From 8c0aff2702fb97323c203d3bc8bc3b3a4610d5ab Mon Sep 17 00:00:00 2001 From: CI Date: Mon, 30 Sep 2024 11:49:24 +0000 Subject: [PATCH] Build branch multiple_fixes with version multiple_fixes (55878e4) Build pipeline: viash-hub.rnaseq.multiple-fixes-jmwt2 Source commit: https://github.com/viash-hub/rnaseq/commit/55878e4519aa920a419bb99a9b3afc8307b6c6e3 Source message: output markduplicates metrics --- assets/multiqc_config.yml | 15 ++-- src/cat_fastq/config.vsh.yaml | 4 +- .../genome_alignment_and_quant/main.nf | 2 +- src/workflows/post_processing/config.vsh.yaml | 2 +- src/workflows/post_processing/main.nf | 21 ++--- src/workflows/quality_control/main.nf | 1 + src/workflows/rnaseq/config.vsh.yaml | 30 ++++--- src/workflows/rnaseq/main.nf | 1 + .../executable/bbmap_bbsplit/.config.vsh.yaml | 4 +- target/executable/bbmap_bbsplit/bbmap_bbsplit | 6 +- .../bedtools_genomecov/.config.vsh.yaml | 4 +- .../bedtools_genomecov/bedtools_genomecov | 6 +- .../cat_additional_fasta/.config.vsh.yaml | 4 +- .../cat_additional_fasta/cat_additional_fasta | 6 +- target/executable/cat_fastq/.config.vsh.yaml | 8 +- target/executable/cat_fastq/cat_fastq | 14 ++-- target/executable/deseq2_qc/.config.vsh.yaml | 4 +- target/executable/deseq2_qc/deseq2_qc | 6 +- target/executable/dupradar/.config.vsh.yaml | 4 +- target/executable/dupradar/dupradar | 6 +- target/executable/fastqc/.config.vsh.yaml | 4 +- target/executable/fastqc/fastqc | 6 +- .../executable/fq_subsample/.config.vsh.yaml | 4 +- target/executable/fq_subsample/fq_subsample | 6 +- .../executable/getchromsizes/.config.vsh.yaml | 4 +- target/executable/getchromsizes/getchromsizes | 6 +- target/executable/gtf2bed/.config.vsh.yaml | 4 +- target/executable/gtf2bed/gtf2bed | 6 +- target/executable/gtf_filter/.config.vsh.yaml | 4 +- target/executable/gtf_filter/gtf_filter | 6 +- target/executable/gunzip/.config.vsh.yaml | 4 +- target/executable/gunzip/gunzip | 6 +- .../kallisto/kallisto_index/.config.vsh.yaml | 4 +- .../kallisto/kallisto_index/kallisto_index | 6 +- .../kallisto/kallisto_quant/.config.vsh.yaml | 4 +- .../kallisto/kallisto_quant/kallisto_quant | 6 +- .../multiqc_custom_biotype/.config.vsh.yaml | 4 +- .../multiqc_custom_biotype | 6 +- .../picard_markduplicates/.config.vsh.yaml | 4 +- .../picard_markduplicates | 6 +- .../prepare_multiqc_input/.config.vsh.yaml | 4 +- .../prepare_multiqc_input | 6 +- .../.config.vsh.yaml | 4 +- .../preprocess_transcripts_fasta | 6 +- .../preseq_lcextrap/.config.vsh.yaml | 4 +- .../preseq_lcextrap/preseq_lcextrap | 6 +- target/executable/qualimap/.config.vsh.yaml | 4 +- target/executable/qualimap/qualimap | 6 +- .../.config.vsh.yaml | 4 +- .../rsem_calculate_expression | 6 +- .../rsem/rsem_merge_counts/.config.vsh.yaml | 4 +- .../rsem/rsem_merge_counts/rsem_merge_counts | 6 +- .../rseqc/rseqc_bamstat/.config.vsh.yaml | 4 +- .../rseqc/rseqc_bamstat/rseqc_bamstat | 6 +- .../rseqc_inferexperiment/.config.vsh.yaml | 4 +- .../rseqc_inferexperiment | 6 +- .../rseqc_innerdistance/.config.vsh.yaml | 4 +- .../rseqc_innerdistance/rseqc_innerdistance | 6 +- .../rseqc_junctionannotation/.config.vsh.yaml | 4 +- .../rseqc_junctionannotation | 6 +- .../rseqc_junctionsaturation/.config.vsh.yaml | 4 +- .../rseqc_junctionsaturation | 6 +- .../rseqc_readdistribution/.config.vsh.yaml | 4 +- .../rseqc_readdistribution | 6 +- .../rseqc_readduplication/.config.vsh.yaml | 4 +- .../rseqc_readduplication | 6 +- .../rseqc/rseqc_tin/.config.vsh.yaml | 4 +- target/executable/rseqc/rseqc_tin/rseqc_tin | 6 +- target/executable/sortmerna/.config.vsh.yaml | 4 +- target/executable/sortmerna/sortmerna | 6 +- target/executable/stringtie/.config.vsh.yaml | 4 +- target/executable/stringtie/stringtie | 6 +- .../summarizedexperiment/.config.vsh.yaml | 4 +- .../summarizedexperiment/summarizedexperiment | 6 +- target/executable/trimgalore/.config.vsh.yaml | 4 +- target/executable/trimgalore/trimgalore | 4 +- target/executable/tx2gene/.config.vsh.yaml | 4 +- target/executable/tx2gene/tx2gene | 6 +- target/executable/tximport/.config.vsh.yaml | 4 +- target/executable/tximport/tximport | 6 +- .../executable/ucsc/bedclip/.config.vsh.yaml | 4 +- target/executable/ucsc/bedclip/bedclip | 6 +- .../ucsc/bedgraphtobigwig/.config.vsh.yaml | 4 +- .../ucsc/bedgraphtobigwig/bedgraphtobigwig | 6 +- .../umitools/umitools_dedup/.config.vsh.yaml | 4 +- .../umitools/umitools_dedup/umitools_dedup | 6 +- .../umitools_extract/.config.vsh.yaml | 4 +- .../umitools_extract/umitools_extract | 6 +- .../umitools_prepareforquant/.config.vsh.yaml | 4 +- .../umitools_prepareforquant | 6 +- .../.config.vsh.yaml | 4 +- .../genome_alignment_and_quant | 2 +- .../merge_quant_results/.config.vsh.yaml | 4 +- .../post_processing/.config.vsh.yaml | 6 +- .../workflows/post_processing/post_processing | 25 +++--- .../workflows/pre_processing/.config.vsh.yaml | 4 +- .../workflows/prepare_genome/.config.vsh.yaml | 4 +- .../.config.vsh.yaml | 4 +- .../quality_control/.config.vsh.yaml | 4 +- .../workflows/quality_control/quality_control | 1 + .../workflows/rnaseq/.config.vsh.yaml | 41 ++++++---- target/executable/workflows/rnaseq/rnaseq | 79 ++++++++++++------- .../nextflow/bbmap_bbsplit/.config.vsh.yaml | 4 +- target/nextflow/bbmap_bbsplit/main.nf | 4 +- .../bedtools_genomecov/.config.vsh.yaml | 4 +- target/nextflow/bedtools_genomecov/main.nf | 4 +- .../cat_additional_fasta/.config.vsh.yaml | 4 +- target/nextflow/cat_additional_fasta/main.nf | 4 +- target/nextflow/cat_fastq/.config.vsh.yaml | 8 +- target/nextflow/cat_fastq/main.nf | 8 +- target/nextflow/deseq2_qc/.config.vsh.yaml | 4 +- target/nextflow/deseq2_qc/main.nf | 4 +- target/nextflow/dupradar/.config.vsh.yaml | 4 +- target/nextflow/dupradar/main.nf | 4 +- target/nextflow/fastqc/.config.vsh.yaml | 4 +- target/nextflow/fastqc/main.nf | 4 +- target/nextflow/fq_subsample/.config.vsh.yaml | 4 +- target/nextflow/fq_subsample/main.nf | 4 +- .../nextflow/getchromsizes/.config.vsh.yaml | 4 +- target/nextflow/getchromsizes/main.nf | 4 +- target/nextflow/gtf2bed/.config.vsh.yaml | 4 +- target/nextflow/gtf2bed/main.nf | 4 +- target/nextflow/gtf_filter/.config.vsh.yaml | 4 +- target/nextflow/gtf_filter/main.nf | 4 +- target/nextflow/gunzip/.config.vsh.yaml | 4 +- target/nextflow/gunzip/main.nf | 4 +- .../kallisto/kallisto_index/.config.vsh.yaml | 4 +- .../nextflow/kallisto/kallisto_index/main.nf | 4 +- .../kallisto/kallisto_quant/.config.vsh.yaml | 4 +- .../nextflow/kallisto/kallisto_quant/main.nf | 4 +- .../multiqc_custom_biotype/.config.vsh.yaml | 4 +- .../nextflow/multiqc_custom_biotype/main.nf | 4 +- .../picard_markduplicates/.config.vsh.yaml | 4 +- target/nextflow/picard_markduplicates/main.nf | 4 +- .../prepare_multiqc_input/.config.vsh.yaml | 4 +- target/nextflow/prepare_multiqc_input/main.nf | 4 +- .../.config.vsh.yaml | 4 +- .../preprocess_transcripts_fasta/main.nf | 4 +- .../nextflow/preseq_lcextrap/.config.vsh.yaml | 4 +- target/nextflow/preseq_lcextrap/main.nf | 4 +- target/nextflow/qualimap/.config.vsh.yaml | 4 +- target/nextflow/qualimap/main.nf | 4 +- .../.config.vsh.yaml | 4 +- .../rsem/rsem_calculate_expression/main.nf | 4 +- .../rsem/rsem_merge_counts/.config.vsh.yaml | 4 +- .../nextflow/rsem/rsem_merge_counts/main.nf | 4 +- .../rseqc/rseqc_bamstat/.config.vsh.yaml | 4 +- target/nextflow/rseqc/rseqc_bamstat/main.nf | 4 +- .../rseqc_inferexperiment/.config.vsh.yaml | 4 +- .../rseqc/rseqc_inferexperiment/main.nf | 4 +- .../rseqc_innerdistance/.config.vsh.yaml | 4 +- .../rseqc/rseqc_innerdistance/main.nf | 4 +- .../rseqc_junctionannotation/.config.vsh.yaml | 4 +- .../rseqc/rseqc_junctionannotation/main.nf | 4 +- .../rseqc_junctionsaturation/.config.vsh.yaml | 4 +- .../rseqc/rseqc_junctionsaturation/main.nf | 4 +- .../rseqc_readdistribution/.config.vsh.yaml | 4 +- .../rseqc/rseqc_readdistribution/main.nf | 4 +- .../rseqc_readduplication/.config.vsh.yaml | 4 +- .../rseqc/rseqc_readduplication/main.nf | 4 +- .../nextflow/rseqc/rseqc_tin/.config.vsh.yaml | 4 +- target/nextflow/rseqc/rseqc_tin/main.nf | 4 +- target/nextflow/sortmerna/.config.vsh.yaml | 4 +- target/nextflow/sortmerna/main.nf | 4 +- target/nextflow/stringtie/.config.vsh.yaml | 4 +- target/nextflow/stringtie/main.nf | 4 +- .../summarizedexperiment/.config.vsh.yaml | 4 +- target/nextflow/summarizedexperiment/main.nf | 4 +- target/nextflow/trimgalore/.config.vsh.yaml | 4 +- target/nextflow/trimgalore/main.nf | 4 +- target/nextflow/tx2gene/.config.vsh.yaml | 4 +- target/nextflow/tx2gene/main.nf | 4 +- target/nextflow/tximport/.config.vsh.yaml | 4 +- target/nextflow/tximport/main.nf | 4 +- target/nextflow/ucsc/bedclip/.config.vsh.yaml | 4 +- target/nextflow/ucsc/bedclip/main.nf | 4 +- .../ucsc/bedgraphtobigwig/.config.vsh.yaml | 4 +- target/nextflow/ucsc/bedgraphtobigwig/main.nf | 4 +- .../umitools/umitools_dedup/.config.vsh.yaml | 4 +- .../nextflow/umitools/umitools_dedup/main.nf | 4 +- .../umitools_extract/.config.vsh.yaml | 4 +- .../umitools/umitools_extract/main.nf | 4 +- .../umitools_prepareforquant/.config.vsh.yaml | 4 +- .../nextflow/umitools_prepareforquant/main.nf | 4 +- .../.config.vsh.yaml | 4 +- .../genome_alignment_and_quant/main.nf | 6 +- .../merge_quant_results/.config.vsh.yaml | 4 +- .../workflows/merge_quant_results/main.nf | 4 +- .../post_processing/.config.vsh.yaml | 6 +- .../workflows/post_processing/main.nf | 27 ++++--- .../workflows/pre_processing/.config.vsh.yaml | 4 +- .../nextflow/workflows/pre_processing/main.nf | 4 +- .../workflows/prepare_genome/.config.vsh.yaml | 4 +- .../nextflow/workflows/prepare_genome/main.nf | 4 +- .../.config.vsh.yaml | 4 +- .../pseudo_alignment_and_quant/main.nf | 4 +- .../quality_control/.config.vsh.yaml | 4 +- .../workflows/quality_control/main.nf | 5 +- .../workflows/rnaseq/.config.vsh.yaml | 41 ++++++---- target/nextflow/workflows/rnaseq/main.nf | 48 +++++++---- .../workflows/rnaseq/nextflow_schema.json | 11 +++ 201 files changed, 637 insertions(+), 557 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index e37f756..0ac2fb1 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -65,15 +65,14 @@ table_columns_visible: percent_duplicates: False extra_fn_clean_extn: - - ".mapping_quality" - - ".MarkDuplicates_flagstat.output.flagstat" - - ".MarkDuplicates_idxstats.output.idxstats" - - ".MarkDuplicates_stats.output.txt" - - ".genome_sorted_MarkDuplicates.output.bam" - - ".genome_sorted_MarkDuplicates" + # - ".mapping_quality" + # - ".MarkDuplicates_flagstat.output.flagstat" + # - ".MarkDuplicates_idxstats.output.idxstats" + # - ".MarkDuplicates_stats.output.txt" + # - ".genome_sorted_MarkDuplicates.output.bam" + # - ".genome_sorted_MarkDuplicates" - ".read_1" - ".read_2" - - "_merged" # See https://github.com/ewels/MultiQC_TestData/blob/master/data/custom_content/with_config/table_headerconfig/multiqc_config.yaml custom_data: @@ -129,8 +128,6 @@ sp: # hisat2: # fn: "*.hisat2.summary.log" - - # TODO: Add Salmon meta info # salmon: # fn: "*meta_info.json" diff --git a/src/cat_fastq/config.vsh.yaml b/src/cat_fastq/config.vsh.yaml index 929921d..4f8b77b 100644 --- a/src/cat_fastq/config.vsh.yaml +++ b/src/cat_fastq/config.vsh.yaml @@ -25,13 +25,13 @@ argument_groups: - name: "--fastq_1" type: file direction: output - default: $id_r1_merged.fastq + default: $id_r1.fastq description: Concatenated read 1 fastq - name: "--fastq_2" type: file direction: output must_exist: false - default: $id_r2_merged.fastq + default: $id_r2.fastq description: Concatenated read 2 fastq resources: diff --git a/src/workflows/genome_alignment_and_quant/main.nf b/src/workflows/genome_alignment_and_quant/main.nf index 9ba3aee..4734670 100644 --- a/src/workflows/genome_alignment_and_quant/main.nf +++ b/src/workflows/genome_alignment_and_quant/main.nf @@ -284,7 +284,7 @@ workflow run_wf { def mod_state = (state.aligner == 'star_salmon') ? state + [salmon_multiqc: state.quant_out_dir] : state [ id, mod_state ] } - | niceView() + | rsem_calculate_expression.run ( runIf: { id, state -> state.aligner == 'star_rsem' }, fromState: [ diff --git a/src/workflows/post_processing/config.vsh.yaml b/src/workflows/post_processing/config.vsh.yaml index b91e0a0..40ca733 100644 --- a/src/workflows/post_processing/config.vsh.yaml +++ b/src/workflows/post_processing/config.vsh.yaml @@ -79,7 +79,7 @@ argument_groups: - name: "--processed_genome_bam" type: file direction: output - default: $id..genome.bam + default: $id.genome.bam - name: "--genome_bam_index" type: file direction: output diff --git a/src/workflows/post_processing/main.nf b/src/workflows/post_processing/main.nf index 80b15e0..9c60291 100644 --- a/src/workflows/post_processing/main.nf +++ b/src/workflows/post_processing/main.nf @@ -16,20 +16,20 @@ workflow run_wf { "extra_picard_args": "extra_picard_args" ], toState: [ - "genome_bam": "output_bam", + "processed_genome_bam": "output_bam", "markduplicates_metrics": "metrics" ] ) | samtools_sort.run ( runIf: { id, state -> !state.skip_markduplicates && !state.with_umi }, - fromState: [ "input": "genome_bam" ], - toState: [ "genome_bam": "output" ], + fromState: [ "input": "processed_genome_bam" ], + toState: [ "processed_genome_bam": "output" ], key: "genome_sorted_MarkDuplicates" ) | samtools_index.run ( runIf: { id, state -> !state.skip_markduplicates && !state.with_umi }, fromState: [ - "input": "genome_bam", + "input": "processed_genome_bam", "csi": "bam_csi_index" ], toState: [ "genome_bam_index": "output" ], @@ -38,7 +38,7 @@ workflow run_wf { | samtools_stats.run ( runIf: { id, state -> !state.skip_markduplicates && !state.with_umi }, fromState: [ - "input": "genome_bam", + "input": "processed_genome_bam", "bai": "genome_bam_index" ], toState: [ "genome_bam_stats": "output" ], @@ -47,7 +47,7 @@ workflow run_wf { | samtools_flagstat.run ( runIf: { id, state -> !state.skip_markduplicates && !state.with_umi }, fromState: [ - "bam": "genome_bam", + "bam": "processed_genome_bam", "bai": "genome_bam_index" ], toState: [ "genome_bam_flagstat": "output" ], @@ -56,7 +56,7 @@ workflow run_wf { | samtools_idxstats.run( runIf: { id, state -> !state.skip_markduplicates && !state.with_umi }, fromState: [ - "bam": "genome_bam", + "bam": "processed_genome_bam", "bai": "genome_bam_index" ], toState: [ "genome_bam_idxstats": "output" ], @@ -67,7 +67,7 @@ workflow run_wf { runIf: { id, state -> !state.skip_stringtie }, fromState: [ "strandedness": "strandedness", - "bam": "genome_bam", + "bam": "processed_genome_bam", "annotation_gtf": "gtf", "extra_stringtie_args": "extra_stringtie_args" ], @@ -85,7 +85,7 @@ workflow run_wf { runIf: { id, state -> !state.skip_bigwig }, fromState: [ "strandedness": "strandedness", - "bam": "genome_bam", + "bam": "processed_genome_bam", "extra_bedtools_args": "extra_bedtools_args" ], toState: [ @@ -138,9 +138,10 @@ workflow run_wf { def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() } [ id, mod_state ] } + | niceView() | setState ( - "processed_genome_bam": "genome_bam", + "processed_genome_bam": "processed_genome_bam", "genome_bam_index": "genome_bam_index", "genome_bam_stats": "genome_bam_stats", "genome_bam_flagstat": "genome_bam_flagstat", diff --git a/src/workflows/quality_control/main.nf b/src/workflows/quality_control/main.nf index d74e758..c142272 100644 --- a/src/workflows/quality_control/main.nf +++ b/src/workflows/quality_control/main.nf @@ -723,6 +723,7 @@ workflow run_wf { "title": "multiqc_title", "input": "multiqc_input", ], + args: [exclude_modules: "general_stats"], toState: [ "multiqc_report": "output_report", "multiqc_data": "output_data", diff --git a/src/workflows/rnaseq/config.vsh.yaml b/src/workflows/rnaseq/config.vsh.yaml index 151cb77..4526e8c 100644 --- a/src/workflows/rnaseq/config.vsh.yaml +++ b/src/workflows/rnaseq/config.vsh.yaml @@ -492,23 +492,23 @@ argument_groups: - name: "--star_alignment" type: file direction: output - default: STAR_alignment/$id + default: STAR/$id - name: "--genome_bam_sorted" type: file direction: output - default: STAR_alignment/genome_processed/$id.genome.bam + default: STAR/genome_processed/$id.genome.bam - name: "--genome_bam_index" type: file direction: output - default: STAR_alignment/genome_processed/$id.genome.bam.bai + default: STAR/genome_processed/$id.genome.bam.bai - name: "--transcriptome_bam" type: file direction: output - default: STAR_alignment/transcriptome_processed/$id.transcriptome.bam + default: STAR/transcriptome_processed/$id.transcriptome.bam - name: "--transcriptome_bam_index" type: file direction: output - default: