id.$key.discarded.discarded`. The output file containing reads that were discarded due to too low quality or too many uncalled bases", - "help_text": "Type: `file`, required, default: `$id.$key.discarded.discarded`. The output file containing reads that were discarded due to too low quality or too many uncalled bases. Can be compressed with gzip." + "description": "Type: `file`, required, default: `$id.$key.discarded`. The output file containing reads that were discarded due to too low quality or too many uncalled bases", + "help_text": "Type: `file`, required, default: `$id.$key.discarded`. The output file containing reads that were discarded due to too low quality or too many uncalled bases. Can be compressed with gzip." , - "default":"$id.$key.discarded.discarded" + "default":"$id.$key.discarded" } diff --git a/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml b/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml index f2bd283d..1729163e 100644 --- a/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml +++ b/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml @@ -266,16 +266,16 @@ build_info: engine: "docker|native" output: "target/nextflow/qualimap/qualimap_rnaseq" executable: "target/nextflow/qualimap/qualimap_rnaseq/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/qualimap/qualimap_rnaseq/main.nf b/target/nextflow/qualimap/qualimap_rnaseq/main.nf index eade0ca2..aeaef477 100644 --- a/target/nextflow/qualimap/qualimap_rnaseq/main.nf +++ b/target/nextflow/qualimap/qualimap_rnaseq/main.nf @@ -1,6 +1,6 @@ // qualimap_rnaseq main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3363,16 +3358,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/qualimap/qualimap_rnaseq", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3823,7 +3818,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3837,6 +3832,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/qualimap/qualimap_rnaseq/nextflow_schema.json b/target/nextflow/qualimap/qualimap_rnaseq/nextflow_schema.json index 37135d51..47e34c91 100644 --- a/target/nextflow/qualimap/qualimap_rnaseq/nextflow_schema.json +++ b/target/nextflow/qualimap/qualimap_rnaseq/nextflow_schema.json @@ -58,10 +58,10 @@ "counts": { "type": "string", - "description": "Type: `file`, default: `$id.$key.counts.counts`. Output file for computed counts", - "help_text": "Type: `file`, default: `$id.$key.counts.counts`. Output file for computed counts." + "description": "Type: `file`, default: `$id.$key.counts`. Output file for computed counts", + "help_text": "Type: `file`, default: `$id.$key.counts`. Output file for computed counts." , - "default":"$id.$key.counts.counts" + "default":"$id.$key.counts" } diff --git a/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml b/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml index 0ea605da..a5ce9e04 100644 --- a/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml +++ b/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml @@ -854,16 +854,16 @@ build_info: engine: "docker|native" output: "target/nextflow/rsem/rsem_calculate_expression" executable: "target/nextflow/rsem/rsem_calculate_expression/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/rsem/rsem_calculate_expression/main.nf b/target/nextflow/rsem/rsem_calculate_expression/main.nf index 7520419c..b0c0a61b 100644 --- a/target/nextflow/rsem/rsem_calculate_expression/main.nf +++ b/target/nextflow/rsem/rsem_calculate_expression/main.nf @@ -1,6 +1,6 @@ // rsem_calculate_expression main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -82,64 +82,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -151,10 +143,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3895,16 +3890,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/rsem/rsem_calculate_expression", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -4456,7 +4451,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -4470,6 +4465,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml b/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml index 8a67dfd8..9bd2ec3f 100644 --- a/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml +++ b/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml @@ -418,16 +418,16 @@ build_info: engine: "docker|native" output: "target/nextflow/rsem/rsem_prepare_reference" executable: "target/nextflow/rsem/rsem_prepare_reference/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/rsem/rsem_prepare_reference/main.nf b/target/nextflow/rsem/rsem_prepare_reference/main.nf index 3e5e9b9c..7014ee86 100644 --- a/target/nextflow/rsem/rsem_prepare_reference/main.nf +++ b/target/nextflow/rsem/rsem_prepare_reference/main.nf @@ -1,6 +1,6 @@ // rsem_prepare_reference main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3479,16 +3474,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/rsem/rsem_prepare_reference", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3940,7 +3935,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3954,6 +3949,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/rsem/rsem_prepare_reference/nextflow_schema.json b/target/nextflow/rsem/rsem_prepare_reference/nextflow_schema.json index 1a04a5e7..1d5c516f 100644 --- a/target/nextflow/rsem/rsem_prepare_reference/nextflow_schema.json +++ b/target/nextflow/rsem/rsem_prepare_reference/nextflow_schema.json @@ -47,10 +47,10 @@ "output": { "type": "string", - "description": "Type: `file`, required, default: `$id.$key.output.output`. Directory containing reference files generated by RSEM", - "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Directory containing reference files generated by RSEM." + "description": "Type: `file`, required, default: `$id.$key.output`. Directory containing reference files generated by RSEM", + "help_text": "Type: `file`, required, default: `$id.$key.output`. Directory containing reference files generated by RSEM." , - "default":"$id.$key.output.output" + "default":"$id.$key.output" } diff --git a/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml index 1b76d900..a54902df 100644 --- a/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml @@ -177,16 +177,16 @@ build_info: engine: "docker|native" output: "target/nextflow/rseqc/rseqc_bamstat" executable: "target/nextflow/rseqc/rseqc_bamstat/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/rseqc/rseqc_bamstat/main.nf b/target/nextflow/rseqc/rseqc_bamstat/main.nf index 43fb7de1..20ba5b3c 100644 --- a/target/nextflow/rseqc/rseqc_bamstat/main.nf +++ b/target/nextflow/rseqc/rseqc_bamstat/main.nf @@ -1,6 +1,6 @@ // rseqc_bamstat main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3270,16 +3265,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/rseqc/rseqc_bamstat", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3680,7 +3675,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3694,6 +3689,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/rseqc/rseqc_bamstat/nextflow_schema.json b/target/nextflow/rseqc/rseqc_bamstat/nextflow_schema.json index e84def6b..4b31a3da 100644 --- a/target/nextflow/rseqc/rseqc_bamstat/nextflow_schema.json +++ b/target/nextflow/rseqc/rseqc_bamstat/nextflow_schema.json @@ -47,10 +47,10 @@ "output": { "type": "string", - "description": "Type: `file`, default: `$id.$key.output.output`. Output file (txt) with mapping quality statistics", - "help_text": "Type: `file`, default: `$id.$key.output.output`. Output file (txt) with mapping quality statistics." + "description": "Type: `file`, default: `$id.$key.output`. Output file (txt) with mapping quality statistics", + "help_text": "Type: `file`, default: `$id.$key.output`. Output file (txt) with mapping quality statistics." , - "default":"$id.$key.output.output" + "default":"$id.$key.output" } diff --git a/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml index 2af29811..22eda52d 100644 --- a/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml @@ -203,16 +203,16 @@ build_info: engine: "docker|native" output: "target/nextflow/rseqc/rseqc_inferexperiment" executable: "target/nextflow/rseqc/rseqc_inferexperiment/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/rseqc/rseqc_inferexperiment/main.nf b/target/nextflow/rseqc/rseqc_inferexperiment/main.nf index b151d7db..e25aafc6 100644 --- a/target/nextflow/rseqc/rseqc_inferexperiment/main.nf +++ b/target/nextflow/rseqc/rseqc_inferexperiment/main.nf @@ -1,6 +1,6 @@ // rseqc_inferexperiment main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3303,16 +3298,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/rseqc/rseqc_inferexperiment", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3716,7 +3711,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3730,6 +3725,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/rseqc/rseqc_inner_distance/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_inner_distance/.config.vsh.yaml index 6d706c4f..be20f97f 100644 --- a/target/nextflow/rseqc/rseqc_inner_distance/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_inner_distance/.config.vsh.yaml @@ -296,16 +296,16 @@ build_info: engine: "docker|native" output: "target/nextflow/rseqc/rseqc_inner_distance" executable: "target/nextflow/rseqc/rseqc_inner_distance/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/rseqc/rseqc_inner_distance/main.nf b/target/nextflow/rseqc/rseqc_inner_distance/main.nf index b4d92ad5..10945a94 100644 --- a/target/nextflow/rseqc/rseqc_inner_distance/main.nf +++ b/target/nextflow/rseqc/rseqc_inner_distance/main.nf @@ -1,6 +1,6 @@ // rseqc_inner_distance main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3403,16 +3398,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/rseqc/rseqc_inner_distance", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3839,7 +3834,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3853,6 +3848,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/rseqc/rseqc_inner_distance/nextflow_schema.json b/target/nextflow/rseqc/rseqc_inner_distance/nextflow_schema.json index 9f62271a..6bcd0c8a 100644 --- a/target/nextflow/rseqc/rseqc_inner_distance/nextflow_schema.json +++ b/target/nextflow/rseqc/rseqc_inner_distance/nextflow_schema.json @@ -107,10 +107,10 @@ "output_stats": { "type": "string", - "description": "Type: `file`, default: `$id.$key.output_stats.output_stats`. output file (txt) with summary statistics of inner distances of paired reads", - "help_text": "Type: `file`, default: `$id.$key.output_stats.output_stats`. output file (txt) with summary statistics of inner distances of paired reads" + "description": "Type: `file`, default: `$id.$key.output_stats`. output file (txt) with summary statistics of inner distances of paired reads", + "help_text": "Type: `file`, default: `$id.$key.output_stats`. output file (txt) with summary statistics of inner distances of paired reads" , - "default":"$id.$key.output_stats.output_stats" + "default":"$id.$key.output_stats" } @@ -118,10 +118,10 @@ "output_dist": { "type": "string", - "description": "Type: `file`, default: `$id.$key.output_dist.output_dist`. output file (txt) with inner distances of all paired reads", - "help_text": "Type: `file`, default: `$id.$key.output_dist.output_dist`. output file (txt) with inner distances of all paired reads" + "description": "Type: `file`, default: `$id.$key.output_dist`. output file (txt) with inner distances of all paired reads", + "help_text": "Type: `file`, default: `$id.$key.output_dist`. output file (txt) with inner distances of all paired reads" , - "default":"$id.$key.output_dist.output_dist" + "default":"$id.$key.output_dist" } @@ -129,10 +129,10 @@ "output_freq": { "type": "string", - "description": "Type: `file`, default: `$id.$key.output_freq.output_freq`. output file (txt) with frequencies of inner distances of all paired reads", - "help_text": "Type: `file`, default: `$id.$key.output_freq.output_freq`. output file (txt) with frequencies of inner distances of all paired reads" + "description": "Type: `file`, default: `$id.$key.output_freq`. output file (txt) with frequencies of inner distances of all paired reads", + "help_text": "Type: `file`, default: `$id.$key.output_freq`. output file (txt) with frequencies of inner distances of all paired reads" , - "default":"$id.$key.output_freq.output_freq" + "default":"$id.$key.output_freq" } @@ -140,10 +140,10 @@ "output_plot": { "type": "string", - "description": "Type: `file`, default: `$id.$key.output_plot.output_plot`. output file (pdf) with histogram plot of of inner distances of all paired reads", - "help_text": "Type: `file`, default: `$id.$key.output_plot.output_plot`. output file (pdf) with histogram plot of of inner distances of all paired reads" + "description": "Type: `file`, default: `$id.$key.output_plot`. output file (pdf) with histogram plot of of inner distances of all paired reads", + "help_text": "Type: `file`, default: `$id.$key.output_plot`. output file (pdf) with histogram plot of of inner distances of all paired reads" , - "default":"$id.$key.output_plot.output_plot" + "default":"$id.$key.output_plot" } @@ -151,10 +151,10 @@ "output_plot_r": { "type": "string", - "description": "Type: `file`, default: `$id.$key.output_plot_r.output_plot_r`. output file (R) with script of histogram plot of of inner distances of all paired reads", - "help_text": "Type: `file`, default: `$id.$key.output_plot_r.output_plot_r`. output file (R) with script of histogram plot of of inner distances of all paired reads" + "description": "Type: `file`, default: `$id.$key.output_plot_r`. output file (R) with script of histogram plot of of inner distances of all paired reads", + "help_text": "Type: `file`, default: `$id.$key.output_plot_r`. output file (R) with script of histogram plot of of inner distances of all paired reads" , - "default":"$id.$key.output_plot_r.output_plot_r" + "default":"$id.$key.output_plot_r" } diff --git a/target/nextflow/salmon/salmon_index/.config.vsh.yaml b/target/nextflow/salmon/salmon_index/.config.vsh.yaml index c375d463..568099c5 100644 --- a/target/nextflow/salmon/salmon_index/.config.vsh.yaml +++ b/target/nextflow/salmon/salmon_index/.config.vsh.yaml @@ -279,16 +279,16 @@ build_info: engine: "docker|native" output: "target/nextflow/salmon/salmon_index" executable: "target/nextflow/salmon/salmon_index/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/salmon/salmon_index/main.nf b/target/nextflow/salmon/salmon_index/main.nf index 045195f6..b378b131 100644 --- a/target/nextflow/salmon/salmon_index/main.nf +++ b/target/nextflow/salmon/salmon_index/main.nf @@ -1,6 +1,6 @@ // salmon_index main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3363,16 +3358,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/salmon/salmon_index", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3828,7 +3823,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3842,6 +3837,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/salmon/salmon_index/nextflow_schema.json b/target/nextflow/salmon/salmon_index/nextflow_schema.json index d21c0eee..5e67d15f 100644 --- a/target/nextflow/salmon/salmon_index/nextflow_schema.json +++ b/target/nextflow/salmon/salmon_index/nextflow_schema.json @@ -153,10 +153,10 @@ "index": { "type": "string", - "description": "Type: `file`, required, default: `$id.$key.index.index`, example: `Salmon_index`. Salmon index\n", - "help_text": "Type: `file`, required, default: `$id.$key.index.index`, example: `Salmon_index`. Salmon index\n" + "description": "Type: `file`, required, default: `$id.$key.index`, example: `Salmon_index`. Salmon index\n", + "help_text": "Type: `file`, required, default: `$id.$key.index`, example: `Salmon_index`. Salmon index\n" , - "default":"$id.$key.index.index" + "default":"$id.$key.index" } diff --git a/target/nextflow/salmon/salmon_quant/.config.vsh.yaml b/target/nextflow/salmon/salmon_quant/.config.vsh.yaml index 2ce481e2..e5eafd49 100644 --- a/target/nextflow/salmon/salmon_quant/.config.vsh.yaml +++ b/target/nextflow/salmon/salmon_quant/.config.vsh.yaml @@ -1175,16 +1175,16 @@ build_info: engine: "docker|native" output: "target/nextflow/salmon/salmon_quant" executable: "target/nextflow/salmon/salmon_quant/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/salmon/salmon_quant/main.nf b/target/nextflow/salmon/salmon_quant/main.nf index dea9c3f1..2634d293 100644 --- a/target/nextflow/salmon/salmon_quant/main.nf +++ b/target/nextflow/salmon/salmon_quant/main.nf @@ -1,6 +1,6 @@ // salmon_quant main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -4198,16 +4193,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/salmon/salmon_quant", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -4843,7 +4838,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -4857,6 +4852,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/salmon/salmon_quant/nextflow_schema.json b/target/nextflow/salmon/salmon_quant/nextflow_schema.json index 16d210f5..2b1c3f37 100644 --- a/target/nextflow/salmon/salmon_quant/nextflow_schema.json +++ b/target/nextflow/salmon/salmon_quant/nextflow_schema.json @@ -152,10 +152,10 @@ "output": { "type": "string", - "description": "Type: `file`, required, default: `$id.