STAR_alignment/transcriptome_processed/$id.transcriptome.bam.bai + default: STAR/transcriptome_processed/$id.transcriptome.bam.bai # samtools - name: "--genome_bam_stats" @@ -541,6 +541,10 @@ argument_groups: type: file direction: output default: STAR_Salmon/$id + - name: "--salmon_quant_results_file" + type: file + direction: output + default: STAR_Salmon/$id/quant.sf - name: "--pseudo_quant_results" type: file direction: output @@ -577,37 +581,37 @@ argument_groups: - name: "--tpm_gene" type: file direction: output - default: alignment_quantification/gene_tpm.tsv + default: transcript_quantification/gene_tpm.tsv - name: "--counts_gene" type: file direction: output - default: alignment_quantification/gene_counts.tsv + default: transcript_quantification/gene_counts.tsv - name: "--counts_gene_length_scaled" type: file direction: output - default: alignment_quantification/gene_counts_length_scaled.tsv + default: transcript_quantification/gene_counts_length_scaled.tsv - name: "--counts_gene_scaled" type: file direction: output - default: alignment_quantification/gene_counts_scaled.tsv + default: transcript_quantification/gene_counts_scaled.tsv - name: "--tpm_transcript" type: file direction: output - default: alignment_quantification/transcript_tpm.tsv + default: transcript_quantification/transcript_tpm.tsv - name: "--counts_transcript" type: file direction: output - default: alignment_quantification/transcript_counts.tsv + default: transcript_quantification/transcript_counts.tsv - name: "--quant_merged_summarizedexperiment" type: file direction: output - default: alignment_quantification/summarizedexperiment + default: transcript_quantification/summarizedexperiment # MarkDuplicates - name: "--markduplicates_metrics" type: file direction: output - default: picard/$id.sorted.MarkDuplicates.metrics.txt + default: picard/$id.MarkDuplicates.metrics.txt # StringTie - name: "--stringtie_transcript_gtf" diff --git a/src/workflows/rnaseq/main.nf b/src/workflows/rnaseq/main.nf index 8a22197..d9e10b1 100644 --- a/src/workflows/rnaseq/main.nf +++ b/src/workflows/rnaseq/main.nf @@ -477,6 +477,7 @@ workflow run_wf { "transcriptome_bam_idxstats": "transcriptome_bam_idxstats", "salmon_quant_results": "quant_out_dir", "pseudo_quant_results": "pseudo_quant_out_dir", + "markduplicates_metrics": "markduplicates_metrics", "stringtie_transcript_gtf": "stringtie_transcript_gtf", "stringtie_coverage_gtf": "stringtie_coverage_gtf", "stringtie_abundance": "stringtie_abundance", diff --git a/target/executable/bbmap_bbsplit/.config.vsh.yaml b/target/executable/bbmap_bbsplit/.config.vsh.yaml index fb51071..fe2e053 100644 --- a/target/executable/bbmap_bbsplit/.config.vsh.yaml +++ b/target/executable/bbmap_bbsplit/.config.vsh.yaml @@ -238,8 +238,8 @@ build_info: output: "target/executable/bbmap_bbsplit" executable: "target/executable/bbmap_bbsplit/bbmap_bbsplit" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/bbmap_bbsplit/bbmap_bbsplit b/target/executable/bbmap_bbsplit/bbmap_bbsplit index b9f9c39..cd7fc86 100755 --- a/target/executable/bbmap_bbsplit/bbmap_bbsplit +++ b/target/executable/bbmap_bbsplit/bbmap_bbsplit @@ -506,9 +506,9 @@ tar xzf BBMap_39.01.tar.gz && \ cp -r bbmap/* /usr/local/bin LABEL org.opencontainers.image.description="Companion container for running component bbmap_bbsplit" -LABEL org.opencontainers.image.created="2024-09-30T07:15:18Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:29Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/bedtools_genomecov/.config.vsh.yaml b/target/executable/bedtools_genomecov/.config.vsh.yaml index c6b5f07..9f362ba 100644 --- a/target/executable/bedtools_genomecov/.config.vsh.yaml +++ b/target/executable/bedtools_genomecov/.config.vsh.yaml @@ -178,8 +178,8 @@ build_info: output: "target/executable/bedtools_genomecov" executable: "target/executable/bedtools_genomecov/bedtools_genomecov" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/bedtools_genomecov/bedtools_genomecov b/target/executable/bedtools_genomecov/bedtools_genomecov index e2e87f6..3d9eece 100755 --- a/target/executable/bedtools_genomecov/bedtools_genomecov +++ b/target/executable/bedtools_genomecov/bedtools_genomecov @@ -481,9 +481,9 @@ mv bedtools.static /usr/local/bin/bedtools && \ chmod a+x /usr/local/bin/bedtools LABEL org.opencontainers.image.description="Companion container for running component bedtools_genomecov" -LABEL org.opencontainers.image.created="2024-09-30T07:15:18Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:29Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/cat_additional_fasta/.config.vsh.yaml b/target/executable/cat_additional_fasta/.config.vsh.yaml index 295eff3..39b3ea9 100644 --- a/target/executable/cat_additional_fasta/.config.vsh.yaml +++ b/target/executable/cat_additional_fasta/.config.vsh.yaml @@ -182,8 +182,8 @@ build_info: output: "target/executable/cat_additional_fasta" executable: "target/executable/cat_additional_fasta/cat_additional_fasta" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/cat_additional_fasta/cat_additional_fasta b/target/executable/cat_additional_fasta/cat_additional_fasta index 90169b7..29fd1b1 100755 --- a/target/executable/cat_additional_fasta/cat_additional_fasta +++ b/target/executable/cat_additional_fasta/cat_additional_fasta @@ -480,9 +480,9 @@ function ViashDockerfile { FROM python:latest ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component cat_additional_fasta" -LABEL org.opencontainers.image.created="2024-09-30T07:15:25Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:37Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/cat_fastq/.config.vsh.yaml b/target/executable/cat_fastq/.config.vsh.yaml index 328f39b..12c4cb4 100644 --- a/target/executable/cat_fastq/.config.vsh.yaml +++ b/target/executable/cat_fastq/.config.vsh.yaml @@ -30,7 +30,7 @@ argument_groups: description: "Concatenated read 1 fastq" info: null default: - - "$id_r1_merged.fastq" + - "$id_r1.fastq" must_exist: true create_parent: true required: false @@ -42,7 +42,7 @@ argument_groups: description: "Concatenated read 2 fastq" info: null default: - - "$id_r2_merged.fastq" + - "$id_r2.fastq" must_exist: false create_parent: true required: false @@ -169,8 +169,8 @@ build_info: output: "target/executable/cat_fastq" executable: "target/executable/cat_fastq/cat_fastq" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/cat_fastq/cat_fastq b/target/executable/cat_fastq/cat_fastq index 3b14491..d55b481 100755 --- a/target/executable/cat_fastq/cat_fastq +++ b/target/executable/cat_fastq/cat_fastq @@ -187,12 +187,12 @@ function ViashHelp { echo "Output:" echo " --fastq_1" echo " type: file, output, file must exist" - echo " default: \$id_r1_merged.fastq" + echo " default: \$id_r1.fastq" echo " Concatenated read 1 fastq" echo "" echo " --fastq_2" echo " type: file, output" - echo " default: \$id_r2_merged.fastq" + echo " default: \$id_r2.fastq" echo " Concatenated read 2 fastq" } @@ -472,9 +472,9 @@ function ViashDockerfile { FROM ubuntu:22.04 ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component cat_fastq" -LABEL org.opencontainers.image.created="2024-09-30T07:15:26Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:37Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER @@ -869,10 +869,10 @@ fi # filling in defaults if [ -z ${VIASH_PAR_FASTQ_1+x} ]; then - VIASH_PAR_FASTQ_1="\$id_r1_merged.fastq" + VIASH_PAR_FASTQ_1="\$id_r1.fastq" fi if [ -z ${VIASH_PAR_FASTQ_2+x} ]; then - VIASH_PAR_FASTQ_2="\$id_r2_merged.fastq" + VIASH_PAR_FASTQ_2="\$id_r2.fastq" fi # check whether required files exist diff --git a/target/executable/deseq2_qc/.config.vsh.yaml b/target/executable/deseq2_qc/.config.vsh.yaml index 0b1c35a..23e13c1 100644 --- a/target/executable/deseq2_qc/.config.vsh.yaml +++ b/target/executable/deseq2_qc/.config.vsh.yaml @@ -237,8 +237,8 @@ build_info: output: "target/executable/deseq2_qc" executable: "target/executable/deseq2_qc/deseq2_qc" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/deseq2_qc/deseq2_qc b/target/executable/deseq2_qc/deseq2_qc index de9eb5b..18cb5ad 100755 --- a/target/executable/deseq2_qc/deseq2_qc +++ b/target/executable/deseq2_qc/deseq2_qc @@ -502,9 +502,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag Rscript -e 'remotes::install_url(c("https://cran.r-project.org/src/contrib/Archive/matrixStats/matrixStats_1.1.0.tar.gz"), repos = "https://cran.rstudio.com")' LABEL org.opencontainers.image.description="Companion container for running component deseq2_qc" -LABEL org.opencontainers.image.created="2024-09-30T07:15:35Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:47Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/dupradar/.config.vsh.yaml b/target/executable/dupradar/.config.vsh.yaml index 2ff7324..2ddae4b 100644 --- a/target/executable/dupradar/.config.vsh.yaml +++ b/target/executable/dupradar/.config.vsh.yaml @@ -266,8 +266,8 @@ build_info: output: "target/executable/dupradar" executable: "target/executable/dupradar/dupradar" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/dupradar/dupradar b/target/executable/dupradar/dupradar index 3b1be76..ac51f92 100755 --- a/target/executable/dupradar/dupradar +++ b/target/executable/dupradar/dupradar @@ -520,9 +520,9 @@ RUN Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.pa Rscript -e 'if (!requireNamespace("dupRadar", quietly = TRUE)) BiocManager::install("dupRadar")' LABEL org.opencontainers.image.description="Companion container for running component dupradar" -LABEL org.opencontainers.image.created="2024-09-30T07:15:27Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:38Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/fastqc/.config.vsh.yaml b/target/executable/fastqc/.config.vsh.yaml index af17ff0..3058ce9 100644 --- a/target/executable/fastqc/.config.vsh.yaml +++ b/target/executable/fastqc/.config.vsh.yaml @@ -198,8 +198,8 @@ build_info: output: "target/executable/fastqc" executable: "target/executable/fastqc/fastqc" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/fastqc/fastqc b/target/executable/fastqc/fastqc index 32410ab..3c74606 100755 --- a/target/executable/fastqc/fastqc +++ b/target/executable/fastqc/fastqc @@ -490,9 +490,9 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component fastqc" -LABEL org.opencontainers.image.created="2024-09-30T07:15:19Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:30Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/fq_subsample/.config.vsh.yaml b/target/executable/fq_subsample/.config.vsh.yaml index c34ffc9..f128068 100644 --- a/target/executable/fq_subsample/.config.vsh.yaml +++ b/target/executable/fq_subsample/.config.vsh.yaml @@ -177,8 +177,8 @@ build_info: output: "target/executable/fq_subsample" executable: "target/executable/fq_subsample/fq_subsample" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/fq_subsample/fq_subsample b/target/executable/fq_subsample/fq_subsample index 734a432..e6f57f0 100755 --- a/target/executable/fq_subsample/fq_subsample +++ b/target/executable/fq_subsample/fq_subsample @@ -485,9 +485,9 @@ cargo install --locked --path . && \ mv /usr/local/fq/target/release/fq /usr/local/bin/ LABEL org.opencontainers.image.description="Companion container for running component fq_subsample" -LABEL org.opencontainers.image.created="2024-09-30T07:15:19Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:30Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/getchromsizes/.config.vsh.yaml b/target/executable/getchromsizes/.config.vsh.yaml index 99f3aa7..abdd5e9 100644 --- a/target/executable/getchromsizes/.config.vsh.yaml +++ b/target/executable/getchromsizes/.config.vsh.yaml @@ -167,8 +167,8 @@ build_info: output: "target/executable/getchromsizes" executable: "target/executable/getchromsizes/getchromsizes" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/getchromsizes/getchromsizes b/target/executable/getchromsizes/getchromsizes index 0ae4e40..404085c 100755 --- a/target/executable/getchromsizes/getchromsizes +++ b/target/executable/getchromsizes/getchromsizes @@ -480,9 +480,9 @@ make && \ make install LABEL org.opencontainers.image.description="Companion container for running component getchromsizes" -LABEL org.opencontainers.image.created="2024-09-30T07:15:20Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:31Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/gtf2bed/.config.vsh.yaml b/target/executable/gtf2bed/.config.vsh.yaml index dc4b624..2b32650 100644 --- a/target/executable/gtf2bed/.config.vsh.yaml +++ b/target/executable/gtf2bed/.config.vsh.yaml @@ -145,8 +145,8 @@ build_info: output: "target/executable/gtf2bed" executable: "target/executable/gtf2bed/gtf2bed" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/gtf2bed/gtf2bed b/target/executable/gtf2bed/gtf2bed index f4458fc..0ba1a1a 100755 --- a/target/executable/gtf2bed/gtf2bed +++ b/target/executable/gtf2bed/gtf2bed @@ -466,9 +466,9 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component gtf2bed" -LABEL org.opencontainers.image.created="2024-09-30T07:15:31Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:42Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/gtf_filter/.config.vsh.yaml b/target/executable/gtf_filter/.config.vsh.yaml index 6dfdc3b..918ca94 100644 --- a/target/executable/gtf_filter/.config.vsh.yaml +++ b/target/executable/gtf_filter/.config.vsh.yaml @@ -155,8 +155,8 @@ build_info: output: "target/executable/gtf_filter" executable: "target/executable/gtf_filter/gtf_filter" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/gtf_filter/gtf_filter b/target/executable/gtf_filter/gtf_filter index 5e9d73f..d5fd989 100755 --- a/target/executable/gtf_filter/gtf_filter +++ b/target/executable/gtf_filter/gtf_filter @@ -470,9 +470,9 @@ function ViashDockerfile { FROM python:latest ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component gtf_filter" -LABEL org.opencontainers.image.created="2024-09-30T07:15:34Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:46Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/gunzip/.config.vsh.yaml b/target/executable/gunzip/.config.vsh.yaml index 7846252..dd459fd 100644 --- a/target/executable/gunzip/.config.vsh.yaml +++ b/target/executable/gunzip/.config.vsh.yaml @@ -144,8 +144,8 @@ build_info: output: "target/executable/gunzip" executable: "target/executable/gunzip/gunzip" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/gunzip/gunzip b/target/executable/gunzip/gunzip index 11210a1..f7c83bc 100755 --- a/target/executable/gunzip/gunzip +++ b/target/executable/gunzip/gunzip @@ -466,9 +466,9 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component gunzip" -LABEL org.opencontainers.image.created="2024-09-30T07:15:20Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:31Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/kallisto/kallisto_index/.config.vsh.yaml b/target/executable/kallisto/kallisto_index/.config.vsh.yaml index aca24c2..eb3b2bd 100644 --- a/target/executable/kallisto/kallisto_index/.config.vsh.yaml +++ b/target/executable/kallisto/kallisto_index/.config.vsh.yaml @@ -155,8 +155,8 @@ build_info: output: "target/executable/kallisto/kallisto_index" executable: "target/executable/kallisto/kallisto_index/kallisto_index" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/kallisto/kallisto_index/kallisto_index b/target/executable/kallisto/kallisto_index/kallisto_index index b370ff0..b6fdd22 100755 --- a/target/executable/kallisto/kallisto_index/kallisto_index +++ b/target/executable/kallisto/kallisto_index/kallisto_index @@ -471,9 +471,9 @@ 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="2024-09-30T07:15:32Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:44Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml index 792012a..53f33b0 100644 --- a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml +++ b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml @@ -253,8 +253,8 @@ build_info: output: "target/executable/kallisto/kallisto_quant" executable: "target/executable/kallisto/kallisto_quant/kallisto_quant" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/kallisto/kallisto_quant/kallisto_quant b/target/executable/kallisto/kallisto_quant/kallisto_quant index 3cfff21..4d59135 100755 --- a/target/executable/kallisto/kallisto_quant/kallisto_quant +++ b/target/executable/kallisto/kallisto_quant/kallisto_quant @@ -515,9 +515,9 @@ 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_quant" -LABEL