$key.output.output`, example: `quant_output`. Output quantification directory", - "help_text": "Type: `file`, required, default: `$id.$key.output.output`, example: `quant_output`. Output quantification directory.\n" + "description": "Type: `file`, required, default: `$id.$key.output`, example: `quant_output`. Output quantification directory", + "help_text": "Type: `file`, required, default: `$id.$key.output`, example: `quant_output`. Output quantification directory.\n" , - "default":"$id.$key.output.output" + "default":"$id.$key.output" } @@ -584,10 +584,10 @@ "aux_dir": { "type": "string", - "description": "Type: `file`, default: `$id.$key.aux_dir.aux_dir`, example: `aux_info`. The sub-directory of the quantification directory where auxiliary information e", - "help_text": "Type: `file`, default: `$id.$key.aux_dir.aux_dir`, example: `aux_info`. The sub-directory of the quantification directory where auxiliary information e.g. bootstraps, bias parameters, etc. will be written.\n" + "description": "Type: `file`, default: `$id.$key.aux_dir`, example: `aux_info`. The sub-directory of the quantification directory where auxiliary information e", + "help_text": "Type: `file`, default: `$id.$key.aux_dir`, example: `aux_info`. The sub-directory of the quantification directory where auxiliary information e.g. bootstraps, bias parameters, etc. will be written.\n" , - "default":"$id.$key.aux_dir.aux_dir" + "default":"$id.$key.aux_dir" } diff --git a/target/nextflow/samtools/samtools_collate/.config.vsh.yaml b/target/nextflow/samtools/samtools_collate/.config.vsh.yaml index 56ca290f..4a7d0a38 100644 --- a/target/nextflow/samtools/samtools_collate/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_collate/.config.vsh.yaml @@ -266,16 +266,16 @@ build_info: engine: "docker|native" output: "target/nextflow/samtools/samtools_collate" executable: "target/nextflow/samtools/samtools_collate/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/samtools/samtools_collate/main.nf b/target/nextflow/samtools/samtools_collate/main.nf index a9efdc68..2b4c8baa 100644 --- a/target/nextflow/samtools/samtools_collate/main.nf +++ b/target/nextflow/samtools/samtools_collate/main.nf @@ -1,6 +1,6 @@ // samtools_collate main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3374,16 +3369,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_collate", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3810,7 +3805,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3824,6 +3819,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/samtools/samtools_collate/nextflow_schema.json b/target/nextflow/samtools/samtools_collate/nextflow_schema.json index dc33ceb5..c50e595c 100644 --- a/target/nextflow/samtools/samtools_collate/nextflow_schema.json +++ b/target/nextflow/samtools/samtools_collate/nextflow_schema.json @@ -47,10 +47,10 @@ "output": { "type": "string", - "description": "Type: `file`, required, default: `$id.$key.output.output`. The output filename", - "help_text": "Type: `file`, required, default: `$id.$key.output.output`. The output filename." + "description": "Type: `file`, required, default: `$id.$key.output`. The output filename", + "help_text": "Type: `file`, required, default: `$id.$key.output`. The output filename." , - "default":"$id.$key.output.output" + "default":"$id.$key.output" } diff --git a/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml b/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml index 9f259834..84bd3ae1 100644 --- a/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml @@ -245,16 +245,16 @@ build_info: engine: "docker|native" output: "target/nextflow/samtools/samtools_faidx" executable: "target/nextflow/samtools/samtools_faidx/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/samtools/samtools_faidx/main.nf b/target/nextflow/samtools/samtools_faidx/main.nf index f6b7dd23..c0df42ff 100644 --- a/target/nextflow/samtools/samtools_faidx/main.nf +++ b/target/nextflow/samtools/samtools_faidx/main.nf @@ -1,6 +1,6 @@ // samtools_faidx main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3346,16 +3341,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_faidx", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3776,7 +3771,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3790,6 +3785,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml b/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml index 2dd7f9ce..24d07ec3 100644 --- a/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml @@ -435,16 +435,16 @@ build_info: engine: "docker|native" output: "target/nextflow/samtools/samtools_fasta" executable: "target/nextflow/samtools/samtools_fasta/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/samtools/samtools_fasta/main.nf b/target/nextflow/samtools/samtools_fasta/main.nf index b0d6582d..fa5b500c 100644 --- a/target/nextflow/samtools/samtools_fasta/main.nf +++ b/target/nextflow/samtools/samtools_fasta/main.nf @@ -1,6 +1,6 @@ // samtools_fasta main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3538,16 +3533,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_fasta", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -4012,7 +4007,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -4026,6 +4021,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/samtools/samtools_fasta/nextflow_schema.json b/target/nextflow/samtools/samtools_fasta/nextflow_schema.json index 0d14b9b7..f7a9a5dc 100644 --- a/target/nextflow/samtools/samtools_fasta/nextflow_schema.json +++ b/target/nextflow/samtools/samtools_fasta/nextflow_schema.json @@ -37,10 +37,10 @@ "output": { "type": "string", - "description": "Type: `file`, required, default: `$id.$key.output.output`. output FASTA file", - "help_text": "Type: `file`, required, default: `$id.$key.output.output`. output FASTA file" + "description": "Type: `file`, required, default: `$id.$key.output`. output FASTA file", + "help_text": "Type: `file`, required, default: `$id.$key.output`. output FASTA file" , - "default":"$id.$key.output.output" + "default":"$id.$key.output" } @@ -122,10 +122,10 @@ "read1": { "type": "string", - "description": "Type: `file`, default: `$id.$key.read1.read1`. Write reads with the READ1 FLAG set (and READ2 not set) to FILE instead of outputting them", - "help_text": "Type: `file`, default: `$id.$key.read1.read1`. Write reads with the READ1 FLAG set (and READ2 not set) to FILE instead of outputting them. \nIf the -s option is used, only paired reads will be written to this file.\n" + "description": "Type: `file`, default: `$id.$key.read1`. Write reads with the READ1 FLAG set (and READ2 not set) to FILE instead of outputting them", + "help_text": "Type: `file`, default: `$id.$key.read1`. Write reads with the READ1 FLAG set (and READ2 not set) to FILE instead of outputting them. \nIf the -s option is used, only paired reads will be written to this file.\n" , - "default":"$id.$key.read1.read1" + "default":"$id.$key.read1" } @@ -133,10 +133,10 @@ "read2": { "type": "string", - "description": "Type: `file`, default: `$id.$key.read2.read2`. Write reads with the READ2 FLAG set (and READ1 not set) to FILE instead of outputting them", - "help_text": "Type: `file`, default: `$id.$key.read2.read2`. Write reads with the READ2 FLAG set (and READ1 not set) to FILE instead of outputting them. \nIf the -s option is used, only paired reads will be written to this file.\n" + "description": "Type: `file`, default: `$id.$key.read2`. Write reads with the READ2 FLAG set (and READ1 not set) to FILE instead of outputting them", + "help_text": "Type: `file`, default: `$id.$key.read2`. Write reads with the READ2 FLAG set (and READ1 not set) to FILE instead of outputting them. \nIf the -s option is used, only paired reads will be written to this file.\n" , - "default":"$id.$key.read2.read2" + "default":"$id.$key.read2" } @@ -144,10 +144,10 @@ "output_reads": { "type": "string", - "description": "Type: `file`, default: `$id.$key.output_reads.output_reads`. Write reads with either READ1 FLAG or READ2 flag set to FILE instead of outputting them to stdout", - "help_text": "Type: `file`, default: `$id.$key.output_reads.output_reads`. Write reads with either READ1 FLAG or READ2 flag set to FILE instead of outputting them to stdout. \nThis is equivalent to -1 FILE -2 FILE.\n" + "description": "Type: `file`, default: `$id.$key.output_reads`. Write reads with either READ1 FLAG or READ2 flag set to FILE instead of outputting them to stdout", + "help_text": "Type: `file`, default: `$id.$key.output_reads`. Write reads with either READ1 FLAG or READ2 flag set to FILE instead of outputting them to stdout. \nThis is equivalent to -1 FILE -2 FILE.\n" , - "default":"$id.$key.output_reads.output_reads" + "default":"$id.$key.output_reads" } @@ -155,10 +155,10 @@ "output_reads_both": { "type": "string", - "description": "Type: `file`, default: `$id.$key.output_reads_both.output_reads_both`. Write reads where the READ1 and READ2 FLAG bits set are either both set or both unset to FILE \ninstead of outputting them", - "help_text": "Type: `file`, default: `$id.$key.output_reads_both.output_reads_both`. Write reads where the READ1 and READ2 FLAG bits set are either both set or both unset to FILE \ninstead of outputting them.\n" + "description": "Type: `file`, default: `$id.$key.output_reads_both`. Write reads where the READ1 and READ2 FLAG bits set are either both set or both unset to FILE \ninstead of outputting them", + "help_text": "Type: `file`, default: `$id.$key.output_reads_both`. Write reads where the READ1 and READ2 FLAG bits set are either both set or both unset to FILE \ninstead of outputting them.\n" , - "default":"$id.$key.output_reads_both.output_reads_both" + "default":"$id.$key.output_reads_both" } diff --git a/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml b/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml index 208fb8a3..25131374 100644 --- a/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml @@ -435,16 +435,16 @@ build_info: engine: "docker|native" output: "target/nextflow/samtools/samtools_fastq" executable: "target/nextflow/samtools/samtools_fastq/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/samtools/samtools_fastq/main.nf b/target/nextflow/samtools/samtools_fastq/main.nf index a0c2656b..0f3128e4 100644 --- a/target/nextflow/samtools/samtools_fastq/main.nf +++ b/target/nextflow/samtools/samtools_fastq/main.nf @@ -1,6 +1,6 @@ // samtools_fastq main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3538,16 +3533,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_fastq", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -4012,7 +4007,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -4026,6 +4021,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/samtools/samtools_fastq/nextflow_schema.json b/target/nextflow/samtools/samtools_fastq/nextflow_schema.json index b1bdb1a1..98acdf76 100644 --- a/target/nextflow/samtools/samtools_fastq/nextflow_schema.json +++ b/target/nextflow/samtools/samtools_fastq/nextflow_schema.json @@ -37,10 +37,10 @@ "output": { "type": "string", - "description": "Type: `file`, required, default: `$id.$key.output.output`. output FASTQ file", - "help_text": "Type: `file`, required, default: `$id.$key.output.output`. output FASTQ file" + "description": "Type: `file`, required, default: `$id.$key.output`. output FASTQ file", + "help_text": "Type: `file`, required, default: `$id.$key.output`. output FASTQ file" , - "default":"$id.$key.output.output" + "default":"$id.$key.output" } @@ -122,10 +122,10 @@ "read1": { "type": "string", - "description": "Type: `file`, default: `$id.$key.read1.read1`. Write reads with the READ1 FLAG set (and READ2 not set) to FILE instead of outputting them", - "help_text": "Type: `file`, default: `$id.$key.read1.read1`. Write reads with the READ1 FLAG set (and READ2 not set) to FILE instead of outputting them. \nIf the -s option is used, only paired reads will be written to this file.\n" + "description": "Type: `file`, default: `$id.$key.read1`. Write reads with the READ1 FLAG set (and READ2 not set) to FILE instead of outputting them", + "help_text": "Type: `file`, default: `$id.$key.read1`. Write reads with the READ1 FLAG set (and READ2 not set) to FILE instead of outputting them. \nIf the -s option is used, only paired reads will be written to this file.\n" , - "default":"$id.$key.read1.read1" + "default":"$id.$key.read1" } @@ -133,10 +133,10 @@ "read2": { "type": "string", - "description": "Type: `file`, default: `$id.$key.read2.read2`. Write reads with the READ2 FLAG set (and READ1 not set) to FILE instead of outputting them", - "help_text": "Type: `file`, default: `$id.$key.read2.read2`. Write reads with the READ2 FLAG set (and READ1 not set) to FILE instead of outputting them. \nIf the -s option is used, only paired reads will be written to this file.\n" + "description": "Type: `file`, default: `$id.$key.read2`. Write reads with the READ2 FLAG set (and READ1 not set) to FILE instead of outputting them", + "help_text": "Type: `file`, default: `$id.$key.read2`. Write reads with the READ2 FLAG set (and READ1 not set) to FILE instead of outputting them. \nIf the -s option is used, only paired reads will be written to this file.\n" , - "default":"$id.$key.read2.read2" + "default":"$id.$key.read2" } @@ -144,10 +144,10 @@ "output_reads": { "type": "string", - "description": "Type: `file`, default: `$id.$key.output_reads.output_reads`. Write reads with either READ1 FLAG or READ2 flag set to FILE instead of outputting them to stdout", - "help_text": "Type: `file`, default: `$id.$key.output_reads.output_reads`. Write reads with either READ1 FLAG or READ2 flag set to FILE instead of outputting them to stdout. \nThis is equivalent to -1 FILE -2 FILE.\n" + "description": "Type: `file`, default: `$id.$key.output_reads`. Write reads with either READ1 FLAG or READ2 flag set to FILE instead of outputting them to stdout", + "help_text": "Type: `file`, default: `$id.$key.output_reads`. Write reads with either READ1 FLAG or READ2 flag set to FILE instead of outputting them to stdout. \nThis is equivalent to -1 FILE -2 FILE.\n" , - "default":"$id.$key.output_reads.output_reads" + "default":"$id.$key.output_reads" } @@ -155,10 +155,10 @@ "output_reads_both": { "type": "string", - "description": "Type: `file`, default: `$id.$key.output_reads_both.output_reads_both`. Write reads where the READ1 and READ2 FLAG bits set are either both set or both unset to FILE \ninstead of outputting them", - "help_text": "Type: `file`, default: `$id.$key.output_reads_both.output_reads_both`. Write reads where the READ1 and READ2 FLAG bits set are either both set or both unset to FILE \ninstead of outputting them.\n" + "description": "Type: `file`, default: `$id.$key.output_reads_both`. Write reads where the READ1 and READ2 FLAG bits set are either both set or both unset to FILE \ninstead of outputting them", + "help_text": "Type: `file`, default: `$id.$key.output_reads_both`. Write reads where the READ1 and READ2 FLAG bits set are either both set or both unset to FILE \ninstead of outputting them.\n" , - "default":"$id.$key.output_reads_both.output_reads_both" + "default":"$id.$key.output_reads_both" } diff --git a/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml b/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml index c126bc1e..0c863fe1 100644 --- a/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml @@ -175,16 +175,16 @@ build_info: engine: "docker|native" output: "target/nextflow/samtools/samtools_flagstat" executable: "target/nextflow/samtools/samtools_flagstat/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/samtools/samtools_flagstat/main.nf b/target/nextflow/samtools/samtools_flagstat/main.nf index b7073bc2..4df049e3 100644 --- a/target/nextflow/samtools/samtools_flagstat/main.nf +++ b/target/nextflow/samtools/samtools_flagstat/main.nf @@ -1,6 +1,6 @@ // samtools_flagstat main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3262,16 +3257,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_flagstat", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3672,7 +3667,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3686,6 +3681,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml b/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml index f5be8d87..4e44998d 100644 --- a/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml @@ -185,16 +185,16 @@ build_info: engine: "docker|native" output: "target/nextflow/samtools/samtools_idxstats" executable: "target/nextflow/samtools/samtools_idxstats/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/samtools/samtools_idxstats/main.nf b/target/nextflow/samtools/samtools_idxstats/main.nf index 0ba7e3d1..79091b13 100644 --- a/target/nextflow/samtools/samtools_idxstats/main.nf +++ b/target/nextflow/samtools/samtools_idxstats/main.nf @@ -1,6 +1,6 @@ // samtools_idxstats main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3274,16 +3269,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_idxstats", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3682,7 +3677,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3696,6 +3691,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/samtools/samtools_index/.config.vsh.yaml b/target/nextflow/samtools/samtools_index/.config.vsh.yaml index c333d91f..1103c3f7 100644 --- a/target/nextflow/samtools/samtools_index/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_index/.config.vsh.yaml @@ -191,16 +191,16 @@ build_info: engine: "docker|native" output: "target/nextflow/samtools/samtools_index" executable: "target/nextflow/samtools/samtools_index/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/samtools/samtools_index/main.nf b/target/nextflow/samtools/samtools_index/main.nf index 0af9b611..a48e6ccb 100644 --- a/target/nextflow/samtools/samtools_index/main.nf +++ b/target/nextflow/samtools/samtools_index/main.nf @@ -1,6 +1,6 @@ // samtools_index main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3287,16 +3282,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_index", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3706,7 +3701,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3720,6 +3715,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/samtools/samtools_sort/.config.vsh.yaml b/target/nextflow/samtools/samtools_sort/.config.vsh.yaml index 7b6da8a8..99e8af42 100644 --- a/target/nextflow/samtools/samtools_sort/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_sort/.config.vsh.yaml @@ -334,16 +334,16 @@ build_info: engine: "docker|native" output: "target/nextflow/samtools/samtools_sort" executable: "target/nextflow/samtools/samtools_sort/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/samtools/samtools_sort/main.nf b/target/nextflow/samtools/samtools_sort/main.nf index 8202a1bf..177ac270 100644 --- a/target/nextflow/samtools/samtools_sort/main.nf +++ b/target/nextflow/samtools/samtools_sort/main.nf @@ -1,6 +1,6 @@ // samtools_sort main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3459,16 +3454,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_sort", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3926,7 +3921,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3940,6 +3935,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/samtools/samtools_stats/.config.vsh.yaml b/target/nextflow/samtools/samtools_stats/.config.vsh.yaml index d95f577a..166980f3 100644 --- a/target/nextflow/samtools/samtools_stats/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_stats/.config.vsh.yaml @@ -403,16 +403,16 @@ build_info: engine: "docker|native" output: "target/nextflow/samtools/samtools_stats" executable: "target/nextflow/samtools/samtools_stats/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/samtools/samtools_stats/main.nf b/target/nextflow/samtools/samtools_stats/main.nf index ac2f2ae6..6c2f627f 100644 --- a/target/nextflow/samtools/samtools_stats/main.nf +++ b/target/nextflow/samtools/samtools_stats/main.nf @@ -1,6 +1,6 @@ // samtools_stats main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3529,16 +3524,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_stats", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3988,7 +3983,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -4002,6 +3997,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/samtools/samtools_view/.config.vsh.yaml b/target/nextflow/samtools/samtools_view/.config.vsh.yaml index ed95cc52..c23f9161 100644 --- a/target/nextflow/samtools/samtools_view/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_view/.config.vsh.yaml @@ -667,16 +667,16 @@ build_info: engine: "docker|native" output: "target/nextflow/samtools/samtools_view" executable: "target/nextflow/samtools/samtools_view/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/samtools/samtools_view/main.nf b/target/nextflow/samtools/samtools_view/main.nf index a1530878..825e7d17 100644 --- a/target/nextflow/samtools/samtools_view/main.nf +++ b/target/nextflow/samtools/samtools_view/main.nf @@ -1,6 +1,6 @@ // samtools_view main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3710,16 +3705,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_view", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -4230,7 +4225,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -4244,6 +4239,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml b/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml index 2af213c0..b2bc68e4 100644 --- a/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml +++ b/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml @@ -175,16 +175,16 @@ build_info: engine: "docker|native" output: "target/nextflow/seqtk/seqtk_sample" executable: "target/nextflow/seqtk/seqtk_sample/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/seqtk/seqtk_sample/main.nf b/target/nextflow/seqtk/seqtk_sample/main.nf index ac4d7cbe..56e2111a 100644 --- a/target/nextflow/seqtk/seqtk_sample/main.nf +++ b/target/nextflow/seqtk/seqtk_sample/main.nf @@ -1,6 +1,6 @@ // seqtk_sample main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3264,16 +3259,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/seqtk/seqtk_sample", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3676,7 +3671,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3690,6 +3685,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/seqtk/seqtk_sample/nextflow_schema.json b/target/nextflow/seqtk/seqtk_sample/nextflow_schema.json index 34bd4219..96e02772 100644 --- a/target/nextflow/seqtk/seqtk_sample/nextflow_schema.json +++ b/target/nextflow/seqtk/seqtk_sample/nextflow_schema.json @@ -37,10 +37,10 @@ "output": { "type": "string", - "description": "Type: `file`, required, default: `$id.$key.output.output`. The output FASTA/Q file", - "help_text": "Type: `file`, required, default: `$id.$key.output.output`. The output FASTA/Q file." + "description": "Type: `file`, required, default: `$id.$key.output`. The output FASTA/Q file", + "help_text": "Type: `file`, required, default: `$id.$key.output`. The output FASTA/Q file." , - "default":"$id.$key.output.output" + "default":"$id.$key.output" } diff --git a/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml b/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml index f2ef68bc..9a45f911 100644 --- a/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml +++ b/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml @@ -198,16 +198,16 @@ build_info: engine: "docker|native" output: "target/nextflow/seqtk/seqtk_subseq" executable: "target/nextflow/seqtk/seqtk_subseq/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/seqtk/seqtk_subseq/main.nf b/target/nextflow/seqtk/seqtk_subseq/main.nf index d5172c0f..f622ef6f 100644 --- a/target/nextflow/seqtk/seqtk_subseq/main.nf +++ b/target/nextflow/seqtk/seqtk_subseq/main.nf @@ -1,6 +1,6 @@ // seqtk_subseq main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3294,16 +3289,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/seqtk/seqtk_subseq", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3711,7 +3706,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3725,6 +3720,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/seqtk/seqtk_subseq/nextflow_schema.json b/target/nextflow/seqtk/seqtk_subseq/nextflow_schema.json index d5f9f16a..18b4a19b 100644 --- a/target/nextflow/seqtk/seqtk_subseq/nextflow_schema.json +++ b/target/nextflow/seqtk/seqtk_subseq/nextflow_schema.json @@ -47,10 +47,10 @@ "output": { "type": "string", - "description": "Type: `file`, required, default: `$id.$key.output.fa`. The output FASTA/Q file", - "help_text": "Type: `file`, required, default: `$id.$key.output.fa`. The output FASTA/Q file." + "description": "Type: `file`, required, default: `output.fa`. The output FASTA/Q file", + "help_text": "Type: `file`, required, default: `output.fa`. The output FASTA/Q file." , - "default":"$id.