org.opencontainers.image.created="2024-09-30T07:15:32Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:44Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/multiqc_custom_biotype/.config.vsh.yaml b/target/executable/multiqc_custom_biotype/.config.vsh.yaml index caec3cd..8508180 100644 --- a/target/executable/multiqc_custom_biotype/.config.vsh.yaml +++ b/target/executable/multiqc_custom_biotype/.config.vsh.yaml @@ -170,8 +170,8 @@ build_info: output: "target/executable/multiqc_custom_biotype" executable: "target/executable/multiqc_custom_biotype/multiqc_custom_biotype" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/multiqc_custom_biotype/multiqc_custom_biotype b/target/executable/multiqc_custom_biotype/multiqc_custom_biotype index 2a9ae0e..7e7caae 100755 --- a/target/executable/multiqc_custom_biotype/multiqc_custom_biotype +++ b/target/executable/multiqc_custom_biotype/multiqc_custom_biotype @@ -481,9 +481,9 @@ RUN apt-get update && \ RUN pip install --upgrade pip LABEL org.opencontainers.image.description="Companion container for running component multiqc_custom_biotype" -LABEL org.opencontainers.image.created="2024-09-30T07:15:27Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:38Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/picard_markduplicates/.config.vsh.yaml b/target/executable/picard_markduplicates/.config.vsh.yaml index 44d0d9e..da0aff2 100644 --- a/target/executable/picard_markduplicates/.config.vsh.yaml +++ b/target/executable/picard_markduplicates/.config.vsh.yaml @@ -207,8 +207,8 @@ build_info: output: "target/executable/picard_markduplicates" executable: "target/executable/picard_markduplicates/picard_markduplicates" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/picard_markduplicates/picard_markduplicates b/target/executable/picard_markduplicates/picard_markduplicates index b2c0902..784bd08 100755 --- a/target/executable/picard_markduplicates/picard_markduplicates +++ b/target/executable/picard_markduplicates/picard_markduplicates @@ -494,9 +494,9 @@ wget --no-check-certificate https://github.com/broadinstitute/picard/releases/do mv picard.jar /usr/local/bin LABEL org.opencontainers.image.description="Companion container for running component picard_markduplicates" -LABEL org.opencontainers.image.created="2024-09-30T07:15:34Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:46Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/prepare_multiqc_input/.config.vsh.yaml b/target/executable/prepare_multiqc_input/.config.vsh.yaml index 3db4d8f..577ea87 100644 --- a/target/executable/prepare_multiqc_input/.config.vsh.yaml +++ b/target/executable/prepare_multiqc_input/.config.vsh.yaml @@ -409,8 +409,8 @@ build_info: output: "target/executable/prepare_multiqc_input" executable: "target/executable/prepare_multiqc_input/prepare_multiqc_input" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/prepare_multiqc_input/prepare_multiqc_input b/target/executable/prepare_multiqc_input/prepare_multiqc_input index 9496d5a..8ba158a 100755 --- a/target/executable/prepare_multiqc_input/prepare_multiqc_input +++ b/target/executable/prepare_multiqc_input/prepare_multiqc_input @@ -557,9 +557,9 @@ function ViashDockerfile { FROM ubuntu:22.04 ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component prepare_multiqc_input" -LABEL org.opencontainers.image.created="2024-09-30T07:15:30Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:42Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml b/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml index 8a3b76c..52cef23 100644 --- a/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml +++ b/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml @@ -138,8 +138,8 @@ build_info: output: "target/executable/preprocess_transcripts_fasta" executable: "target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta b/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta index 94346d7..b64c412 100755 --- a/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta +++ b/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta @@ -462,9 +462,9 @@ function ViashDockerfile { FROM ubuntu:22.04 ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component preprocess_transcripts_fasta" -LABEL org.opencontainers.image.created="2024-09-30T07:15:30Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:41Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/preseq_lcextrap/.config.vsh.yaml b/target/executable/preseq_lcextrap/.config.vsh.yaml index bea730e..b785df4 100644 --- a/target/executable/preseq_lcextrap/.config.vsh.yaml +++ b/target/executable/preseq_lcextrap/.config.vsh.yaml @@ -191,8 +191,8 @@ build_info: output: "target/executable/preseq_lcextrap" executable: "target/executable/preseq_lcextrap/preseq_lcextrap" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/preseq_lcextrap/preseq_lcextrap b/target/executable/preseq_lcextrap/preseq_lcextrap index 84c42c1..3d75b9c 100755 --- a/target/executable/preseq_lcextrap/preseq_lcextrap +++ b/target/executable/preseq_lcextrap/preseq_lcextrap @@ -495,9 +495,9 @@ mkdir build && cd build && \ make && make install && make HAVE_HTSLIB=1 all LABEL org.opencontainers.image.description="Companion container for running component preseq_lcextrap" -LABEL org.opencontainers.image.created="2024-09-30T07:15:20Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:31Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/qualimap/.config.vsh.yaml b/target/executable/qualimap/.config.vsh.yaml index c9168b7..8ed9d7a 100644 --- a/target/executable/qualimap/.config.vsh.yaml +++ b/target/executable/qualimap/.config.vsh.yaml @@ -271,8 +271,8 @@ build_info: output: "target/executable/qualimap" executable: "target/executable/qualimap/qualimap" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/qualimap/qualimap b/target/executable/qualimap/qualimap index 459d05b..3e9540f 100755 --- a/target/executable/qualimap/qualimap +++ b/target/executable/qualimap/qualimap @@ -537,9 +537,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag Rscript -e 'remotes::install_cran(c("optparse"), repos = "https://cran.rstudio.com")' LABEL org.opencontainers.image.description="Companion container for running component qualimap" -LABEL org.opencontainers.image.created="2024-09-30T07:15:19Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:30Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml b/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml index b6787a7..6aa3ed0 100644 --- a/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml +++ b/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml @@ -299,8 +299,8 @@ build_info: output: "target/executable/rsem/rsem_calculate_expression" executable: "target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression b/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression index 15551c9..69991fe 100755 --- a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression +++ b/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression @@ -542,9 +542,9 @@ echo 'export PATH=$PATH:/usr/local/bin' >> ~/.bashrc && \ /bin/bash -c "source /etc/profile && source ~/.bashrc && echo $PATH && which STAR" LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_calculate_expression" -LABEL org.opencontainers.image.created="2024-09-30T07:15:32Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:43Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml b/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml index e3f2126..1fbe91e 100644 --- a/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml +++ b/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml @@ -182,8 +182,8 @@ build_info: output: "target/executable/rsem/rsem_merge_counts" executable: "target/executable/rsem/rsem_merge_counts/rsem_merge_counts" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rsem/rsem_merge_counts/rsem_merge_counts b/target/executable/rsem/rsem_merge_counts/rsem_merge_counts index fe7690f..f4f230e 100755 --- a/target/executable/rsem/rsem_merge_counts/rsem_merge_counts +++ b/target/executable/rsem/rsem_merge_counts/rsem_merge_counts @@ -483,9 +483,9 @@ function ViashDockerfile { FROM ubuntu:22.04 ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_merge_counts" -LABEL org.opencontainers.image.created="2024-09-30T07:15:31Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:43Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml b/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml index b065fdc..969f240 100644 --- a/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml @@ -163,8 +163,8 @@ build_info: output: "target/executable/rseqc/rseqc_bamstat" executable: "target/executable/rseqc/rseqc_bamstat/rseqc_bamstat" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat b/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat index 0bf42ee..ab58429 100755 --- a/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat +++ b/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat @@ -477,9 +477,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_bamstat" -LABEL org.opencontainers.image.created="2024-09-30T07:15:29Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:41Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml b/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml index b3d4cb6..d617a1e 100644 --- a/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml @@ -186,8 +186,8 @@ build_info: output: "target/executable/rseqc/rseqc_inferexperiment" executable: "target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment b/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment index aea74ad..90ea0c3 100755 --- a/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment +++ b/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment @@ -487,9 +487,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_inferexperiment" -LABEL org.opencontainers.image.created="2024-09-30T07:15:27Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:39Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml b/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml index a981793..0a0531e 100644 --- a/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml @@ -272,8 +272,8 @@ build_info: output: "target/executable/rseqc/rseqc_innerdistance" executable: "target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance b/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance index f09313f..7ae6cfc 100755 --- a/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance +++ b/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance @@ -529,9 +529,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_innerdistance" -LABEL org.opencontainers.image.created="2024-09-30T07:15:29Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:40Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml b/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml index 0c389c9..c863719 100644 --- a/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml @@ -260,8 +260,8 @@ build_info: output: "target/executable/rseqc/rseqc_junctionannotation" executable: "target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation b/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation index 78ca45c..43e9ae6 100755 --- a/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation +++ b/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation @@ -519,9 +519,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_junctionannotation" -LABEL org.opencontainers.image.created="2024-09-30T07:15:29Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:40Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml b/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml index 49b8c6c..0660974 100644 --- a/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml @@ -249,8 +249,8 @@ build_info: output: "target/executable/rseqc/rseqc_junctionsaturation" executable: "target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation b/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation index 069d0fa..70cc36d 100755 --- a/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation +++ b/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation @@ -522,9 +522,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_junctionsaturation" -LABEL org.opencontainers.image.created="2024-09-30T07:15:28Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:40Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml b/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml index d3b73ba..093b64a 100644 --- a/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml @@ -162,8 +162,8 @@ build_info: output: "target/executable/rseqc/rseqc_readdistribution" executable: "target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution b/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution index a412b48..c3525b9 100755 --- a/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution +++ b/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution @@ -474,9 +474,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_readdistribution" -LABEL org.opencontainers.image.created="2024-09-30T07:15:30Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:41Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml b/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml index cc534cd..3e488e1 100644 --- a/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml @@ -211,8 +211,8 @@ build_info: output: "target/executable/rseqc/rseqc_readduplication" executable: "target/executable/rseqc/rseqc_readduplication/rseqc_readduplication" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication b/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication index c0c67d6..af6c98c 100755 --- a/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication +++ b/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication @@ -499,9 +499,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_readduplication" -LABEL org.opencontainers.image.created="2024-09-30T07:15:28Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:39Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_tin/.config.vsh.yaml b/target/executable/rseqc/rseqc_tin/.config.vsh.yaml index f23874e..2840d9e 100644 --- a/target/executable/rseqc/rseqc_tin/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_tin/.config.vsh.yaml @@ -214,8 +214,8 @@ build_info: output: "target/executable/rseqc/rseqc_tin" executable: "target/executable/rseqc/rseqc_tin/rseqc_tin" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rseqc/rseqc_tin/rseqc_tin b/target/executable/rseqc/rseqc_tin/rseqc_tin index 88d51d1..a65eba5 100755 --- a/target/executable/rseqc/rseqc_tin/rseqc_tin +++ b/target/executable/rseqc/rseqc_tin/rseqc_tin @@ -501,9 +501,9 @@ RUN apt-get update && \ RUN pip3 install RSeQC LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_tin" -LABEL org.opencontainers.image.created="2024-09-30T07:15:28Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:39Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/sortmerna/.config.vsh.yaml b/target/executable/sortmerna/.config.vsh.yaml index d2c3d15..750366e 100644 --- a/target/executable/sortmerna/.config.vsh.yaml +++ b/target/executable/sortmerna/.config.vsh.yaml @@ -198,8 +198,8 @@ build_info: output: "target/executable/sortmerna" executable: "target/executable/sortmerna/sortmerna" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/sortmerna/sortmerna b/target/executable/sortmerna/sortmerna index 1f23aa9..a08dcb9 100755 --- a/target/executable/sortmerna/sortmerna +++ b/target/executable/sortmerna/sortmerna @@ -492,9 +492,9 @@ wget --no-check-certificate https://github.com/sortmerna/sortmerna/releases/down bash sortmerna-4.3.6-Linux.sh --skip-license LABEL org.opencontainers.image.description="Companion container for running component sortmerna" -LABEL org.opencontainers.image.created="2024-09-30T07:15:34Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:46Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/stringtie/.config.vsh.yaml b/target/executable/stringtie/.config.vsh.yaml index 60ae24b..211567b 100644 --- a/target/executable/stringtie/.config.vsh.yaml +++ b/target/executable/stringtie/.config.vsh.yaml @@ -216,8 +216,8 @@ build_info: output: "target/executable/stringtie" executable: "target/executable/stringtie/stringtie" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/stringtie/stringtie b/target/executable/stringtie/stringtie index 6b33336..d729279 100755 --- a/target/executable/stringtie/stringtie +++ b/target/executable/stringtie/stringtie @@ -496,9 +496,9 @@ tar -xzf stringtie-2.2.1.Linux_x86_64.tar.gz && \ cp stringtie-2.2.1.Linux_x86_64/stringtie /usr/local/bin/ LABEL org.opencontainers.image.description="Companion container for running component stringtie" -LABEL org.opencontainers.image.created="2024-09-30T07:15:31Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:43Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/summarizedexperiment/.config.vsh.yaml b/target/executable/summarizedexperiment/.config.vsh.yaml index bd9b788..fbcb9ca 100644 --- a/target/executable/summarizedexperiment/.config.vsh.yaml +++ b/target/executable/summarizedexperiment/.config.vsh.yaml @@ -199,8 +199,8 @@ build_info: output: "target/executable/summarizedexperiment" executable: "target/executable/summarizedexperiment/summarizedexperiment" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/summarizedexperiment/summarizedexperiment b/target/executable/summarizedexperiment/summarizedexperiment index 907ce28..4a7d775 100755 --- a/target/executable/summarizedexperiment/summarizedexperiment +++ b/target/executable/summarizedexperiment/summarizedexperiment @@ -487,9 +487,9 @@ RUN Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.pa Rscript -e 'if (!requireNamespace("tximeta", quietly = TRUE)) BiocManager::install("tximeta")' LABEL org.opencontainers.image.description="Companion container for running component summarizedexperiment" -LABEL org.opencontainers.image.created="2024-09-30T07:15:35Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:47Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/trimgalore/.config.vsh.yaml b/target/executable/trimgalore/.config.vsh.yaml index 898d214..6cda973 100644 --- a/target/executable/trimgalore/.config.vsh.yaml +++ b/target/executable/trimgalore/.config.vsh.yaml @@ -788,8 +788,8 @@ build_info: output: "target/executable/trimgalore" executable: "target/executable/trimgalore/trimgalore" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/trimgalore/trimgalore b/target/executable/trimgalore/trimgalore index 2e8a60b..16b1c61 100755 --- a/target/executable/trimgalore/trimgalore +++ b/target/executable/trimgalore/trimgalore @@ -858,9 +858,9 @@ ENTRYPOINT [] RUN echo "TrimGalore: `trim_galore --version | sed -n 's/.