$key.output.fa" + "default":"output.fa" } diff --git a/target/nextflow/sgdemux/.config.vsh.yaml b/target/nextflow/sgdemux/.config.vsh.yaml index 088271d8..d5b06d0f 100644 --- a/target/nextflow/sgdemux/.config.vsh.yaml +++ b/target/nextflow/sgdemux/.config.vsh.yaml @@ -431,16 +431,16 @@ build_info: engine: "docker|native" output: "target/nextflow/sgdemux" executable: "target/nextflow/sgdemux/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/sgdemux/main.nf b/target/nextflow/sgdemux/main.nf index a5a0a5c5..5c6c5977 100644 --- a/target/nextflow/sgdemux/main.nf +++ b/target/nextflow/sgdemux/main.nf @@ -1,6 +1,6 @@ // sgdemux main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3537,16 +3532,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/sgdemux", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -4070,7 +4065,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -4084,6 +4079,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/sgdemux/nextflow_schema.json b/target/nextflow/sgdemux/nextflow_schema.json index b295e944..69413464 100644 --- a/target/nextflow/sgdemux/nextflow_schema.json +++ b/target/nextflow/sgdemux/nextflow_schema.json @@ -223,10 +223,10 @@ "sample_fastq": { "type": "string", - "description": "Type: `file`, required, default: `$id.$key.sample_fastq.sample_fastq`, example: `output`. The directory containing demultiplexed sample FASTQ files", - "help_text": "Type: `file`, required, default: `$id.$key.sample_fastq.sample_fastq`, example: `output`. The directory containing demultiplexed sample FASTQ files." + "description": "Type: `file`, required, default: `$id.$key.sample_fastq`, example: `output`. The directory containing demultiplexed sample FASTQ files", + "help_text": "Type: `file`, required, default: `$id.$key.sample_fastq`, example: `output`. The directory containing demultiplexed sample FASTQ files." , - "default":"$id.$key.sample_fastq.sample_fastq" + "default":"$id.$key.sample_fastq" } diff --git a/target/nextflow/snpeff/.config.vsh.yaml b/target/nextflow/snpeff/.config.vsh.yaml index 37d5c9c4..7ed0695e 100644 --- a/target/nextflow/snpeff/.config.vsh.yaml +++ b/target/nextflow/snpeff/.config.vsh.yaml @@ -630,16 +630,16 @@ build_info: engine: "docker|native" output: "target/nextflow/snpeff" executable: "target/nextflow/snpeff/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/snpeff/main.nf b/target/nextflow/snpeff/main.nf index 792c30a2..4f41cf7e 100644 --- a/target/nextflow/snpeff/main.nf +++ b/target/nextflow/snpeff/main.nf @@ -1,6 +1,6 @@ // snpeff main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -82,64 +82,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -151,10 +143,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3789,16 +3784,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/snpeff", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -4401,7 +4396,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -4415,6 +4410,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/snpeff/nextflow_schema.json b/target/nextflow/snpeff/nextflow_schema.json index 2b4f5c52..1cbca5d1 100644 --- a/target/nextflow/snpeff/nextflow_schema.json +++ b/target/nextflow/snpeff/nextflow_schema.json @@ -58,10 +58,10 @@ "summary": { "type": "string", - "description": "Type: `file`, default: `$id.$key.summary.summary`, example: `summary_dir`. Summary file directory", - "help_text": "Type: `file`, default: `$id.$key.summary.summary`, example: `summary_dir`. Summary file directory." + "description": "Type: `file`, default: `$id.$key.summary`, example: `summary_dir`. Summary file directory", + "help_text": "Type: `file`, default: `$id.$key.summary`, example: `summary_dir`. Summary file directory." , - "default":"$id.$key.summary.summary" + "default":"$id.$key.summary" } @@ -69,10 +69,10 @@ "genes": { "type": "string", - "description": "Type: `file`, default: `$id.$key.genes.genes`, example: `genes_dir`. Txt file directory", - "help_text": "Type: `file`, default: `$id.$key.genes.genes`, example: `genes_dir`. Txt file directory." + "description": "Type: `file`, default: `$id.$key.genes`, example: `genes_dir`. Txt file directory", + "help_text": "Type: `file`, default: `$id.$key.genes`, example: `genes_dir`. Txt file directory." , - "default":"$id.$key.genes.genes" + "default":"$id.$key.genes" } diff --git a/target/nextflow/sortmerna/.config.vsh.yaml b/target/nextflow/sortmerna/.config.vsh.yaml index da269111..9ef7fa4b 100644 --- a/target/nextflow/sortmerna/.config.vsh.yaml +++ b/target/nextflow/sortmerna/.config.vsh.yaml @@ -596,16 +596,16 @@ build_info: engine: "docker|native" output: "target/nextflow/sortmerna" executable: "target/nextflow/sortmerna/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/sortmerna/main.nf b/target/nextflow/sortmerna/main.nf index 90399e99..138c7ed3 100644 --- a/target/nextflow/sortmerna/main.nf +++ b/target/nextflow/sortmerna/main.nf @@ -1,6 +1,6 @@ // sortmerna main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -82,64 +82,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -151,10 +143,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3694,16 +3689,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/sortmerna", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -4238,7 +4233,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -4252,6 +4247,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/sortmerna/nextflow_schema.json b/target/nextflow/sortmerna/nextflow_schema.json index c0e0df62..f3c2fcdc 100644 --- a/target/nextflow/sortmerna/nextflow_schema.json +++ b/target/nextflow/sortmerna/nextflow_schema.json @@ -79,10 +79,10 @@ "output": { "type": "string", - "description": "Type: `file`, default: `$id.$key.output.output`. Directory and file prefix for aligned output", - "help_text": "Type: `file`, default: `$id.$key.output.output`. Directory and file prefix for aligned output. The appropriate extension: \n(fasta|fastq|blast|sam|etc) is automatically added.\nIf \u0027dir\u0027 is not specified, the output is created in the WORKDIR/out/.\nIf \u0027pfx\u0027 is not specified, the prefix \u0027aligned\u0027 is used.\n" + "description": "Type: `file`, default: `$id.$key.output`. Directory and file prefix for aligned output", + "help_text": "Type: `file`, default: `$id.$key.output`. Directory and file prefix for aligned output. The appropriate extension: \n(fasta|fastq|blast|sam|etc) is automatically added.\nIf \u0027dir\u0027 is not specified, the output is created in the WORKDIR/out/.\nIf \u0027pfx\u0027 is not specified, the prefix \u0027aligned\u0027 is used.\n" , - "default":"$id.$key.output.output" + "default":"$id.$key.output" } @@ -90,10 +90,10 @@ "other": { "type": "string", - "description": "Type: `file`, default: `$id.$key.other.other`. Create Non-aligned reads output file with this path/prefix", - "help_text": "Type: `file`, default: `$id.$key.other.other`. Create Non-aligned reads output file with this path/prefix. Must be used with fastx." + "description": "Type: `file`, default: `$id.$key.other`. Create Non-aligned reads output file with this path/prefix", + "help_text": "Type: `file`, default: `$id.$key.other`. Create Non-aligned reads output file with this path/prefix. Must be used with fastx." , - "default":"$id.$key.other.other" + "default":"$id.$key.other" } diff --git a/target/nextflow/star/star_align_reads/.config.vsh.yaml b/target/nextflow/star/star_align_reads/.config.vsh.yaml index 6ab1b5ea..dd0abf70 100644 --- a/target/nextflow/star/star_align_reads/.config.vsh.yaml +++ b/target/nextflow/star/star_align_reads/.config.vsh.yaml @@ -2665,16 +2665,16 @@ build_info: engine: "docker|native" output: "target/nextflow/star/star_align_reads" executable: "target/nextflow/star/star_align_reads/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/star/star_align_reads/main.nf b/target/nextflow/star/star_align_reads/main.nf index 2d3c5ee7..3079420d 100644 --- a/target/nextflow/star/star_align_reads/main.nf +++ b/target/nextflow/star/star_align_reads/main.nf @@ -1,6 +1,6 @@ // star_align_reads main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -86,64 +86,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -155,10 +147,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -6177,16 +6172,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/star/star_align_reads", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -6217,7 +6212,7 @@ meta = [ // inner workflow hook def innerWorkflowFactory(args) { def rawScript = '''set -e -tempscript=".viash_script.sh" +tempscript=".viash_script.py" cat > "$tempscript" << VIASHMAIN import tempfile import subprocess @@ -6880,7 +6875,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -6894,6 +6889,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/star/star_genome_generate/.config.vsh.yaml b/target/nextflow/star/star_genome_generate/.config.vsh.yaml index 6608f1d2..b3defa85 100644 --- a/target/nextflow/star/star_genome_generate/.config.vsh.yaml +++ b/target/nextflow/star/star_genome_generate/.config.vsh.yaml @@ -335,16 +335,16 @@ build_info: engine: "docker|native" output: "target/nextflow/star/star_genome_generate" executable: "target/nextflow/star/star_genome_generate/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/star/star_genome_generate/main.nf b/target/nextflow/star/star_genome_generate/main.nf index 635a67fb..bc93e825 100644 --- a/target/nextflow/star/star_genome_generate/main.nf +++ b/target/nextflow/star/star_genome_generate/main.nf @@ -1,6 +1,6 @@ // star_genome_generate main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3429,16 +3424,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/star/star_genome_generate", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3871,7 +3866,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3885,6 +3880,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/star/star_genome_generate/nextflow_schema.json b/target/nextflow/star/star_genome_generate/nextflow_schema.json index e8aadf16..27f6172f 100644 --- a/target/nextflow/star/star_genome_generate/nextflow_schema.json +++ b/target/nextflow/star/star_genome_generate/nextflow_schema.json @@ -187,10 +187,10 @@ "index": { "type": "string", - "description": "Type: `file`, required, default: `$id.$key.index.index`. STAR index directory", - "help_text": "Type: `file`, required, default: `$id.$key.index.index`. STAR index directory." + "description": "Type: `file`, required, default: `STAR_index`. STAR index directory", + "help_text": "Type: `file`, required, default: `STAR_index`. STAR index directory." , - "default":"$id.$key.index.index" + "default":"STAR_index" } diff --git a/target/nextflow/trimgalore/.config.vsh.yaml b/target/nextflow/trimgalore/.config.vsh.yaml index e5d39e63..92c914d0 100644 --- a/target/nextflow/trimgalore/.config.vsh.yaml +++ b/target/nextflow/trimgalore/.config.vsh.yaml @@ -772,16 +772,16 @@ build_info: engine: "docker|native" output: "target/nextflow/trimgalore" executable: "target/nextflow/trimgalore/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/trimgalore/main.nf b/target/nextflow/trimgalore/main.nf index 484acfb0..ed828083 100644 --- a/target/nextflow/trimgalore/main.nf +++ b/target/nextflow/trimgalore/main.nf @@ -1,6 +1,6 @@ // trimgalore main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3794,16 +3789,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/trimgalore", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -4373,7 +4368,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -4387,6 +4382,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/trimgalore/nextflow_schema.json b/target/nextflow/trimgalore/nextflow_schema.json index 9ee3b485..b022cc47 100644 --- a/target/nextflow/trimgalore/nextflow_schema.json +++ b/target/nextflow/trimgalore/nextflow_schema.json @@ -527,10 +527,10 @@ "output_dir": { "type": "string", - "description": "Type: `file`, required, default: `$id.$key.output_dir.output_dir`. If specified all output will be written to this directory instead of the current directory", - "help_text": "Type: `file`, required, default: `$id.$key.output_dir.output_dir`. If specified all output will be written to this directory instead of the current directory." + "description": "Type: `file`, required, default: `trimmed_output`. If specified all output will be written to this directory instead of the current directory", + "help_text": "Type: `file`, required, default: `trimmed_output`. If specified all output will be written to this directory instead of the current directory." , - "default":"$id.$key.output_dir.output_dir" + "default":"trimmed_output" } diff --git a/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml b/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml index 71ff2835..154533ed 100644 --- a/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml +++ b/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml @@ -613,16 +613,16 @@ build_info: engine: "docker|native" output: "target/nextflow/umi_tools/umi_tools_dedup" executable: "target/nextflow/umi_tools/umi_tools_dedup/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/umi_tools/umi_tools_dedup/main.nf b/target/nextflow/umi_tools/umi_tools_dedup/main.nf index 6ed322ee..bd438349 100644 --- a/target/nextflow/umi_tools/umi_tools_dedup/main.nf +++ b/target/nextflow/umi_tools/umi_tools_dedup/main.nf @@ -1,6 +1,6 @@ // umi_tools_dedup main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3721,16 +3716,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/umi_tools/umi_tools_dedup", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -4243,7 +4238,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -4257,6 +4252,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/umi_tools/umi_tools_dedup/nextflow_schema.json b/target/nextflow/umi_tools/umi_tools_dedup/nextflow_schema.json index 58ecde0e..979543bd 100644 --- a/target/nextflow/umi_tools/umi_tools_dedup/nextflow_schema.json +++ b/target/nextflow/umi_tools/umi_tools_dedup/nextflow_schema.json @@ -68,10 +68,10 @@ "output": { "type": "string", - "description": "Type: `file`, required, default: `$id.$key.output.output`. Deduplicated BAM file", - "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Deduplicated BAM file." + "description": "Type: `file`, required, default: `$id.$key.output`. Deduplicated BAM file", + "help_text": "Type: `file`, required, default: `$id.$key.output`. Deduplicated BAM file." , - "default":"$id.$key.output.output" + "default":"$id.$key.output" } diff --git a/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml b/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml index a3121e85..8652e6b4 100644 --- a/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml +++ b/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml @@ -436,16 +436,16 @@ build_info: engine: "docker|native" output: "target/nextflow/umi_tools/umi_tools_extract" executable: "target/nextflow/umi_tools/umi_tools_extract/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/umi_tools/umi_tools_extract/main.nf b/target/nextflow/umi_tools/umi_tools_extract/main.nf index 533deea7..94f4060e 100644 --- a/target/nextflow/umi_tools/umi_tools_extract/main.nf +++ b/target/nextflow/umi_tools/umi_tools_extract/main.nf @@ -1,6 +1,6 @@ // umi_tools_extract main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -82,64 +82,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -151,10 +143,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3533,16 +3528,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/umi_tools/umi_tools_extract", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -4044,7 +4039,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -4058,6 +4053,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/umi_tools/umi_tools_extract/nextflow_schema.json b/target/nextflow/umi_tools/umi_tools_extract/nextflow_schema.json index 927e039b..e8f0501a 100644 --- a/target/nextflow/umi_tools/umi_tools_extract/nextflow_schema.json +++ b/target/nextflow/umi_tools/umi_tools_extract/nextflow_schema.json @@ -67,10 +67,10 @@ "output": { "type": "string", - "description": "Type: `file`, required, default: `$id.$key.output.output`. Output file for read 1", - "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Output file for read 1." + "description": "Type: `file`, required, default: `$id.$key.output`. Output file for read 1", + "help_text": "Type: `file`, required, default: `$id.$key.output`. Output file for read 1." , - "default":"$id.$key.output.output" + "default":"$id.$key.output" } @@ -78,10 +78,10 @@ "read2_out": { "type": "string", - "description": "Type: `file`, default: `$id.$key.read2_out.read2_out`. Output file for read 2", - "help_text": "Type: `file`, default: `$id.$key.read2_out.read2_out`. Output file for read 2." + "description": "Type: `file`, default: `$id.$key.read2_out`. Output file for read 2", + "help_text": "Type: `file`, default: `$id.$key.read2_out`. Output file for read 2." , - "default":"$id.$key.read2_out.read2_out" + "default":"$id.$key.read2_out" } @@ -269,10 +269,10 @@ "log": { "type": "string", - "description": "Type: `file`, default: `$id.$key.log.log`. File with logging information", - "help_text": "Type: `file`, default: `$id.$key.log.log`. File with logging information." + "description": "Type: `file`, default: `$id.$key.log`. File with logging information", + "help_text": "Type: `file`, default: `$id.