*version\s\+\([0-9]\+\.[0-9]\+\.[0-9]\+\).*/\1/p'`" > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component trimgalore" -LABEL org.opencontainers.image.created="2024-09-30T07:15:33Z" +LABEL org.opencontainers.image.created="2024-09-30T11:39:45Z" LABEL org.opencontainers.image.source="https://github.com/FelixKrueger/TrimGalore" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/tx2gene/.config.vsh.yaml b/target/executable/tx2gene/.config.vsh.yaml index c25ed48..5d02141 100644 --- a/target/executable/tx2gene/.config.vsh.yaml +++ b/target/executable/tx2gene/.config.vsh.yaml @@ -192,8 +192,8 @@ build_info: output: "target/executable/tx2gene" executable: "target/executable/tx2gene/tx2gene" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/tx2gene/tx2gene b/target/executable/tx2gene/tx2gene index dd1b6d7..b3d14a6 100755 --- a/target/executable/tx2gene/tx2gene +++ b/target/executable/tx2gene/tx2gene @@ -487,9 +487,9 @@ RUN apt-get update && \ RUN pip install --upgrade pip LABEL org.opencontainers.image.description="Companion container for running component tx2gene" -LABEL org.opencontainers.image.created="2024-09-30T07:15:31Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:42Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/tximport/.config.vsh.yaml b/target/executable/tximport/.config.vsh.yaml index 07598cc..0908144 100644 --- a/target/executable/tximport/.config.vsh.yaml +++ b/target/executable/tximport/.config.vsh.yaml @@ -247,8 +247,8 @@ build_info: output: "target/executable/tximport" executable: "target/executable/tximport/tximport" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/tximport/tximport b/target/executable/tximport/tximport index 5879b58..b9f6811 100755 --- a/target/executable/tximport/tximport +++ b/target/executable/tximport/tximport @@ -508,9 +508,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag Rscript -e 'remotes::install_cran(c("jsonlite"), repos = "https://cran.rstudio.com")' LABEL org.opencontainers.image.description="Companion container for running component tximport" -LABEL org.opencontainers.image.created="2024-09-30T07:15:25Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:36Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/ucsc/bedclip/.config.vsh.yaml b/target/executable/ucsc/bedclip/.config.vsh.yaml index ab06846..4762938 100644 --- a/target/executable/ucsc/bedclip/.config.vsh.yaml +++ b/target/executable/ucsc/bedclip/.config.vsh.yaml @@ -164,8 +164,8 @@ build_info: output: "target/executable/ucsc/bedclip" executable: "target/executable/ucsc/bedclip/bedclip" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/ucsc/bedclip/bedclip b/target/executable/ucsc/bedclip/bedclip index 2dbdd1b..7e052c1 100755 --- a/target/executable/ucsc/bedclip/bedclip +++ b/target/executable/ucsc/bedclip/bedclip @@ -473,9 +473,9 @@ RUN apt-get update && \ RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedClip /usr/local/bin/ LABEL org.opencontainers.image.description="Companion container for running component ucsc bedclip" -LABEL org.opencontainers.image.created="2024-09-30T07:15:26Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:37Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml b/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml index 39a7bf5..a51f5c0 100644 --- a/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml +++ b/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml @@ -164,8 +164,8 @@ build_info: output: "target/executable/ucsc/bedgraphtobigwig" executable: "target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig b/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig index c6e03a9..e872a8e 100755 --- a/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig +++ b/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig @@ -473,9 +473,9 @@ RUN apt-get update && \ RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedGraphToBigWig /usr/local/bin/ LABEL org.opencontainers.image.description="Companion container for running component ucsc bedgraphtobigwig" -LABEL org.opencontainers.image.created="2024-09-30T07:15:26Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:38Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/umitools/umitools_dedup/.config.vsh.yaml b/target/executable/umitools/umitools_dedup/.config.vsh.yaml index ad64664..71a641b 100644 --- a/target/executable/umitools/umitools_dedup/.config.vsh.yaml +++ b/target/executable/umitools/umitools_dedup/.config.vsh.yaml @@ -195,8 +195,8 @@ build_info: output: "target/executable/umitools/umitools_dedup" executable: "target/executable/umitools/umitools_dedup/umitools_dedup" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/umitools/umitools_dedup/umitools_dedup b/target/executable/umitools/umitools_dedup/umitools_dedup index a227866..b7238cf 100755 --- a/target/executable/umitools/umitools_dedup/umitools_dedup +++ b/target/executable/umitools/umitools_dedup/umitools_dedup @@ -489,9 +489,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "umi_tools" LABEL org.opencontainers.image.description="Companion container for running component umitools umitools_dedup" -LABEL org.opencontainers.image.created="2024-09-30T07:15:33Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:44Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/umitools/umitools_extract/.config.vsh.yaml b/target/executable/umitools/umitools_extract/.config.vsh.yaml index 690c1e0..ff9f634 100644 --- a/target/executable/umitools/umitools_extract/.config.vsh.yaml +++ b/target/executable/umitools/umitools_extract/.config.vsh.yaml @@ -253,8 +253,8 @@ build_info: output: "target/executable/umitools/umitools_extract" executable: "target/executable/umitools/umitools_extract/umitools_extract" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/umitools/umitools_extract/umitools_extract b/target/executable/umitools/umitools_extract/umitools_extract index 7f68e3e..59efee1 100755 --- a/target/executable/umitools/umitools_extract/umitools_extract +++ b/target/executable/umitools/umitools_extract/umitools_extract @@ -521,9 +521,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "umi_tools" LABEL org.opencontainers.image.description="Companion container for running component umitools umitools_extract" -LABEL org.opencontainers.image.created="2024-09-30T07:15:33Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:45Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/umitools_prepareforquant/.config.vsh.yaml b/target/executable/umitools_prepareforquant/.config.vsh.yaml index cdc52d7..8b29e1c 100644 --- a/target/executable/umitools_prepareforquant/.config.vsh.yaml +++ b/target/executable/umitools_prepareforquant/.config.vsh.yaml @@ -156,8 +156,8 @@ build_info: output: "target/executable/umitools_prepareforquant" executable: "target/executable/umitools_prepareforquant/umitools_prepareforquant" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/umitools_prepareforquant/umitools_prepareforquant b/target/executable/umitools_prepareforquant/umitools_prepareforquant index de782d4..21118e2 100755 --- a/target/executable/umitools_prepareforquant/umitools_prepareforquant +++ b/target/executable/umitools_prepareforquant/umitools_prepareforquant @@ -473,9 +473,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "umi_tools" "pysam" LABEL org.opencontainers.image.description="Companion container for running component umitools_prepareforquant" -LABEL org.opencontainers.image.created="2024-09-30T07:15:35Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb" +LABEL org.opencontainers.image.created="2024-09-30T11:39:47Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="55878e4519aa920a419bb99a9b3afc8307b6c6e3" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml b/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml index 90674b9..b6c64b2 100644 --- a/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml +++ b/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml @@ -603,8 +603,8 @@ build_info: output: "target/executable/workflows/genome_alignment_and_quant" executable: "target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort" diff --git a/target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant b/target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant index b522878..b24d218 100755 --- a/target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant +++ b/target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant @@ -1635,7 +1635,7 @@ workflow run_wf { def mod_state = (state.aligner == 'star_salmon') ? state + [salmon_multiqc: state.quant_out_dir] : state [ id, mod_state ] } - | niceView() + | rsem_calculate_expression.run ( runIf: { id, state -> state.aligner == 'star_rsem' }, fromState: [ diff --git a/target/executable/workflows/merge_quant_results/.config.vsh.yaml b/target/executable/workflows/merge_quant_results/.config.vsh.yaml index 0da79e4..28ea150 100644 --- a/target/executable/workflows/merge_quant_results/.config.vsh.yaml +++ b/target/executable/workflows/merge_quant_results/.config.vsh.yaml @@ -278,8 +278,8 @@ build_info: output: "target/executable/workflows/merge_quant_results" executable: "target/executable/workflows/merge_quant_results/merge_quant_results" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/tx2gene" - "target/nextflow/tximport" diff --git a/target/executable/workflows/post_processing/.config.vsh.yaml b/target/executable/workflows/post_processing/.config.vsh.yaml index f0f92d7..530f6f7 100644 --- a/target/executable/workflows/post_processing/.config.vsh.yaml +++ b/target/executable/workflows/post_processing/.config.vsh.yaml @@ -199,7 +199,7 @@ argument_groups: name: "--processed_genome_bam" info: null default: - - "$id..genome.bam" + - "$id.genome.bam" must_exist: true create_parent: true required: false @@ -486,8 +486,8 @@ build_info: output: "target/executable/workflows/post_processing" executable: "target/executable/workflows/post_processing/post_processing" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/picard_markduplicates" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort" diff --git a/target/executable/workflows/post_processing/post_processing b/target/executable/workflows/post_processing/post_processing index ad15b5c..6b6f14f 100755 --- a/target/executable/workflows/post_processing/post_processing +++ b/target/executable/workflows/post_processing/post_processing @@ -269,7 +269,7 @@ function ViashHelp { echo "Output:" echo " --processed_genome_bam" echo " type: file, output, file must exist" - echo " default: \$id..genome.bam" + echo " default: \$id.genome.bam" echo "" echo " --genome_bam_index" echo " type: file, output, file must exist" @@ -887,7 +887,7 @@ if [ -z ${VIASH_PAR_WITH_UMI+x} ]; then VIASH_PAR_WITH_UMI="false" fi if [ -z ${VIASH_PAR_PROCESSED_GENOME_BAM+x} ]; then - VIASH_PAR_PROCESSED_GENOME_BAM="\$id..genome.bam" + VIASH_PAR_PROCESSED_GENOME_BAM="\$id.genome.bam" fi if [ -z ${VIASH_PAR_GENOME_BAM_INDEX+x} ]; then VIASH_PAR_GENOME_BAM_INDEX="\$id.genome.bam.bai" @@ -1185,20 +1185,20 @@ workflow run_wf { "extra_picard_args": "extra_picard_args" ], toState: [ - "genome_bam": "output_bam", + "processed_genome_bam": "output_bam", "markduplicates_metrics": "metrics" ] ) | samtools_sort.run ( runIf: { id, state -> !state.skip_markduplicates && !state.with_umi }, - fromState: [ "input": "genome_bam" ], - toState: [ "genome_bam": "output" ], + fromState: [ "input": "processed_genome_bam" ], + toState: [ "processed_genome_bam": "output" ], key: "genome_sorted_MarkDuplicates" ) | samtools_index.run ( runIf: { id, state -> !state.skip_markduplicates && !state.with_umi }, fromState: [ - "input": "genome_bam", + "input": "processed_genome_bam", "csi": "bam_csi_index" ], toState: [ "genome_bam_index": "output" ], @@ -1207,7 +1207,7 @@ workflow run_wf { | samtools_stats.run ( runIf: { id, state -> !state.skip_markduplicates && !state.with_umi }, fromState: [ - "input": "genome_bam", + "input": "processed_genome_bam", "bai": "genome_bam_index" ], toState: [ "genome_bam_stats": "output" ], @@ -1216,7 +1216,7 @@ workflow run_wf { | samtools_flagstat.run ( runIf: { id, state -> !state.skip_markduplicates && !state.with_umi }, fromState: [ - "bam": "genome_bam", + "bam": "processed_genome_bam", "bai": "genome_bam_index" ], toState: [ "genome_bam_flagstat": "output" ], @@ -1225,7 +1225,7 @@ workflow run_wf { | samtools_idxstats.run( runIf: { id, state -> !state.skip_markduplicates && !state.with_umi }, fromState: [ - "bam": "genome_bam", + "bam": "processed_genome_bam", "bai": "genome_bam_index" ], toState: [ "genome_bam_idxstats": "output" ], @@ -1236,7 +1236,7 @@ workflow run_wf { runIf: { id, state -> !state.skip_stringtie }, fromState: [ "strandedness": "strandedness", - "bam": "genome_bam", + "bam": "processed_genome_bam", "annotation_gtf": "gtf", "extra_stringtie_args": "extra_stringtie_args" ], @@ -1254,7 +1254,7 @@ workflow run_wf { runIf: { id, state -> !state.skip_bigwig }, fromState: [ "strandedness": "strandedness", - "bam": "genome_bam", + "bam": "processed_genome_bam", "extra_bedtools_args": "extra_bedtools_args" ], toState: [ @@ -1307,9 +1307,10 @@ workflow run_wf { def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() } [ id, mod_state ] } + | niceView() | setState ( - "processed_genome_bam": "genome_bam", + "processed_genome_bam": "processed_genome_bam", "genome_bam_index": "genome_bam_index", "genome_bam_stats": "genome_bam_stats", "genome_bam_flagstat": "genome_bam_flagstat", diff --git a/target/executable/workflows/pre_processing/.config.vsh.yaml b/target/executable/workflows/pre_processing/.config.vsh.yaml index d8c8d3a..7e00006 100644 --- a/target/executable/workflows/pre_processing/.config.vsh.yaml +++ b/target/executable/workflows/pre_processing/.config.vsh.yaml @@ -673,8 +673,8 @@ build_info: output: "target/executable/workflows/pre_processing" executable: "target/executable/workflows/pre_processing/pre_processing" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/fastqc" - "target/nextflow/umitools/umitools_extract" diff --git a/target/executable/workflows/prepare_genome/.config.vsh.yaml b/target/executable/workflows/prepare_genome/.config.vsh.yaml index a69e47e..151c58d 100644 --- a/target/executable/workflows/prepare_genome/.config.vsh.yaml +++ b/target/executable/workflows/prepare_genome/.config.vsh.yaml @@ -496,8 +496,8 @@ build_info: output: "target/executable/workflows/prepare_genome" executable: "target/executable/workflows/prepare_genome/prepare_genome" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/gunzip" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread" diff --git a/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml b/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml index 1a41217..a8bd4d1 100644 --- a/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml +++ b/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml @@ -283,8 +283,8 @@ build_info: output: "target/executable/workflows/pseudo_alignment_and_quant" executable: "target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant" - "target/nextflow/kallisto/kallisto_quant" diff --git a/target/executable/workflows/quality_control/.config.vsh.yaml b/target/executable/workflows/quality_control/.config.vsh.yaml index ad74eb3..47e664e 100644 --- a/target/executable/workflows/quality_control/.config.vsh.yaml +++ b/target/executable/workflows/quality_control/.config.vsh.yaml @@ -1596,8 +1596,8 @@ build_info: output: "target/executable/workflows/quality_control" executable: "target/executable/workflows/quality_control/quality_control" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/rseqc/rseqc_bamstat" - "target/nextflow/rseqc/rseqc_inferexperiment" diff --git a/target/executable/workflows/quality_control/quality_control b/target/executable/workflows/quality_control/quality_control index d699ac5..56effd9 100755 --- a/target/executable/workflows/quality_control/quality_control +++ b/target/executable/workflows/quality_control/quality_control @@ -4092,6 +4092,7 @@ workflow run_wf { "title": "multiqc_title", "input": "multiqc_input", ], + args: [exclude_modules: "general_stats"], toState: [ "multiqc_report": "output_report", "multiqc_data": "output_data", diff --git a/target/executable/workflows/rnaseq/.config.vsh.yaml b/target/executable/workflows/rnaseq/.config.vsh.yaml index 7335a78..edb3372 100644 --- a/target/executable/workflows/rnaseq/.config.vsh.yaml +++ b/target/executable/workflows/rnaseq/.config.vsh.yaml @@ -1051,7 +1051,7 @@ argument_groups: name: "--star_alignment" info: null default: - - "STAR_alignment/$id" + - "STAR/$id" must_exist: true create_parent: true required: false @@ -1062,7 +1062,7 @@ argument_groups: name: "--genome_bam_sorted" info: null default: - - "STAR_alignment/genome_processed/$id.genome.bam" + - "STAR/genome_processed/$id.genome.bam" must_exist: true create_parent: true required: false @@ -1073,7 +1073,7 @@ argument_groups: name: "--genome_bam_index" info: null default: - - "STAR_alignment/genome_processed/$id.genome.bam.bai" + - "STAR/genome_processed/$id.genome.bam.bai" must_exist: true create_parent: true required: false @@ -1084,7 +1084,7 @@ argument_groups: name: "--transcriptome_bam" info: null default: - - "STAR_alignment/transcriptome_processed/$id.transcriptome.bam" + - "STAR/transcriptome_processed/$id.transcriptome.bam" must_exist: true create_parent: true required: false @@ -1095,7 +1095,7 @@ argument_groups: name: "--transcriptome_bam_index" info: null default: - - "STAR_alignment/transcriptome_processed/$id.transcriptome.bam.bai" + - "STAR/transcriptome_processed/$id.transcriptome.bam.bai" must_exist: true create_parent: true required: false @@ -1179,6 +1179,17 @@ argument_groups: direction: "output" multiple: false multiple_sep: ";" + - type: "file" + name: "--salmon_quant_results_file" + info: null + default: + - "STAR_Salmon/$id/quant.sf" + must_exist: true + create_parent: true + required: false + direction: "output" + multiple: false + multiple_sep: ";" - type: "file" name: "--pseudo_quant_results" info: null @@ -1254,7 +1265,7 @@ argument_groups: name: "--tpm_gene" info: null default: - - "alignment_quantification/gene_tpm.tsv" + - "transcript_quantification/gene_tpm.tsv" must_exist: true create_parent: true required: false @@ -1265,7 +1276,7 @@ argument_groups: name: "--counts_gene" info: null default: - - "alignment_quantification/gene_counts.tsv" + - "transcript_quantification/gene_counts.tsv" must_exist: true create_parent: true required: false @@ -1276,7 +1287,7 @@ argument_groups: name: "--counts_gene_length_scaled" info: null default: - - "alignment_quantification/gene_counts_length_scaled.tsv" + - "transcript_quantification/gene_counts_length_scaled.tsv" must_exist: true create_parent: true required: false @@ -1287,7 +1298,7 @@ argument_groups: name: "--counts_gene_scaled" info: null default: - - "alignment_quantification/gene_counts_scaled.tsv" + - "transcript_quantification/gene_counts_scaled.tsv" must_exist: true create_parent: true required: false @@ -1298,7 +1309,7 @@ argument_groups: name: "--tpm_transcript" info: null default: - - "alignment_quantification/transcript_tpm.tsv" + - "transcript_quantification/transcript_tpm.tsv" must_exist: true create_parent: true required: false @@ -1309,7 +1320,7 @@ argument_groups: name: "--counts_transcript" info: null default: - - "alignment_quantification/transcript_counts.tsv" + - "transcript_quantification/transcript_counts.tsv" must_exist: true create_parent: true required: false @@ -1320,7 +1331,7 @@ argument_groups: name: "--quant_merged_summarizedexperiment" info: null default: - - "alignment_quantification/summarizedexperiment" + - "transcript_quantification/summarizedexperiment" must_exist: true create_parent: true required: false @@ -1331,7 +1342,7 @@ argument_groups: name: "--markduplicates_metrics" info: null default: - - "picard/$id.sorted.MarkDuplicates.metrics.txt" + - "picard/$id.MarkDuplicates.metrics.txt" must_exist: true create_parent: true required: false @@ -2106,8 +2117,8 @@ build_info: output: "target/executable/workflows/rnaseq" executable: "target/executable/workflows/rnaseq/rnaseq" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/workflows/prepare_genome" - "target/nextflow/cat_fastq" diff --git a/target/executable/workflows/rnaseq/rnaseq b/target/executable/workflows/rnaseq/rnaseq index f0eb778..5b0761e 100755 --- a/target/executable/workflows/rnaseq/rnaseq +++ b/target/executable/workflows/rnaseq/rnaseq @@ -693,24 +693,23 @@ function ViashHelp { echo "" echo " --star_alignment" echo " type: file, output, file must exist" - echo " default: STAR_alignment/\$id" + echo " default: STAR/\$id" echo "" echo " --genome_bam_sorted" echo " type: file, output, file must exist" - echo " default: STAR_alignment/genome_processed/\$id.genome.bam" + echo " default: STAR/genome_processed/\$id.genome.bam" echo "" echo " --genome_bam_index" echo " type: file, output, file must exist" - echo " default: STAR_alignment/genome_processed/\$id.genome.bam.bai" + echo " default: STAR/genome_processed/\$id.genome.bam.bai" echo "" echo " --transcriptome_bam" echo " type: file, output, file must exist" - echo " default: STAR_alignment/transcriptome_processed/\$id.transcriptome.bam" + echo " default: STAR/transcriptome_processed/\$id.transcriptome.bam" echo "" echo " --transcriptome_bam_index" echo " type: file, output, file must exist" - echo " default:" - echo "STAR_alignment/transcriptome_processed/\$id.transcriptome.bam.bai" + echo " default: STAR/transcriptome_processed/\$id.transcriptome.bam.bai" echo "" echo " --genome_bam_stats" echo " type: file, output, file must exist" @@ -740,6 +739,10 @@ function ViashHelp { echo " type: file, output, file must exist" echo " default: STAR_Salmon/\$id" echo "" + echo " --salmon_quant_results_file" + echo " type: file, output, file must exist" + echo " default: STAR_Salmon/\$id/quant.sf" + echo "" echo " --pseudo_quant_results" echo " type: file, output, file must exist" echo " default: Pseudo_align_quant/\$id" @@ -771,35 +774,35 @@ function ViashHelp { echo "" echo " --tpm_gene" echo " type: file, output, file must exist" - echo " default: alignment_quantification/gene_tpm.tsv" + echo " default: transcript_quantification/gene_tpm.tsv" echo "" echo " --counts_gene" echo " type: file, output, file must exist" - echo " default: alignment_quantification/gene_counts.tsv" + echo " default: transcript_quantification/gene_counts.tsv" echo "" echo " --counts_gene_length_scaled" echo " type: file, output, file must exist" - echo " default: alignment_quantification/gene_counts_length_scaled.tsv" + echo " default: transcript_quantification/gene_counts_length_scaled.tsv" echo "" echo " --counts_gene_scaled" echo " type: file, output, file must exist" - echo " default: alignment_quantification/gene_counts_scaled.tsv" + echo " default: transcript_quantification/gene_counts_scaled.tsv" echo "" echo " --tpm_transcript" echo " type: file, output, file must exist" - echo " default: alignment_quantification/transcript_tpm.tsv" + echo " default: transcript_quantification/transcript_tpm.tsv" echo "" echo " --counts_transcript" echo " type: file, output, file must exist" - echo " default: alignment_quantification/transcript_counts.tsv" + echo " default: transcript_quantification/transcript_counts.tsv" echo "" echo " --quant_merged_summarizedexperiment" echo " type: file, output, file must exist" - echo " default: alignment_quantification/summarizedexperiment" + echo " default: transcript_quantification/summarizedexperiment" echo "" echo " --markduplicates_metrics" echo " type: file, output, file must exist" - echo " default: picard/\$id.sorted.MarkDuplicates.metrics.txt" + echo " default: picard/\$id.MarkDuplicates.metrics.txt" echo "" echo " --stringtie_transcript_gtf" echo " type: file, output, file must exist" @@ -2235,6 +2238,17 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_SALMON_QUANT_RESULTS=$(ViashRemoveFlags "$1") shift 1 ;; + --salmon_quant_results_file) + [ -n "$VIASH_PAR_SALMON_QUANT_RESULTS_FILE" ] && ViashError Bad arguments for option \'--salmon_quant_results_file\': \'$VIASH_PAR_SALMON_QUANT_RESULTS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_SALMON_QUANT_RESULTS_FILE="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --salmon_quant_results_file. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --salmon_quant_results_file=*) + [ -n "$VIASH_PAR_SALMON_QUANT_RESULTS_FILE" ] && ViashError Bad arguments for option \'--salmon_quant_results_file=*\': \'$VIASH_PAR_SALMON_QUANT_RESULTS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_SALMON_QUANT_RESULTS_FILE=$(ViashRemoveFlags "$1") + shift 1 + ;; --pseudo_quant_results) [ -n "$VIASH_PAR_PSEUDO_QUANT_RESULTS" ] && ViashError Bad arguments for option \'--pseudo_quant_results\': \'$VIASH_PAR_PSEUDO_QUANT_RESULTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_PSEUDO_QUANT_RESULTS="$2" @@ -3398,19 +3412,19 @@ if [ -z ${VIASH_PAR_SORTMERNA_LOG+x} ]; then VIASH_PAR_SORTMERNA_LOG="sortmerna/\$id.log" fi if [ -z ${VIASH_PAR_STAR_ALIGNMENT+x} ]; then - VIASH_PAR_STAR_ALIGNMENT="STAR_alignment/\$id" + VIASH_PAR_STAR_ALIGNMENT="STAR/\$id" fi if [ -z ${VIASH_PAR_GENOME_BAM_SORTED+x} ]; then - VIASH_PAR_GENOME_BAM_SORTED="STAR_alignment/genome_processed/\$id.genome.bam" + VIASH_PAR_GENOME_BAM_SORTED="STAR/genome_processed/\$id.genome.bam" fi if [ -z ${VIASH_PAR_GENOME_BAM_INDEX+x} ]; then - VIASH_PAR_GENOME_BAM_INDEX="STAR_alignment/genome_processed/\$id.genome.bam.bai" + VIASH_PAR_GENOME_BAM_INDEX="STAR/genome_processed/\$id.genome.bam.bai" fi if [ -z ${VIASH_PAR_TRANSCRIPTOME_BAM+x} ]; then - VIASH_PAR_TRANSCRIPTOME_BAM="STAR_alignment/transcriptome_processed/\$id.transcriptome.bam" + VIASH_PAR_TRANSCRIPTOME_BAM="STAR/transcriptome_processed/\$id.transcriptome.bam" fi if [ -z ${VIASH_PAR_TRANSCRIPTOME_BAM_INDEX+x} ]; then - VIASH_PAR_TRANSCRIPTOME_BAM_INDEX="STAR_alignment/transcriptome_processed/\$id.transcriptome.bam.bai" + VIASH_PAR_TRANSCRIPTOME_BAM_INDEX="STAR/transcriptome_processed/\$id.transcriptome.bam.bai" fi if [ -z ${VIASH_PAR_GENOME_BAM_STATS+x} ]; then VIASH_PAR_GENOME_BAM_STATS="samtools_stats/\$id.genome.stats" @@ -3433,6 +3447,9 @@ fi if [ -z ${VIASH_PAR_SALMON_QUANT_RESULTS+x} ]; then VIASH_PAR_SALMON_QUANT_RESULTS="STAR_Salmon/\$id" fi +if [ -z ${VIASH_PAR_SALMON_QUANT_RESULTS_FILE+x} ]; then + VIASH_PAR_SALMON_QUANT_RESULTS_FILE="STAR_Salmon/\$id/quant.sf" +fi if [ -z ${VIASH_PAR_PSEUDO_QUANT_RESULTS+x} ]; then VIASH_PAR_PSEUDO_QUANT_RESULTS="Pseudo_align_quant/\$id" fi @@ -3452,28 +3469,28 @@ if [ -z ${VIASH_PAR_BAM_TRANSCRIPT_RSEM+x} ]; then VIASH_PAR_BAM_TRANSCRIPT_RSEM="RSEM/\$id.transcript.bam" fi if [ -z ${VIASH_PAR_TPM_GENE+x} ]; then - VIASH_PAR_TPM_GENE="alignment_quantification/gene_tpm.tsv" + VIASH_PAR_TPM_GENE="transcript_quantification/gene_tpm.tsv" fi if [ -z ${VIASH_PAR_COUNTS_GENE+x} ]; then - VIASH_PAR_COUNTS_GENE="alignment_quantification/gene_counts.tsv" + VIASH_PAR_COUNTS_GENE="transcript_quantification/gene_counts.tsv" fi if [ -z ${VIASH_PAR_COUNTS_GENE_LENGTH_SCALED+x} ]; then - VIASH_PAR_COUNTS_GENE_LENGTH_SCALED="alignment_quantification/gene_counts_length_scaled.tsv" + VIASH_PAR_COUNTS_GENE_LENGTH_SCALED="transcript_quantification/gene_counts_length_scaled.tsv" fi if [ -z ${VIASH_PAR_COUNTS_GENE_SCALED+x} ]; then - VIASH_PAR_COUNTS_GENE_SCALED="alignment_quantification/gene_counts_scaled.tsv" + VIASH_PAR_COUNTS_GENE_SCALED="transcript_quantification/gene_counts_scaled.tsv" fi if [ -z ${VIASH_PAR_TPM_TRANSCRIPT+x} ]; then - VIASH_PAR_TPM_TRANSCRIPT="alignment_quantification/transcript_tpm.tsv" + VIASH_PAR_TPM_TRANSCRIPT="transcript_quantification/transcript_tpm.tsv" fi if [ -z ${VIASH_PAR_COUNTS_TRANSCRIPT+x} ]; then - VIASH_PAR_COUNTS_TRANSCRIPT="alignment_quantification/transcript_counts.tsv" + VIASH_PAR_COUNTS_TRANSCRIPT="transcript_quantification/transcript_counts.tsv" fi if [ -z ${VIASH_PAR_QUANT_MERGED_SUMMARIZEDEXPERIMENT+x} ]; then - VIASH_PAR_QUANT_MERGED_SUMMARIZEDEXPERIMENT="alignment_quantification/summarizedexperiment" + VIASH_PAR_QUANT_MERGED_SUMMARIZEDEXPERIMENT="transcript_quantification/summarizedexperiment" fi if [ -z ${VIASH_PAR_MARKDUPLICATES_METRICS+x} ]; then - VIASH_PAR_MARKDUPLICATES_METRICS="picard/\$id.sorted.MarkDuplicates.metrics.txt" + VIASH_PAR_MARKDUPLICATES_METRICS="picard/\$id.MarkDuplicates.metrics.txt" fi if [ -z ${VIASH_PAR_STRINGTIE_TRANSCRIPT_GTF+x} ]; then VIASH_PAR_STRINGTIE_TRANSCRIPT_GTF="stringtie/\$id.transcripts.gtf" @@ -4192,6 +4209,9 @@ fi if [ ! -z "$VIASH_PAR_SALMON_QUANT_RESULTS" ] && [ ! -d "$(dirname "$VIASH_PAR_SALMON_QUANT_RESULTS")" ]; then mkdir -p "$(dirname "$VIASH_PAR_SALMON_QUANT_RESULTS")" fi +if [ ! -z "$VIASH_PAR_SALMON_QUANT_RESULTS_FILE" ] && [ ! -d "$(dirname "$VIASH_PAR_SALMON_QUANT_RESULTS_FILE")" ]; then + mkdir -p "$(dirname "$VIASH_PAR_SALMON_QUANT_RESULTS_FILE")" +fi if [ ! -z "$VIASH_PAR_PSEUDO_QUANT_RESULTS" ] && [ ! -d "$(dirname "$VIASH_PAR_PSEUDO_QUANT_RESULTS")" ]; then mkdir -p "$(dirname "$VIASH_PAR_PSEUDO_QUANT_RESULTS")" fi @@ -4919,6 +4939,7 @@ workflow run_wf { "transcriptome_bam_idxstats": "transcriptome_bam_idxstats", "salmon_quant_results": "quant_out_dir", "pseudo_quant_results": "pseudo_quant_out_dir", + "markduplicates_metrics": "markduplicates_metrics", "stringtie_transcript_gtf": "stringtie_transcript_gtf", "stringtie_coverage_gtf": "stringtie_coverage_gtf", "stringtie_abundance": "stringtie_abundance", @@ -5172,6 +5193,10 @@ if [ ! -z "$VIASH_PAR_SALMON_QUANT_RESULTS" ] && [ ! -e "$VIASH_PAR_SALMON_QUANT ViashError "Output file '$VIASH_PAR_SALMON_QUANT_RESULTS' does not exist." exit 1 fi +if [ ! -z "$VIASH_PAR_SALMON_QUANT_RESULTS_FILE" ] && [ ! -e "$VIASH_PAR_SALMON_QUANT_RESULTS_FILE" ]; then + ViashError "Output file '$VIASH_PAR_SALMON_QUANT_RESULTS_FILE' does not exist." + exit 1 +fi if [ ! -z "$VIASH_PAR_PSEUDO_QUANT_RESULTS" ] && [ ! -e "$VIASH_PAR_PSEUDO_QUANT_RESULTS" ]; then ViashError "Output file '$VIASH_PAR_PSEUDO_QUANT_RESULTS' does not exist." exit 1 diff --git a/target/nextflow/bbmap_bbsplit/.config.vsh.yaml b/target/nextflow/bbmap_bbsplit/.config.vsh.yaml index 7dc77d4..f4c39b2 100644 --- a/target/nextflow/bbmap_bbsplit/.config.vsh.yaml +++ b/target/nextflow/bbmap_bbsplit/.config.vsh.yaml @@ -238,8 +238,8 @@ build_info: output: "target/nextflow/bbmap_bbsplit" executable: "target/nextflow/bbmap_bbsplit/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/bbmap_bbsplit/main.nf b/target/nextflow/bbmap_bbsplit/main.nf index 720900a..2db3865 100644 --- a/target/nextflow/bbmap_bbsplit/main.nf +++ b/target/nextflow/bbmap_bbsplit/main.nf @@ -3104,8 +3104,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/bbmap_bbsplit", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/bedtools_genomecov/.config.vsh.yaml