$key.log`. File with logging information." , - "default":"$id.$key.log.log" + "default":"$id.$key.log" } @@ -301,10 +301,10 @@ "error": { "type": "string", - "description": "Type: `file`, default: `$id.$key.error.error`. File with error information", - "help_text": "Type: `file`, default: `$id.$key.error.error`. File with error information." + "description": "Type: `file`, default: `$id.$key.error`. File with error information", + "help_text": "Type: `file`, default: `$id.$key.error`. File with error information." , - "default":"$id.$key.error.error" + "default":"$id.$key.error" } @@ -332,10 +332,10 @@ "timeit": { "type": "string", - "description": "Type: `file`, default: `$id.$key.timeit.timeit`. Store timing information in file", - "help_text": "Type: `file`, default: `$id.$key.timeit.timeit`. Store timing information in file." + "description": "Type: `file`, default: `$id.$key.timeit`. Store timing information in file", + "help_text": "Type: `file`, default: `$id.$key.timeit`. Store timing information in file." , - "default":"$id.$key.timeit.timeit" + "default":"$id.$key.timeit" } diff --git a/target/nextflow/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml b/target/nextflow/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml index 05f0a193..5beb60f2 100644 --- a/target/nextflow/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml +++ b/target/nextflow/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml @@ -258,16 +258,16 @@ build_info: engine: "docker|native" output: "target/nextflow/umi_tools/umi_tools_prepareforrsem" executable: "target/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf" - viash_version: "0.9.2" - git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27" + viash_version: "0.9.4" + git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-31-g1efc026" + git_tag: "v0.2.0-32-gc733de2" package_config: name: "biobox" version: "main" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.2" + viash_version: "0.9.4" source: "src" target: "target" config_mods: diff --git a/target/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf b/target/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf index 4821a36b..d471131d 100644 --- a/target/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf +++ b/target/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf @@ -1,6 +1,6 @@ // umi_tools_prepareforrsem main // -// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative +// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data // Intuitive. // @@ -82,64 +82,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi foundClass = "List[${e.foundClass}]" } } else if (par.type == "string") { - // cast to string if need be + // cast to string if need be. only cast if the value is a GString if (value instanceof GString) { - value = value.toString() + value = value as String } expectedClass = value instanceof String ? null : "String" } else if (par.type == "integer") { // cast to integer if need be - if (value instanceof String) { + if (value !instanceof Integer) { try { - value = value.toInteger() + value = value as Integer } catch (NumberFormatException e) { - // do nothing + expectedClass = "Integer" } } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" } else if (par.type == "long") { // cast to long if need be - if (value instanceof String) { + if (value !instanceof Long) { try { - value = value.toLong() + value = value as Long } catch (NumberFormatException e) { - // do nothing + expectedClass = "Long" } } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" } else if (par.type == "double") { // cast to double if need be - if (value instanceof String) { + if (value !instanceof Double) { try { - value = value.toDouble() + value = value as Double } catch (NumberFormatException e) { - // do nothing + expectedClass = "Double" } } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() + } else if (par.type == "float") { + // cast to float if need be + if (value !instanceof Float) { + try { + value = value as Float + } catch (NumberFormatException e) { + expectedClass = "Float" + } } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false + if (value !instanceof Boolean) { + try { + value = value as Boolean + } catch (Exception e) { + expectedClass = "Boolean" } } - expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { // cast to path if need be if (value instanceof String) { @@ -151,10 +143,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi expectedClass = value instanceof Path ? null : "Path" } else if (par.type == "file" && stage == "input" && par.direction == "output") { // cast to string if need be - if (value instanceof GString) { - value = value.toString() + if (value !instanceof String) { + try { + value = value as String + } catch (Exception e) { + expectedClass = "String" + } } - expectedClass = value instanceof String ? null : "String" } else { // didn't find a match for par.type expectedClass = par.type @@ -3355,16 +3350,16 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/umi_tools/umi_tools_prepareforrsem", - "viash_version" : "0.9.2", - "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27", + "viash_version" : "0.9.4", + "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-31-g1efc026" + "git_tag" : "v0.2.0-32-gc733de2" }, "package_config" : { "name" : "biobox", "version" : "main", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.2", + "viash_version" : "0.9.4", "source" : "src", "target" : "target", "config_mods" : [ @@ -3797,7 +3792,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { // create process from temp file def binding = new nextflow.script.ScriptBinding([:]) def session = nextflow.Nextflow.getSession() - def parser = new nextflow.script.ScriptParser(session) + def parser = _getScriptLoader(session) .setModule(true) .setBinding(binding) def moduleScript = parser.runScript(tempFile) @@ -3811,6 +3806,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { return scriptMeta.getProcess(procKey) } +// use Reflection to get a ScriptParser / ScriptLoader +// <25.02.0-edge: new nextflow.script.ScriptParser(session) +// >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session) +def _getScriptLoader(nextflow.Session session) { + // try using the old method + try { + Class scriptParserClass = Class.forName('nextflow.script.ScriptParser') + return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session) + } catch (ClassNotFoundException e) { + // else try with the new method + try { + Class scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory') + def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session) + return createMethod.invoke(null, session) // null because create is static + } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) { + // Handle the case where neither class is found + throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2) + } + } +} + // defaults meta["defaults"] = [ // key to be used to trace the process and determine output names diff --git a/target/nextflow/umi_tools/umi_tools_prepareforrsem/nextflow_schema.json b/target/nextflow/umi_tools/umi_tools_prepareforrsem/nextflow_schema.json index d7e1cd71..98b77e2f 100644 --- a/target/nextflow/umi_tools/umi_tools_prepareforrsem/nextflow_schema.json +++ b/target/nextflow/umi_tools/umi_tools_prepareforrsem/nextflow_schema.json @@ -48,10 +48,10 @@ "log": { "type": "string", - "description": "Type: `file`, default: `$id.$key.log.log`. File with logging information [default = stdout]", - "help_text": "Type: `file`, default: `$id.$key.log.log`. File with logging information [default = stdout]." + "description": "Type: `file`, default: `$id.$key.log`. File with logging information [default = stdout]", + "help_text": "Type: `file`, default: `$id.$key.log`. File with logging information [default = stdout]." , - "default":"$id.$key.log.log" + "default":"$id.$key.log" } @@ -59,10 +59,10 @@ "error": { "type": "string", - "description": "Type: `file`, default: `$id.$key.error.error`. File with error information [default = stderr]", - "help_text": "Type: `file`, default: `$id.$key.error.error`. File with error information [default = stderr]." + "description": "Type: `file`, default: `$id.$key.error`. File with error information [default = stderr]", + "help_text": "Type: `file`, default: `$id.$key.error`. File with error information [default = stderr]." , - "default":"$id.$key.error.error" + "default":"$id.$key.error" }