b/target/nextflow/bedtools_genomecov/.config.vsh.yaml index c032ec3..69365f3 100644 --- a/target/nextflow/bedtools_genomecov/.config.vsh.yaml +++ b/target/nextflow/bedtools_genomecov/.config.vsh.yaml @@ -178,8 +178,8 @@ build_info: output: "target/nextflow/bedtools_genomecov" executable: "target/nextflow/bedtools_genomecov/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/bedtools_genomecov/main.nf b/target/nextflow/bedtools_genomecov/main.nf index b3e55bf..8bc9085 100644 --- a/target/nextflow/bedtools_genomecov/main.nf +++ b/target/nextflow/bedtools_genomecov/main.nf @@ -3031,8 +3031,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/bedtools_genomecov", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/cat_additional_fasta/.config.vsh.yaml b/target/nextflow/cat_additional_fasta/.config.vsh.yaml index a362039..9193f2f 100644 --- a/target/nextflow/cat_additional_fasta/.config.vsh.yaml +++ b/target/nextflow/cat_additional_fasta/.config.vsh.yaml @@ -182,8 +182,8 @@ build_info: output: "target/nextflow/cat_additional_fasta" executable: "target/nextflow/cat_additional_fasta/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/cat_additional_fasta/main.nf b/target/nextflow/cat_additional_fasta/main.nf index cf67de5..d31f2c5 100644 --- a/target/nextflow/cat_additional_fasta/main.nf +++ b/target/nextflow/cat_additional_fasta/main.nf @@ -3032,8 +3032,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/cat_additional_fasta", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/cat_fastq/.config.vsh.yaml b/target/nextflow/cat_fastq/.config.vsh.yaml index ac4e3cf..e1f6cd1 100644 --- a/target/nextflow/cat_fastq/.config.vsh.yaml +++ b/target/nextflow/cat_fastq/.config.vsh.yaml @@ -30,7 +30,7 @@ argument_groups: description: "Concatenated read 1 fastq" info: null default: - - "$id_r1_merged.fastq" + - "$id_r1.fastq" must_exist: true create_parent: true required: false @@ -42,7 +42,7 @@ argument_groups: description: "Concatenated read 2 fastq" info: null default: - - "$id_r2_merged.fastq" + - "$id_r2.fastq" must_exist: false create_parent: true required: false @@ -169,8 +169,8 @@ build_info: output: "target/nextflow/cat_fastq" executable: "target/nextflow/cat_fastq/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/cat_fastq/main.nf b/target/nextflow/cat_fastq/main.nf index 7ea24f2..5594873 100644 --- a/target/nextflow/cat_fastq/main.nf +++ b/target/nextflow/cat_fastq/main.nf @@ -2842,7 +2842,7 @@ meta = [ "name" : "--fastq_1", "description" : "Concatenated read 1 fastq", "default" : [ - "$id_r1_merged.fastq" + "$id_r1.fastq" ], "must_exist" : true, "create_parent" : true, @@ -2856,7 +2856,7 @@ meta = [ "name" : "--fastq_2", "description" : "Concatenated read 2 fastq", "default" : [ - "$id_r2_merged.fastq" + "$id_r2.fastq" ], "must_exist" : false, "create_parent" : true, @@ -3023,8 +3023,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/cat_fastq", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/deseq2_qc/.config.vsh.yaml b/target/nextflow/deseq2_qc/.config.vsh.yaml index e4bdbda..4b0a461 100644 --- a/target/nextflow/deseq2_qc/.config.vsh.yaml +++ b/target/nextflow/deseq2_qc/.config.vsh.yaml @@ -237,8 +237,8 @@ build_info: output: "target/nextflow/deseq2_qc" executable: "target/nextflow/deseq2_qc/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/deseq2_qc/main.nf b/target/nextflow/deseq2_qc/main.nf index 455d9bc..48da8fd 100644 --- a/target/nextflow/deseq2_qc/main.nf +++ b/target/nextflow/deseq2_qc/main.nf @@ -3110,8 +3110,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/deseq2_qc", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/dupradar/.config.vsh.yaml b/target/nextflow/dupradar/.config.vsh.yaml index 04ef101..1b778cf 100644 --- a/target/nextflow/dupradar/.config.vsh.yaml +++ b/target/nextflow/dupradar/.config.vsh.yaml @@ -266,8 +266,8 @@ build_info: output: "target/nextflow/dupradar" executable: "target/nextflow/dupradar/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/dupradar/main.nf b/target/nextflow/dupradar/main.nf index d1328b3..4779246 100644 --- a/target/nextflow/dupradar/main.nf +++ b/target/nextflow/dupradar/main.nf @@ -3136,8 +3136,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/dupradar", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/fastqc/.config.vsh.yaml b/target/nextflow/fastqc/.config.vsh.yaml index 34ca15b..4547cbc 100644 --- a/target/nextflow/fastqc/.config.vsh.yaml +++ b/target/nextflow/fastqc/.config.vsh.yaml @@ -198,8 +198,8 @@ build_info: output: "target/nextflow/fastqc" executable: "target/nextflow/fastqc/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/fastqc/main.nf b/target/nextflow/fastqc/main.nf index a103813..f2efecb 100644 --- a/target/nextflow/fastqc/main.nf +++ b/target/nextflow/fastqc/main.nf @@ -3056,8 +3056,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/fastqc", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/fq_subsample/.config.vsh.yaml b/target/nextflow/fq_subsample/.config.vsh.yaml index 9fad7a1..7adf920 100644 --- a/target/nextflow/fq_subsample/.config.vsh.yaml +++ b/target/nextflow/fq_subsample/.config.vsh.yaml @@ -177,8 +177,8 @@ build_info: output: "target/nextflow/fq_subsample" executable: "target/nextflow/fq_subsample/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/fq_subsample/main.nf b/target/nextflow/fq_subsample/main.nf index 5c3736d..40dcfc6 100644 --- a/target/nextflow/fq_subsample/main.nf +++ b/target/nextflow/fq_subsample/main.nf @@ -3027,8 +3027,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/fq_subsample", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/getchromsizes/.config.vsh.yaml b/target/nextflow/getchromsizes/.config.vsh.yaml index b6d5135..295aa1c 100644 --- a/target/nextflow/getchromsizes/.config.vsh.yaml +++ b/target/nextflow/getchromsizes/.config.vsh.yaml @@ -167,8 +167,8 @@ build_info: output: "target/nextflow/getchromsizes" executable: "target/nextflow/getchromsizes/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/getchromsizes/main.nf b/target/nextflow/getchromsizes/main.nf index 896b467..b4a2386 100644 --- a/target/nextflow/getchromsizes/main.nf +++ b/target/nextflow/getchromsizes/main.nf @@ -3013,8 +3013,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/getchromsizes", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/gtf2bed/.config.vsh.yaml b/target/nextflow/gtf2bed/.config.vsh.yaml index 662f239..4fe0b1f 100644 --- a/target/nextflow/gtf2bed/.config.vsh.yaml +++ b/target/nextflow/gtf2bed/.config.vsh.yaml @@ -145,8 +145,8 @@ build_info: output: "target/nextflow/gtf2bed" executable: "target/nextflow/gtf2bed/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/gtf2bed/main.nf b/target/nextflow/gtf2bed/main.nf index 9cb1653..b205b97 100644 --- a/target/nextflow/gtf2bed/main.nf +++ b/target/nextflow/gtf2bed/main.nf @@ -2995,8 +2995,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/gtf2bed", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/gtf_filter/.config.vsh.yaml b/target/nextflow/gtf_filter/.config.vsh.yaml index 9e17a10..0fb8b46 100644 --- a/target/nextflow/gtf_filter/.config.vsh.yaml +++ b/target/nextflow/gtf_filter/.config.vsh.yaml @@ -155,8 +155,8 @@ build_info: output: "target/nextflow/gtf_filter" executable: "target/nextflow/gtf_filter/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/gtf_filter/main.nf b/target/nextflow/gtf_filter/main.nf index 591b219..092eea5 100644 --- a/target/nextflow/gtf_filter/main.nf +++ b/target/nextflow/gtf_filter/main.nf @@ -3003,8 +3003,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/gtf_filter", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/gunzip/.config.vsh.yaml b/target/nextflow/gunzip/.config.vsh.yaml index 5fec39c..69d0c93 100644 --- a/target/nextflow/gunzip/.config.vsh.yaml +++ b/target/nextflow/gunzip/.config.vsh.yaml @@ -144,8 +144,8 @@ build_info: output: "target/nextflow/gunzip" executable: "target/nextflow/gunzip/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/gunzip/main.nf b/target/nextflow/gunzip/main.nf index e18e223..4e473bd 100644 --- a/target/nextflow/gunzip/main.nf +++ b/target/nextflow/gunzip/main.nf @@ -2992,8 +2992,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/gunzip", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml b/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml index 9426f89..78f51a2 100644 --- a/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml +++ b/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml @@ -155,8 +155,8 @@ build_info: output: "target/nextflow/kallisto/kallisto_index" executable: "target/nextflow/kallisto/kallisto_index/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/kallisto/kallisto_index/main.nf b/target/nextflow/kallisto/kallisto_index/main.nf index 26766c3..2d3736b 100644 --- a/target/nextflow/kallisto/kallisto_index/main.nf +++ b/target/nextflow/kallisto/kallisto_index/main.nf @@ -3002,8 +3002,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/kallisto/kallisto_index", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml b/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml index b18063c..ab09c6b 100644 --- a/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml +++ b/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml @@ -253,8 +253,8 @@ build_info: output: "target/nextflow/kallisto/kallisto_quant" executable: "target/nextflow/kallisto/kallisto_quant/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/kallisto/kallisto_quant/main.nf b/target/nextflow/kallisto/kallisto_quant/main.nf index 96fb786..a3cab5d 100644 --- a/target/nextflow/kallisto/kallisto_quant/main.nf +++ b/target/nextflow/kallisto/kallisto_quant/main.nf @@ -3114,8 +3114,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/kallisto/kallisto_quant", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml b/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml index 6db45e5..16b886f 100644 --- a/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml +++ b/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml @@ -170,8 +170,8 @@ build_info: output: "target/nextflow/multiqc_custom_biotype" executable: "target/nextflow/multiqc_custom_biotype/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/multiqc_custom_biotype/main.nf b/target/nextflow/multiqc_custom_biotype/main.nf index ecd67e3..3810a92 100644 --- a/target/nextflow/multiqc_custom_biotype/main.nf +++ b/target/nextflow/multiqc_custom_biotype/main.nf @@ -3020,8 +3020,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/multiqc_custom_biotype", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/picard_markduplicates/.config.vsh.yaml b/target/nextflow/picard_markduplicates/.config.vsh.yaml index a4cb0e7..907f7b1 100644 --- a/target/nextflow/picard_markduplicates/.config.vsh.yaml +++ b/target/nextflow/picard_markduplicates/.config.vsh.yaml @@ -207,8 +207,8 @@ build_info: output: "target/nextflow/picard_markduplicates" executable: "target/nextflow/picard_markduplicates/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/picard_markduplicates/main.nf b/target/nextflow/picard_markduplicates/main.nf index c5a3ddc..2996a35 100644 --- a/target/nextflow/picard_markduplicates/main.nf +++ b/target/nextflow/picard_markduplicates/main.nf @@ -3063,8 +3063,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/picard_markduplicates", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/prepare_multiqc_input/.config.vsh.yaml b/target/nextflow/prepare_multiqc_input/.config.vsh.yaml index fad4c69..f48d3c0 100644 --- a/target/nextflow/prepare_multiqc_input/.config.vsh.yaml +++ b/target/nextflow/prepare_multiqc_input/.config.vsh.yaml @@ -409,8 +409,8 @@ build_info: output: "target/nextflow/prepare_multiqc_input" executable: "target/nextflow/prepare_multiqc_input/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/prepare_multiqc_input/main.nf b/target/nextflow/prepare_multiqc_input/main.nf index da34f40..8042514 100644 --- a/target/nextflow/prepare_multiqc_input/main.nf +++ b/target/nextflow/prepare_multiqc_input/main.nf @@ -3277,8 +3277,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/prepare_multiqc_input", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml b/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml index 63df6ed..662c4ce 100644 --- a/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml +++ b/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml @@ -138,8 +138,8 @@ build_info: output: "target/nextflow/preprocess_transcripts_fasta" executable: "target/nextflow/preprocess_transcripts_fasta/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/preprocess_transcripts_fasta/main.nf b/target/nextflow/preprocess_transcripts_fasta/main.nf index d6d1c9f..218977b 100644 --- a/target/nextflow/preprocess_transcripts_fasta/main.nf +++ b/target/nextflow/preprocess_transcripts_fasta/main.nf @@ -2982,8 +2982,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/preprocess_transcripts_fasta", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/preseq_lcextrap/.config.vsh.yaml b/target/nextflow/preseq_lcextrap/.config.vsh.yaml index bb3cf56..e8dfa64 100644 --- a/target/nextflow/preseq_lcextrap/.config.vsh.yaml +++ b/target/nextflow/preseq_lcextrap/.config.vsh.yaml @@ -191,8 +191,8 @@ build_info: output: "target/nextflow/preseq_lcextrap" executable: "target/nextflow/preseq_lcextrap/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/preseq_lcextrap/main.nf b/target/nextflow/preseq_lcextrap/main.nf index a81907c..c2771ae 100644 --- a/target/nextflow/preseq_lcextrap/main.nf +++ b/target/nextflow/preseq_lcextrap/main.nf @@ -3035,8 +3035,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/preseq_lcextrap", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/qualimap/.config.vsh.yaml b/target/nextflow/qualimap/.config.vsh.yaml index 75719f2..f49e348 100644 --- a/target/nextflow/qualimap/.config.vsh.yaml +++ b/target/nextflow/qualimap/.config.vsh.yaml @@ -271,8 +271,8 @@ build_info: output: "target/nextflow/qualimap" executable: "target/nextflow/qualimap/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/qualimap/main.nf b/target/nextflow/qualimap/main.nf index 454943d..f2852ea 100644 --- a/target/nextflow/qualimap/main.nf +++ b/target/nextflow/qualimap/main.nf @@ -3144,8 +3144,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/qualimap", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml b/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml index 742c544..91f40ff 100644 --- a/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml +++ b/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml @@ -299,8 +299,8 @@ build_info: output: "target/nextflow/rsem/rsem_calculate_expression" executable: "target/nextflow/rsem/rsem_calculate_expression/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rsem/rsem_calculate_expression/main.nf b/target/nextflow/rsem/rsem_calculate_expression/main.nf index c591cec..50929ac 100644 --- a/target/nextflow/rsem/rsem_calculate_expression/main.nf +++ b/target/nextflow/rsem/rsem_calculate_expression/main.nf @@ -3163,8 +3163,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rsem/rsem_calculate_expression", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml b/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml index 62ad579..bbb1964 100644 --- a/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml +++ b/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml @@ -182,8 +182,8 @@ build_info: output: "target/nextflow/rsem/rsem_merge_counts" executable: "target/nextflow/rsem/rsem_merge_counts/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rsem/rsem_merge_counts/main.nf b/target/nextflow/rsem/rsem_merge_counts/main.nf index 60ba527..ab0d892 100644 --- a/target/nextflow/rsem/rsem_merge_counts/main.nf +++ b/target/nextflow/rsem/rsem_merge_counts/main.nf @@ -3028,8 +3028,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rsem/rsem_merge_counts", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml index cad890e..a5e7d01 100644 --- a/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml @@ -163,8 +163,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_bamstat" executable: "target/nextflow/rseqc/rseqc_bamstat/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rseqc/rseqc_bamstat/main.nf b/target/nextflow/rseqc/rseqc_bamstat/main.nf index 078b1cf..77dc135 100644 --- a/target/nextflow/rseqc/rseqc_bamstat/main.nf +++ b/target/nextflow/rseqc/rseqc_bamstat/main.nf @@ -3016,8 +3016,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_bamstat", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml index 91deacd..8034d6f 100644 --- a/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml @@ -186,8 +186,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_inferexperiment" executable: "target/nextflow/rseqc/rseqc_inferexperiment/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rseqc/rseqc_inferexperiment/main.nf b/target/nextflow/rseqc/rseqc_inferexperiment/main.nf index cee1b2f..b2f9ced 100644 --- a/target/nextflow/rseqc/rseqc_inferexperiment/main.nf +++ b/target/nextflow/rseqc/rseqc_inferexperiment/main.nf @@ -3044,8 +3044,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_inferexperiment", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rseqc/rseqc_innerdistance/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_innerdistance/.config.vsh.yaml index 58644ec..64e82cf 100644 --- a/target/nextflow/rseqc/rseqc_innerdistance/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_innerdistance/.config.vsh.yaml @@ -272,8 +272,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_innerdistance" executable: "target/nextflow/rseqc/rseqc_innerdistance/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rseqc/rseqc_innerdistance/main.nf b/target/nextflow/rseqc/rseqc_innerdistance/main.nf index 77e7f64..56f9828 100644 --- a/target/nextflow/rseqc/rseqc_innerdistance/main.nf +++ b/target/nextflow/rseqc/rseqc_innerdistance/main.nf @@ -3137,8 +3137,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_innerdistance", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml index fb160cd..cd2865c 100644 --- a/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml @@ -260,8 +260,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_junctionannotation" executable: "target/nextflow/rseqc/rseqc_junctionannotation/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rseqc/rseqc_junctionannotation/main.nf b/target/nextflow/rseqc/rseqc_junctionannotation/main.nf index 523a3f8..84098b6 100644 --- a/target/nextflow/rseqc/rseqc_junctionannotation/main.nf +++ b/target/nextflow/rseqc/rseqc_junctionannotation/main.nf @@ -3128,8 +3128,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_junctionannotation", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml index f3d2a45..bb0fac7 100644 --- a/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml @@ -249,8 +249,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_junctionsaturation" executable: "target/nextflow/rseqc/rseqc_junctionsaturation/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf b/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf index 3ed2a7d..de3b498 100644 --- a/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf +++ b/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf @@ -3113,8 +3113,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_junctionsaturation", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml index 35dee3e..9aa85d4 100644 --- a/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml @@ -162,8 +162,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_readdistribution" executable: "target/nextflow/rseqc/rseqc_readdistribution/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rseqc/rseqc_readdistribution/main.nf b/target/nextflow/rseqc/rseqc_readdistribution/main.nf index 374001e..945f88d 100644 --- a/target/nextflow/rseqc/rseqc_readdistribution/main.nf +++ b/target/nextflow/rseqc/rseqc_readdistribution/main.nf @@ -3017,8 +3017,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_readdistribution", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml index 183b2b3..c132a83 100644 --- a/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml @@ -211,8 +211,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_readduplication" executable: "target/nextflow/rseqc/rseqc_readduplication/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rseqc/rseqc_readduplication/main.nf b/target/nextflow/rseqc/rseqc_readduplication/main.nf index 4bbe152..0138258 100644 --- a/target/nextflow/rseqc/rseqc_readduplication/main.nf +++ b/target/nextflow/rseqc/rseqc_readduplication/main.nf @@ -3071,8 +3071,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_readduplication", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml index f10b6ae..5f454d6 100644 --- a/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml @@ -214,8 +214,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_tin" executable: "target/nextflow/rseqc/rseqc_tin/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rseqc/rseqc_tin/main.nf b/target/nextflow/rseqc/rseqc_tin/main.nf index d0963e5..4d215dc 100644 --- a/target/nextflow/rseqc/rseqc_tin/main.nf +++ b/target/nextflow/rseqc/rseqc_tin/main.nf @@ -3076,8 +3076,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_tin", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/sortmerna/.config.vsh.yaml b/target/nextflow/sortmerna/.config.vsh.yaml index dabbcd1..f3d6352 100644 --- a/target/nextflow/sortmerna/.config.vsh.yaml +++ b/target/nextflow/sortmerna/.config.vsh.yaml @@ -198,8 +198,8 @@ build_info: output: "target/nextflow/sortmerna" executable: "target/nextflow/sortmerna/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/sortmerna/main.nf b/target/nextflow/sortmerna/main.nf index 87840ff..668d706 100644 --- a/target/nextflow/sortmerna/main.nf +++ b/target/nextflow/sortmerna/main.nf @@ -3050,8 +3050,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/sortmerna", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/stringtie/.config.vsh.yaml b/target/nextflow/stringtie/.config.vsh.yaml index 43545b3..2ed7eed 100644 --- a/target/nextflow/stringtie/.config.vsh.yaml +++ b/target/nextflow/stringtie/.config.vsh.yaml @@ -216,8 +216,8 @@ build_info: output: "target/nextflow/stringtie" executable: "target/nextflow/stringtie/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/stringtie/main.nf b/target/nextflow/stringtie/main.nf index 100bd0d..56ee977 100644 --- a/target/nextflow/stringtie/main.nf +++ b/target/nextflow/stringtie/main.nf @@ -3073,8 +3073,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/stringtie", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/summarizedexperiment/.config.vsh.yaml b/target/nextflow/summarizedexperiment/.config.vsh.yaml index 5556760..e841890 100644 --- a/target/nextflow/summarizedexperiment/.config.vsh.yaml +++ b/target/nextflow/summarizedexperiment/.config.vsh.yaml @@ -199,8 +199,8 @@ build_info: output: "target/nextflow/summarizedexperiment" executable: "target/nextflow/summarizedexperiment/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/summarizedexperiment/main.nf b/target/nextflow/summarizedexperiment/main.nf index d5bd2e2..5a847b7 100644 --- a/target/nextflow/summarizedexperiment/main.nf +++ b/target/nextflow/summarizedexperiment/main.nf @@ -3054,8 +3054,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/summarizedexperiment", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/trimgalore/.config.vsh.yaml b/target/nextflow/trimgalore/.config.vsh.yaml index 1f9a8d3..5fa597e 100644 --- a/target/nextflow/trimgalore/.config.vsh.yaml +++ b/target/nextflow/trimgalore/.config.vsh.yaml @@ -788,8 +788,8 @@ build_info: output: "target/nextflow/trimgalore" executable: "target/nextflow/trimgalore/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/trimgalore/main.nf b/target/nextflow/trimgalore/main.nf index f8a631f..0072732 100644 --- a/target/nextflow/trimgalore/main.nf +++ b/target/nextflow/trimgalore/main.nf @@ -3576,8 +3576,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/trimgalore", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/tx2gene/.config.vsh.yaml b/target/nextflow/tx2gene/.config.vsh.yaml index 733b1a6..e89a30e 100644 --- a/target/nextflow/tx2gene/.config.vsh.yaml +++ b/target/nextflow/tx2gene/.config.vsh.yaml @@ -192,8 +192,8 @@ build_info: output: "target/nextflow/tx2gene" executable: "target/nextflow/tx2gene/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/tx2gene/main.nf b/target/nextflow/tx2gene/main.nf index d5a9570..f201e1a 100644 --- a/target/nextflow/tx2gene/main.nf +++ b/target/nextflow/tx2gene/main.nf @@ -3049,8 +3049,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/tx2gene", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/tximport/.config.vsh.yaml b/target/nextflow/tximport/.config.vsh.yaml index 7244d11..0d253ee 100644 --- a/target/nextflow/tximport/.config.vsh.yaml +++ b/target/nextflow/tximport/.config.vsh.yaml @@ -247,8 +247,8 @@ build_info: output: "target/nextflow/tximport" executable: "target/nextflow/tximport/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/tximport/main.nf b/target/nextflow/tximport/main.nf index 29e9d8c..7882568 100644 --- a/target/nextflow/tximport/main.nf +++ b/target/nextflow/tximport/main.nf @@ -3114,8 +3114,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/tximport", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/ucsc/bedclip/.config.vsh.yaml b/target/nextflow/ucsc/bedclip/.config.vsh.yaml index 2d4ac7f..0d54349 100644 --- a/target/nextflow/ucsc/bedclip/.config.vsh.yaml +++ b/target/nextflow/ucsc/bedclip/.config.vsh.yaml @@ -164,8 +164,8 @@ build_info: output: "target/nextflow/ucsc/bedclip" executable: "target/nextflow/ucsc/bedclip/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/ucsc/bedclip/main.nf b/target/nextflow/ucsc/bedclip/main.nf index ab23566..287a1cf 100644 --- a/target/nextflow/ucsc/bedclip/main.nf +++ b/target/nextflow/ucsc/bedclip/main.nf @@ -3018,8 +3018,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/ucsc/bedclip", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml b/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml index 0c64dce..bcde132 100644 --- a/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml +++ b/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml @@ -164,8 +164,8 @@ build_info: output: "target/nextflow/ucsc/bedgraphtobigwig" executable: "target/nextflow/ucsc/bedgraphtobigwig/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/ucsc/bedgraphtobigwig/main.nf b/target/nextflow/ucsc/bedgraphtobigwig/main.nf index 83d042f..26315ff 100644 --- a/target/nextflow/ucsc/bedgraphtobigwig/main.nf +++ b/target/nextflow/ucsc/bedgraphtobigwig/main.nf @@ -3018,8 +3018,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/ucsc/bedgraphtobigwig", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/umitools/umitools_dedup/.config.vsh.yaml b/target/nextflow/umitools/umitools_dedup/.config.vsh.yaml index c307ef0..e65ab27 100644 --- a/target/nextflow/umitools/umitools_dedup/.config.vsh.yaml +++ b/target/nextflow/umitools/umitools_dedup/.config.vsh.yaml @@ -195,8 +195,8 @@ build_info: output: "target/nextflow/umitools/umitools_dedup" executable: "target/nextflow/umitools/umitools_dedup/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/umitools/umitools_dedup/main.nf b/target/nextflow/umitools/umitools_dedup/main.nf index ce33562..67022d2 100644 --- a/target/nextflow/umitools/umitools_dedup/main.nf +++ b/target/nextflow/umitools/umitools_dedup/main.nf @@ -3054,8 +3054,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/umitools/umitools_dedup", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/umitools/umitools_extract/.config.vsh.yaml b/target/nextflow/umitools/umitools_extract/.config.vsh.yaml index 70af5a7..22ab4cc 100644 --- a/target/nextflow/umitools/umitools_extract/.config.vsh.yaml +++ b/target/nextflow/umitools/umitools_extract/.config.vsh.yaml @@ -253,8 +253,8 @@ build_info: output: "target/nextflow/umitools/umitools_extract" executable: "target/nextflow/umitools/umitools_extract/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/umitools/umitools_extract/main.nf b/target/nextflow/umitools/umitools_extract/main.nf index 6d18628..e8e391c 100644 --- a/target/nextflow/umitools/umitools_extract/main.nf +++ b/target/nextflow/umitools/umitools_extract/main.nf @@ -3119,8 +3119,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/umitools/umitools_extract", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/umitools_prepareforquant/.config.vsh.yaml b/target/nextflow/umitools_prepareforquant/.config.vsh.yaml index 5928840..a2d64cd 100644 --- a/target/nextflow/umitools_prepareforquant/.config.vsh.yaml +++ b/target/nextflow/umitools_prepareforquant/.config.vsh.yaml @@ -156,8 +156,8 @@ build_info: output: "target/nextflow/umitools_prepareforquant" executable: "target/nextflow/umitools_prepareforquant/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/umitools_prepareforquant/main.nf b/target/nextflow/umitools_prepareforquant/main.nf index b53a124..1f8b12a 100644 --- a/target/nextflow/umitools_prepareforquant/main.nf +++ b/target/nextflow/umitools_prepareforquant/main.nf @@ -3007,8 +3007,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/umitools_prepareforquant", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/workflows/genome_alignment_and_quant/.config.vsh.yaml b/target/nextflow/workflows/genome_alignment_and_quant/.config.vsh.yaml index d3b76a9..4b13390 100644 --- a/target/nextflow/workflows/genome_alignment_and_quant/.config.vsh.yaml +++ b/target/nextflow/workflows/genome_alignment_and_quant/.config.vsh.yaml @@ -603,8 +603,8 @@ build_info: output: "target/nextflow/workflows/genome_alignment_and_quant" executable: "target/nextflow/workflows/genome_alignment_and_quant/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort" diff --git a/target/nextflow/workflows/genome_alignment_and_quant/main.nf b/target/nextflow/workflows/genome_alignment_and_quant/main.nf index ccad37d..66fc2ac 100644 --- a/target/nextflow/workflows/genome_alignment_and_quant/main.nf +++ b/target/nextflow/workflows/genome_alignment_and_quant/main.nf @@ -3531,8 +3531,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/genome_alignment_and_quant", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", @@ -3873,7 +3873,7 @@ workflow run_wf { def mod_state = (state.aligner == 'star_salmon') ? state + [salmon_multiqc: state.quant_out_dir] : state [ id, mod_state ] } - | niceView() + | rsem_calculate_expression.run ( runIf: { id, state -> state.aligner == 'star_rsem' }, fromState: [ diff --git a/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml b/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml index bc44897..ecaeb73 100644 --- a/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml +++ b/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml @@ -278,8 +278,8 @@ build_info: output: "target/nextflow/workflows/merge_quant_results" executable: "target/nextflow/workflows/merge_quant_results/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/tx2gene" - "target/nextflow/tximport" diff --git a/target/nextflow/workflows/merge_quant_results/main.nf b/target/nextflow/workflows/merge_quant_results/main.nf index 864b7fd..ea86e50 100644 --- a/target/nextflow/workflows/merge_quant_results/main.nf +++ b/target/nextflow/workflows/merge_quant_results/main.nf @@ -3149,8 +3149,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/merge_quant_results", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/workflows/post_processing/.config.vsh.yaml b/target/nextflow/workflows/post_processing/.config.vsh.yaml index ca96f59..4ee6210 100644 --- a/target/nextflow/workflows/post_processing/.config.vsh.yaml +++ b/target/nextflow/workflows/post_processing/.config.vsh.yaml @@ -199,7 +199,7 @@ argument_groups: name: "--processed_genome_bam" info: null default: - - "$id..genome.bam" + - "$id.genome.bam" must_exist: true create_parent: true required: false @@ -486,8 +486,8 @@ build_info: output: "target/nextflow/workflows/post_processing" executable: "target/nextflow/workflows/post_processing/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/picard_markduplicates" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort" diff --git a/target/nextflow/workflows/post_processing/main.nf b/target/nextflow/workflows/post_processing/main.nf index 10a6131..eb2ae2b 100644 --- a/target/nextflow/workflows/post_processing/main.nf +++ b/target/nextflow/workflows/post_processing/main.nf @@ -3029,7 +3029,7 @@ meta = [ "type" : "file", "name" : "--processed_genome_bam", "default" : [ - "$id..genome.bam" + "$id.genome.bam" ], "must_exist" : true, "create_parent" : true, @@ -3397,8 +3397,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/post_processing", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", @@ -3471,20 +3471,20 @@ workflow run_wf { "extra_picard_args": "extra_picard_args" ], toState: [ - "genome_bam": "output_bam", + "processed_genome_bam": "output_bam", "markduplicates_metrics": "metrics" ] ) | samtools_sort.run ( runIf: { id, state -> !state.skip_markduplicates && !state.with_umi }, - fromState: [ "input": "genome_bam" ], - toState: [ "genome_bam": "output" ], + fromState: [ "input": "processed_genome_bam" ], + toState: [ "processed_genome_bam": "output" ], key: "genome_sorted_MarkDuplicates" ) | samtools_index.run ( runIf: { id, state -> !state.skip_markduplicates && !state.with_umi }, fromState: [ - "input": "genome_bam", + "input": "processed_genome_bam", "csi": "bam_csi_index" ], toState: [ "genome_bam_index": "output" ], @@ -3493,7 +3493,7 @@ workflow run_wf { | samtools_stats.run ( runIf: { id, state -> !state.skip_markduplicates && !state.with_umi }, fromState: [ - "input": "genome_bam", + "input": "processed_genome_bam", "bai": "genome_bam_index" ], toState: [ "genome_bam_stats": "output" ], @@ -3502,7 +3502,7 @@ workflow run_wf { | samtools_flagstat.run ( runIf: { id, state -> !state.skip_markduplicates && !state.with_umi }, fromState: [ - "bam": "genome_bam", + "bam": "processed_genome_bam", "bai": "genome_bam_index" ], toState: [ "genome_bam_flagstat": "output" ], @@ -3511,7 +3511,7 @@ workflow run_wf { | samtools_idxstats.run( runIf: { id, state -> !state.skip_markduplicates && !state.with_umi }, fromState: [ - "bam": "genome_bam", + "bam": "processed_genome_bam", "bai": "genome_bam_index" ], toState: [ "genome_bam_idxstats": "output" ], @@ -3522,7 +3522,7 @@ workflow run_wf { runIf: { id, state -> !state.skip_stringtie }, fromState: [ "strandedness": "strandedness", - "bam": "genome_bam", + "bam": "processed_genome_bam", "annotation_gtf": "gtf", "extra_stringtie_args": "extra_stringtie_args" ], @@ -3540,7 +3540,7 @@ workflow run_wf { runIf: { id, state -> !state.skip_bigwig }, fromState: [ "strandedness": "strandedness", - "bam": "genome_bam", + "bam": "processed_genome_bam", "extra_bedtools_args": "extra_bedtools_args" ], toState: [ @@ -3593,9 +3593,10 @@ workflow run_wf { def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() } [ id, mod_state ] } + | niceView() | setState ( - "processed_genome_bam": "genome_bam", + "processed_genome_bam": "processed_genome_bam", "genome_bam_index": "genome_bam_index", "genome_bam_stats": "genome_bam_stats", "genome_bam_flagstat": "genome_bam_flagstat", diff --git a/target/nextflow/workflows/pre_processing/.config.vsh.yaml b/target/nextflow/workflows/pre_processing/.config.vsh.yaml index 5d219f2..96d48e5 100644 --- a/target/nextflow/workflows/pre_processing/.config.vsh.yaml +++ b/target/nextflow/workflows/pre_processing/.config.vsh.yaml @@ -673,8 +673,8 @@ build_info: output: "target/nextflow/workflows/pre_processing" executable: "target/nextflow/workflows/pre_processing/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/fastqc" - "target/nextflow/umitools/umitools_extract" diff --git a/target/nextflow/workflows/pre_processing/main.nf b/target/nextflow/workflows/pre_processing/main.nf index 1a5ddb8..6debc47 100644 --- a/target/nextflow/workflows/pre_processing/main.nf +++ b/target/nextflow/workflows/pre_processing/main.nf @@ -3626,8 +3626,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/pre_processing", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/workflows/prepare_genome/.config.vsh.yaml b/target/nextflow/workflows/prepare_genome/.config.vsh.yaml index b9fd063..828f4fd 100644 --- a/target/nextflow/workflows/prepare_genome/.config.vsh.yaml +++ b/target/nextflow/workflows/prepare_genome/.config.vsh.yaml @@ -496,8 +496,8 @@ build_info: output: "target/nextflow/workflows/prepare_genome" executable: "target/nextflow/workflows/prepare_genome/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/gunzip" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread" diff --git a/target/nextflow/workflows/prepare_genome/main.nf b/target/nextflow/workflows/prepare_genome/main.nf index cfcc084..f1604c4 100644 --- a/target/nextflow/workflows/prepare_genome/main.nf +++ b/target/nextflow/workflows/prepare_genome/main.nf @@ -3407,8 +3407,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/prepare_genome", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/workflows/pseudo_alignment_and_quant/.config.vsh.yaml b/target/nextflow/workflows/pseudo_alignment_and_quant/.config.vsh.yaml index 899e630..0350a12 100644 --- a/target/nextflow/workflows/pseudo_alignment_and_quant/.config.vsh.yaml +++ b/target/nextflow/workflows/pseudo_alignment_and_quant/.config.vsh.yaml @@ -283,8 +283,8 @@ build_info: output: "target/nextflow/workflows/pseudo_alignment_and_quant" executable: "target/nextflow/workflows/pseudo_alignment_and_quant/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant" - "target/nextflow/kallisto/kallisto_quant" diff --git a/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf b/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf index 6c7ad31..1fb665e 100644 --- a/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf +++ b/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf @@ -3143,8 +3143,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/pseudo_alignment_and_quant", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/workflows/quality_control/.config.vsh.yaml b/target/nextflow/workflows/quality_control/.config.vsh.yaml index 15eb460..b7433f4 100644 --- a/target/nextflow/workflows/quality_control/.config.vsh.yaml +++ b/target/nextflow/workflows/quality_control/.config.vsh.yaml @@ -1596,8 +1596,8 @@ build_info: output: "target/nextflow/workflows/quality_control" executable: "target/nextflow/workflows/quality_control/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/rseqc/rseqc_bamstat" - "target/nextflow/rseqc/rseqc_inferexperiment" diff --git a/target/nextflow/workflows/quality_control/main.nf b/target/nextflow/workflows/quality_control/main.nf index ec54d2c..00b4abf 100644 --- a/target/nextflow/workflows/quality_control/main.nf +++ b/target/nextflow/workflows/quality_control/main.nf @@ -4676,8 +4676,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/quality_control", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", @@ -5465,6 +5465,7 @@ workflow run_wf { "title": "multiqc_title", "input": "multiqc_input", ], + args: [exclude_modules: "general_stats"], toState: [ "multiqc_report": "output_report", "multiqc_data": "output_data", diff --git a/target/nextflow/workflows/rnaseq/.config.vsh.yaml b/target/nextflow/workflows/rnaseq/.config.vsh.yaml index c1ebddd..877bca6 100644 --- a/target/nextflow/workflows/rnaseq/.config.vsh.yaml +++ b/target/nextflow/workflows/rnaseq/.config.vsh.yaml @@ -1051,7 +1051,7 @@ argument_groups: name: "--star_alignment" info: null default: - - "STAR_alignment/$id" + - "STAR/$id" must_exist: true create_parent: true required: false @@ -1062,7 +1062,7 @@ argument_groups: name: "--genome_bam_sorted" info: null default: - - "STAR_alignment/genome_processed/$id.genome.bam" + - "STAR/genome_processed/$id.genome.bam" must_exist: true create_parent: true required: false @@ -1073,7 +1073,7 @@ argument_groups: name: "--genome_bam_index" info: null default: - - "STAR_alignment/genome_processed/$id.genome.bam.bai" + - "STAR/genome_processed/$id.genome.bam.bai" must_exist: true create_parent: true required: false @@ -1084,7 +1084,7 @@ argument_groups: name: "--transcriptome_bam" info: null default: - - "STAR_alignment/transcriptome_processed/$id.transcriptome.bam" + - "STAR/transcriptome_processed/$id.transcriptome.bam" must_exist: true create_parent: true required: false @@ -1095,7 +1095,7 @@ argument_groups: name: "--transcriptome_bam_index" info: null default: - - "STAR_alignment/transcriptome_processed/$id.transcriptome.bam.bai" + - "STAR/transcriptome_processed/$id.transcriptome.bam.bai" must_exist: true create_parent: true required: false @@ -1179,6 +1179,17 @@ argument_groups: direction: "output" multiple: false multiple_sep: ";" + - type: "file" + name: "--salmon_quant_results_file" + info: null + default: + - "STAR_Salmon/$id/quant.sf" + must_exist: true + create_parent: true + required: false + direction: "output" + multiple: false + multiple_sep: ";" - type: "file" name: "--pseudo_quant_results" info: null @@ -1254,7 +1265,7 @@ argument_groups: name: "--tpm_gene" info: null default: - - "alignment_quantification/gene_tpm.tsv" + - "transcript_quantification/gene_tpm.tsv" must_exist: true create_parent: true required: false @@ -1265,7 +1276,7 @@ argument_groups: name: "--counts_gene" info: null default: - - "alignment_quantification/gene_counts.tsv" + - "transcript_quantification/gene_counts.tsv" must_exist: true create_parent: true required: false @@ -1276,7 +1287,7 @@ argument_groups: name: "--counts_gene_length_scaled" info: null default: - - "alignment_quantification/gene_counts_length_scaled.tsv" + - "transcript_quantification/gene_counts_length_scaled.tsv" must_exist: true create_parent: true required: false @@ -1287,7 +1298,7 @@ argument_groups: name: "--counts_gene_scaled" info: null default: - - "alignment_quantification/gene_counts_scaled.tsv" + - "transcript_quantification/gene_counts_scaled.tsv" must_exist: true create_parent: true required: false @@ -1298,7 +1309,7 @@ argument_groups: name: "--tpm_transcript" info: null default: - - "alignment_quantification/transcript_tpm.tsv" + - "transcript_quantification/transcript_tpm.tsv" must_exist: true create_parent: true required: false @@ -1309,7 +1320,7 @@ argument_groups: name: "--counts_transcript" info: null default: - - "alignment_quantification/transcript_counts.tsv" + - "transcript_quantification/transcript_counts.tsv" must_exist: true create_parent: true required: false @@ -1320,7 +1331,7 @@ argument_groups: name: "--quant_merged_summarizedexperiment" info: null default: - - "alignment_quantification/summarizedexperiment" + - "transcript_quantification/summarizedexperiment" must_exist: true create_parent: true required: false @@ -1331,7 +1342,7 @@ argument_groups: name: "--markduplicates_metrics" info: null default: - - "picard/$id.sorted.MarkDuplicates.metrics.txt" + - "picard/$id.MarkDuplicates.metrics.txt" must_exist: true create_parent: true required: false @@ -2106,8 +2117,8 @@ build_info: output: "target/nextflow/workflows/rnaseq" executable: "target/nextflow/workflows/rnaseq/main.nf" viash_version: "0.9.0" - git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb" - git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + git_commit: "55878e4519aa920a419bb99a9b3afc8307b6c6e3" + git_remote: "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/workflows/prepare_genome" - "target/nextflow/cat_fastq" diff --git a/target/nextflow/workflows/rnaseq/main.nf b/target/nextflow/workflows/rnaseq/main.nf index 5cd47fd..7a01f03 100644 --- a/target/nextflow/workflows/rnaseq/main.nf +++ b/target/nextflow/workflows/rnaseq/main.nf @@ -4015,7 +4015,7 @@ meta = [ "type" : "file", "name" : "--star_alignment", "default" : [ - "STAR_alignment/$id" + "STAR/$id" ], "must_exist" : true, "create_parent" : true, @@ -4028,7 +4028,7 @@ meta = [ "type" : "file", "name" : "--genome_bam_sorted", "default" : [ - "STAR_alignment/genome_processed/$id.genome.bam" + "STAR/genome_processed/$id.genome.bam" ], "must_exist" : true, "create_parent" : true, @@ -4041,7 +4041,7 @@ meta = [ "type" : "file", "name" : "--genome_bam_index", "default" : [ - "STAR_alignment/genome_processed/$id.genome.bam.bai" + "STAR/genome_processed/$id.genome.bam.bai" ], "must_exist" : true, "create_parent" : true, @@ -4054,7 +4054,7 @@ meta = [ "type" : "file", "name" : "--transcriptome_bam", "default" : [ - "STAR_alignment/transcriptome_processed/$id.transcriptome.bam" + "STAR/transcriptome_processed/$id.transcriptome.bam" ], "must_exist" : true, "create_parent" : true, @@ -4067,7 +4067,7 @@ meta = [ "type" : "file", "name" : "--transcriptome_bam_index", "default" : [ - "STAR_alignment/transcriptome_processed/$id.transcriptome.bam.bai" + "STAR/transcriptome_processed/$id.transcriptome.bam.bai" ], "must_exist" : true, "create_parent" : true, @@ -4167,6 +4167,19 @@ meta = [ "multiple" : false, "multiple_sep" : ";" }, + { + "type" : "file", + "name" : "--salmon_quant_results_file", + "default" : [ + "STAR_Salmon/$id/quant.sf" + ], + "must_exist" : true, + "create_parent" : true, + "required" : false, + "direction" : "output", + "multiple" : false, + "multiple_sep" : ";" + }, { "type" : "file", "name" : "--pseudo_quant_results", @@ -4254,7 +4267,7 @@ meta = [ "type" : "file", "name" : "--tpm_gene", "default" : [ - "alignment_quantification/gene_tpm.tsv" + "transcript_quantification/gene_tpm.tsv" ], "must_exist" : true, "create_parent" : true, @@ -4267,7 +4280,7 @@ meta = [ "type" : "file", "name" : "--counts_gene", "default" : [ - "alignment_quantification/gene_counts.tsv" + "transcript_quantification/gene_counts.tsv" ], "must_exist" : true, "create_parent" : true, @@ -4280,7 +4293,7 @@ meta = [ "type" : "file", "name" : "--counts_gene_length_scaled", "default" : [ - "alignment_quantification/gene_counts_length_scaled.tsv" + "transcript_quantification/gene_counts_length_scaled.tsv" ], "must_exist" : true, "create_parent" : true, @@ -4293,7 +4306,7 @@ meta = [ "type" : "file", "name" : "--counts_gene_scaled", "default" : [ - "alignment_quantification/gene_counts_scaled.tsv" + "transcript_quantification/gene_counts_scaled.tsv" ], "must_exist" : true, "create_parent" : true, @@ -4306,7 +4319,7 @@ meta = [ "type" : "file", "name" : "--tpm_transcript", "default" : [ - "alignment_quantification/transcript_tpm.tsv" + "transcript_quantification/transcript_tpm.tsv" ], "must_exist" : true, "create_parent" : true, @@ -4319,7 +4332,7 @@ meta = [ "type" : "file", "name" : "--counts_transcript", "default" : [ - "alignment_quantification/transcript_counts.tsv" + "transcript_quantification/transcript_counts.tsv" ], "must_exist" : true, "create_parent" : true, @@ -4332,7 +4345,7 @@ meta = [ "type" : "file", "name" : "--quant_merged_summarizedexperiment", "default" : [ - "alignment_quantification/summarizedexperiment" + "transcript_quantification/summarizedexperiment" ], "must_exist" : true, "create_parent" : true, @@ -4345,7 +4358,7 @@ meta = [ "type" : "file", "name" : "--markduplicates_metrics", "default" : [ - "picard/$id.sorted.MarkDuplicates.metrics.txt" + "picard/$id.MarkDuplicates.metrics.txt" ], "must_exist" : true, "create_parent" : true, @@ -4878,7 +4891,7 @@ meta = [ "name" : "--dupradar_output_duprate_exp_boxplot", "description" : "path to output file (pdf) of distribution of expression box plot", "default" : [ - "dupradar/box_plot/$id.duprate_exp_boxplot.pdf" + "dupradar/box_''' + '''plot/$id.duprate_exp_boxplot.pdf" ], "must_exist" : true, "create_parent" : true, @@ -4889,7 +4902,7 @@ meta = [ }, { "type" : "file", - "name" : "--duprada''' + '''r_output_duprate_exp_densplot", + "name" : "--dupradar_output_duprate_exp_densplot", "description" : "path to output file (pdf) of 2D density scatter plot of duplicate tag counts", "default" : [ "dupradar/scatter_plot/$id.duprate_exp_densityplot.pdf" @@ -5270,8 +5283,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/rnaseq", "viash_version" : "0.9.0", - "git_commit" : "f3645db764dda85eb0fbd0439e7ca872b46a0dcb", - "git_remote" : "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq" + "git_commit" : "55878e4519aa920a419bb99a9b3afc8307b6c6e3", + "git_remote" : "https://x-access-token:ghs_ltJPjPqiv1bdiWEoMNLoIT9NWntapQ0mtFGy@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", @@ -5802,6 +5815,7 @@ workflow run_wf { "transcriptome_bam_idxstats": "transcriptome_bam_idxstats", "salmon_quant_results": "quant_out_dir", "pseudo_quant_results": "pseudo_quant_out_dir", + "markduplicates_metrics": "markduplicates_metrics", "stringtie_transcript_gtf": "stringtie_transcript_gtf", "stringtie_coverage_gtf": "stringtie_coverage_gtf", "stringtie_abundance": "stringtie_abundance", diff --git a/target/nextflow/workflows/rnaseq/nextflow_schema.json b/target/nextflow/workflows/rnaseq/nextflow_schema.json index c646b4e..cb85c7f 100644 --- a/target/nextflow/workflows/rnaseq/nextflow_schema.json +++ b/target/nextflow/workflows/rnaseq/nextflow_schema.json @@ -1360,6 +1360,17 @@ } + , + "salmon_quant_results_file": { + "type": + "string", + "description": "Type: `file`, default: `$id.$key.salmon_quant_results_file.sf`. ", + "help_text": "Type: `file`, default: `$id.$key.salmon_quant_results_file.sf`. " + , + "default": "$id.$key.salmon_quant_results_file.sf" + } + + , "pseudo_quant_results": { "type":