diff --git a/src/workflows/genome_alignment_and_quant/main.nf b/src/workflows/genome_alignment_and_quant/main.nf index f2c2aa9..ceb0ee1 100644 --- a/src/workflows/genome_alignment_and_quant/main.nf +++ b/src/workflows/genome_alignment_and_quant/main.nf @@ -1,3 +1,5 @@ +// TODO: Improve logic of this wf, e.g. by splitting up in 2 subwfs +// TODO: See if this can be aligned with the pseudo-alignment branch of the logic workflow run_wf { take: input_ch diff --git a/src/workflows/pseudo_alignment_and_quant/main.nf b/src/workflows/pseudo_alignment_and_quant/main.nf index e275962..43cf36d 100644 --- a/src/workflows/pseudo_alignment_and_quant/main.nf +++ b/src/workflows/pseudo_alignment_and_quant/main.nf @@ -1,3 +1,4 @@ +// TODO: See if the logic of this can be aligned with the STAR aligner logic workflow run_wf { take: input_ch diff --git a/src/workflows/quality_control/main.nf b/src/workflows/quality_control/main.nf index 35ba2e9..7ff8e0f 100644 --- a/src/workflows/quality_control/main.nf +++ b/src/workflows/quality_control/main.nf @@ -240,6 +240,7 @@ workflow run_wf { def skip_qc = list.collect { id, state -> state.skip_qc }.unique()[0] def skip_align = list.collect { id, state -> state.skip_align }.unique()[0] def skip_pseudo_align = list.collect { id, state -> state.skip_pseudo_align }.unique()[0] + // TODO: Are these checks necessary? def quant_results = list.collect { id, state -> (state.quant_results_file instanceof java.nio.file.Path && state.quant_results_file.exists()) ? state.quant_results_file : @@ -538,6 +539,7 @@ workflow run_wf { ) | niceView() // Get list of samples that failed trimming, mapping, and strand check for MultiQC report + // TODO: Refactor this to a process/step | map { id, state -> def fail_trimming_header = ["Sample", "Reads after trimming"] def fail_trimming_multiqc = "" @@ -666,6 +668,7 @@ workflow run_wf { | map { list -> [list[0], list[1] + list[2]] } | map { id, state -> + // TODO: Check this, necessary for setState def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() } [ id, mod_state ] } diff --git a/src/workflows/rnaseq/config.vsh.yaml b/src/workflows/rnaseq/config.vsh.yaml index 5a8cf97..55cf7ae 100644 --- a/src/workflows/rnaseq/config.vsh.yaml +++ b/src/workflows/rnaseq/config.vsh.yaml @@ -912,7 +912,7 @@ argument_groups: type: file direction: output default: pseudo_alignment_quantification/quant_merged_summarizedexperiment - + resources: - type: nextflow_script path: main.nf diff --git a/src/workflows/rnaseq/main.nf b/src/workflows/rnaseq/main.nf index 902974d..28684bd 100644 --- a/src/workflows/rnaseq/main.nf +++ b/src/workflows/rnaseq/main.nf @@ -5,222 +5,473 @@ workflow run_wf { main: reference_ch = input_ch - | map { id, state -> - def biotype = state.gencode ? "gene_type" : state.featurecounts_group_type - def filter_gtf = - ( - ( !state.skip_alignment && state.aligner) // Condition 1: Alignment is required and aligner is set - || ( !state.skip_pseudo_alignment && state.pseudo_aligner ) // Condition 2: Pseudoalignment is required and pseudoaligner is set - || ( !state.transcript_fasta ) // Condition 3: Transcript FASTA file is not provided - ) - && - ( !state.skip_gtf_filter ) // Condition 4: --skip_gtf_filter is not provided - [ id, state + [ biotype: biotype, filter_gtf: filter_gtf ] ] - } - - | toSortedList - - | map { list -> - [ "ref", - [ fasta: list.collect { id, state -> state.fasta }.unique()[0], - gtf: list.collect { id, state -> state.gtf }.unique()[0], - gff: list.collect { id, state -> state.gff }.unique()[0], - additional_fasta: list.collect { id, state -> state.additional_fasta }.unique()[0], - transcript_fasta:list.collect { id, state -> state.transcript_fasta }.unique()[0], - gene_bed: list.collect { id, state -> state.gene_bed }.unique()[0], - bbsplit_fasta_list: list.collect { id, state -> state.bbsplit_fasta_list }.unique()[0], - aligner: list.collect { id, state -> state.aligner }.unique()[0], - pseudo_aligner: list.collect { id, state -> state.pseudo_aligner }.unique()[0], - star_index: list.collect { id, state -> state.star_index }.unique()[0], - rsem_index: list.collect { id, state -> state.rsem_index }.unique()[0], - salmon_index: list.collect { id, state -> state.salmon_index }.unique()[0], - kallisto_index: list.collect { id, state -> state.kallisto_index }.unique()[0], - // splicesites: list.collect { id, state -> state.splicesites }.unique()[0], - // hisat2_index: list.collect { id, state -> state.hisat2_index }.unique()[0], - bbsplit_index: list.collect { id, state -> state.bbsplit_index }.unique()[0], - skip_bbsplit: list.collect { id, state -> state.skip_bbsplit }.unique()[0], - gencode: list.collect { id, state -> state.gencode }.unique()[0], - biotype: list.collect { id, state -> state.biotype }.unique()[0], - filter_gtf: list.collect { id, state -> state.filter_gtf }.unique()[0], - pseudo_aligner_kmer_size: list.collect { id, state -> state.pseudo_aligner_kmer_size }.unique()[0] ] - ] - } + | map { id, state -> + def biotype = state.gencode ? "gene_type" : state.featurecounts_group_type + def filter_gtf = + ( + ( !state.skip_alignment && state.aligner) // Condition 1: Alignment is required and aligner is set + || ( !state.skip_pseudo_alignment && state.pseudo_aligner ) // Condition 2: Pseudoalignment is required and pseudoaligner is set + || ( !state.transcript_fasta ) // Condition 3: Transcript FASTA file is not provided + ) + && + ( !state.skip_gtf_filter ) // Condition 4: --skip_gtf_filter is not provided + [ id, state + [ biotype: biotype, filter_gtf: filter_gtf ] ] + } + + | toSortedList + + | map { list -> + [ "ref", + [ fasta: list.collect { id, state -> state.fasta }.unique()[0], + gtf: list.collect { id, state -> state.gtf }.unique()[0], + gff: list.collect { id, state -> state.gff }.unique()[0], + additional_fasta: list.collect { id, state -> state.additional_fasta }.unique()[0], + transcript_fasta:list.collect { id, state -> state.transcript_fasta }.unique()[0], + gene_bed: list.collect { id, state -> state.gene_bed }.unique()[0], + bbsplit_fasta_list: list.collect { id, state -> state.bbsplit_fasta_list }.unique()[0], + aligner: list.collect { id, state -> state.aligner }.unique()[0], + pseudo_aligner: list.collect { id, state -> state.pseudo_aligner }.unique()[0], + star_index: list.collect { id, state -> state.star_index }.unique()[0], + rsem_index: list.collect { id, state -> state.rsem_index }.unique()[0], + salmon_index: list.collect { id, state -> state.salmon_index }.unique()[0], + kallisto_index: list.collect { id, state -> state.kallisto_index }.unique()[0], + // splicesites: list.collect { id, state -> state.splicesites }.unique()[0], + // hisat2_index: list.collect { id, state -> state.hisat2_index }.unique()[0], + bbsplit_index: list.collect { id, state -> state.bbsplit_index }.unique()[0], + skip_bbsplit: list.collect { id, state -> state.skip_bbsplit }.unique()[0], + gencode: list.collect { id, state -> state.gencode }.unique()[0], + biotype: list.collect { id, state -> state.biotype }.unique()[0], + filter_gtf: list.collect { id, state -> state.filter_gtf }.unique()[0], + pseudo_aligner_kmer_size: list.collect { id, state -> state.pseudo_aligner_kmer_size }.unique()[0] ] + ] + } - // prepare all the necessary files for reference genome - | prepare_genome.run ( - fromState: [ - "fasta": "fasta", - "gtf": "gtf", - "gff": "gff", - "additional_fasta": "additional_fasta", - "transcript_fasta": "transcript_fasta", - "gene_bed": "gene_bed", - "bbsplit_fasta_list": "bbsplit_fasta_list", - "star_index": "star_index", - "rsem_index": "rsem_index", - "salmon_index": "salmon_index", - "kallisto_index": "kallisto_index", - "pseudo_aligner_kmer_size": "pseudo_aligner_kmer_size", - // "splicesites": "splicesites", - // "hisat2_index": "hisat2_index", - "bbsplit_index": "bbsplit_index", - "skip_bbsplit": "skip_bbsplit", - "gencode": "gencode", - "biotype": "biotype", - "filter_gtf": "filter_gtf", - "aligner": "aligner", - "pseudo_aligner": "pseudo_aligner", - "skip_alignment": "skip_alignment" - ], - toState: [ - "fasta": "uncompressed_fasta", - "gtf": "gtf_uncompressed", - "transcript_fasta": "transcript_fasta_uncompressed", - "fai": "fai", - "chrom_sizes": "chrom_sizes", - "bbsplit_index": "bbsplit_index_uncompressed", - "star_index": "star_index_uncompressed", - "salmon_index": "salmon_index_uncompressed", - "kallisto_index": "kallisto_index_uncompressed", - "gene_bed": "gene_bed_uncompressed" - ] - ) + // prepare all the necessary files for reference genome + | prepare_genome.run ( + fromState: [ + "fasta": "fasta", + "gtf": "gtf", + "gff": "gff", + "additional_fasta": "additional_fasta", + "transcript_fasta": "transcript_fasta", + "gene_bed": "gene_bed", + "bbsplit_fasta_list": "bbsplit_fasta_list", + "star_index": "star_index", + "rsem_index": "rsem_index", + "salmon_index": "salmon_index", + "kallisto_index": "kallisto_index", + "pseudo_aligner_kmer_size": "pseudo_aligner_kmer_size", + // "splicesites": "splicesites", + // "hisat2_index": "hisat2_index", + "bbsplit_index": "bbsplit_index", + "skip_bbsplit": "skip_bbsplit", + "gencode": "gencode", + "biotype": "biotype", + "filter_gtf": "filter_gtf", + "aligner": "aligner", + "pseudo_aligner": "pseudo_aligner", + "skip_alignment": "skip_alignment" + ], + toState: [ + "fasta": "uncompressed_fasta", + "gtf": "gtf_uncompressed", + "transcript_fasta": "transcript_fasta_uncompressed", + "fai": "fai", + "chrom_sizes": "chrom_sizes", + "bbsplit_index": "bbsplit_index_uncompressed", + "star_index": "star_index_uncompressed", + "salmon_index": "salmon_index_uncompressed", + "kallisto_index": "kallisto_index_uncompressed", + "gene_bed": "gene_bed_uncompressed" + ] + ) - // Check if contigs in genome fasta file > 512 Mbp - | map { id, state -> - (isBelowMaxContigSize(state.fai)) ? [id, state] : [id, state + [bam_csi_index: true]] - } + // Check if contigs in genome fasta file > 512 Mbp + // TODO: check where this is required and move if necessary + | map { id, state -> + (isBelowMaxContigSize(state.fai)) ? [id, state] : [id, state + [bam_csi_index: true]] + } - | map { list -> list[1]} + // Pick out the state + | map { list -> list[1]} analysis_ch = input_ch - | combine(reference_ch) + | combine(reference_ch) - | map { list -> [list[0], list[1] + list[2]] } + | map { list -> [list[0], list[1] + list[2]] } - // Concatenate FastQ files from same sample if required - | cat_fastq.run ( - fromState: [ - "read_1": "fastq_1", - "read_2": "fastq_2" - ], - toState: [ - "fastq_1": "fastq_1", - "fastq_2": "fastq_2" - ] - ) + // Concatenate FastQ files from same sample if required + | cat_fastq.run ( + fromState: [ + "read_1": "fastq_1", + "read_2": "fastq_2" + ], + toState: [ + "fastq_1": "fastq_1", + "fastq_2": "fastq_2" + ] + ) - // Pre-process fastq files - | pre_processing.run ( - fromState: [ - "id": "id", - "fastq_1": "fastq_1", - "fastq_2": "fastq_2", - "umitools_bc_pattern": "umitools_bc_pattern", - "umitools_bc_pattern2": "umitools_bc_pattern2", - "strandedness": "strandedness", - "transcript_fasta": "transcript_fasta", - "gtf": "gtf", - "with_umi": "with_umi", - "bbsplit_index": "bbsplit_index", - "bbsplit_fasta_list": "bbsplit_fasta_list", - "bc_pattern": "bc_pattern", - "ribo_database_manifest": "ribo_database_manifest", - "salmon_index": "salmon_index", - "skip_qc": "skip_qc", - "skip_fastqc": "skip_fastqc", - "skip_skip_umi_extract": "skip_umi_extract", - "umi_discard_read": "umi_discard_read", - "skip_trimming": "skip_trimming", - "trimmer": "trimmer", - "skip_bbsplit": "skip_bbsplit", - "remove_ribo_rna": "remove_ribo_rna" - ], - toState: [ + // Pre-process fastq files + | pre_processing.run ( + fromState: [ + "id": "id", + "fastq_1": "fastq_1", + "fastq_2": "fastq_2", + "umitools_bc_pattern": "umitools_bc_pattern", + "umitools_bc_pattern2": "umitools_bc_pattern2", + "strandedness": "strandedness", + "transcript_fasta": "transcript_fasta", + "gtf": "gtf", + "with_umi": "with_umi", + "bbsplit_index": "bbsplit_index", + "bbsplit_fasta_list": "bbsplit_fasta_list", + "bc_pattern": "bc_pattern", + "ribo_database_manifest": "ribo_database_manifest", + "salmon_index": "salmon_index", + "skip_qc": "skip_qc", + "skip_fastqc": "skip_fastqc", + "skip_skip_umi_extract": "skip_umi_extract", + "umi_discard_read": "umi_discard_read", + "skip_trimming": "skip_trimming", + "trimmer": "trimmer", + "skip_bbsplit": "skip_bbsplit", + "remove_ribo_rna": "remove_ribo_rna" + ], + toState: [ + "fastqc_html_1": "fastqc_html_1", + "fastqc_html_2": "fastqc_html_2", + "fastqc_zip_1": "fastqc_zip_1", + "fastqc_zip_2": "fastqc_zip_2", + "fastq_1": "qc_output1", + "fastq_2": "qc_output2", + "trim_log_1": "trim_log_1", + "trim_log_2": "trim_log_2", + "trim_zip_1": "trim_zip_1", + "trim_zip_2": "trim_zip_2", + "trim_html_1": "trim_html_1", + "trim_html_2": "trim_html_2", + "passed_trimmed_reads": "passed_trimmed_reads", + "num_trimmed_reads": "num_trimmed_reads", + "sortmerna_log": "sortmerna_log", + "salmon_quant_output": "salmon_quant_output", + "fastp_failed_trim": "failed_trim", + "fastp_failed_trim_unpaired1": "failed_trim_unpaired1", + "fastp_failed_trim_unpaired2": "failed_trim_unpaired2", + "fastp_trim_json": "trim_json", + "fastp_trim_html": "trim_html", + "fastp_trim_merged_out": "trim_merged_out" + ] + ) + + // Infer strandedness from Salmon pseudo-alignment results + // TODO: Turn this into a workflow step and include as a dependency + | map { id, state -> + (state.strandedness == 'auto') ? + [ id, state + [strandedness: getSalmonInferredStrandedness(state.salmon_quant_output)] ] : + [id, state] + } + + // Filter FastQ files based on minimum trimmed read count after adapter trimming + // TODO: Turn this into a workflow step and include as a dependency + | map { id, state -> + def input = state.fastq_2 ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ] + def num_reads = (state.skip_trimming) ? + state.min_trimmed_reads + 1 : + ( + (state.trimmer == "fastp") ? + getFastpReadsAfterFiltering(state.fastp_trim_json) : + ( + (!state.skip_trimming && input.size() == 2) ? + getTrimGaloreReadsAfterFiltering(state.trim_log_2) : + getTrimGaloreReadsAfterFiltering(state.trim_log_1) + ) + ) + def passed_trimmed_reads = + (state.skip_trimming || (num_reads >= state.min_trimmed_reads)) ? + true : + false + [ id, state + [num_trimmed_reads: num_reads, passed_trimmed_reads: passed_trimmed_reads] ] + } + + // Genome alignment and quantification + | genome_alignment_and_quant.run ( + runIf: { id, state -> !state.skip_alignment && state.passed_trimmed_reads }, + fromState: [ + "id": "id", + "fastq_1": "fastq_1", + "fastq_2": "fastq_2", + "strandedness": "strandedness", + "gtf": "gtf", + "transcript_fasta": "transcript_fasta", + "bam_csi_index": "bam_csi_index", + "aligner": "aligner", + "rsem_index": "rsem_index", + "star_index": "star_index", + "extra_star_align_args": "extra_star_align_args", + "star_ignore_sjdbgtf": "star_ignore_sjdbgtf", + "seq_platform": "seq_platform", + "seq_center": "seq_center", + "with_umi": "with_umi", + "umi_dedup_stats": "umi_dedup_stats", + "gtf_group_features": "gtf_group_features", + "gtf_extra_attributes": "gtf_extra_attributes", + "salmon_quant_libtype": "salmon_quant_libtype", + "salmon_index": "salmon_index", + "extra_rsem_calculate_expression_args": "extra_rsem_calculate_expression_args" + ], + toState: [ + "star_multiqc": "star_multiqc", + "rsem_multiqc": "rsem_multiqc", + "salmon_multiqc": "salmon_multiqc", + "genome_bam_sorted": "genome_bam_sorted", + "genome_bam_index": "genome_bam_index", + "genome_bam_stats": "genome_bam_stats", + "genome_bam_flagstat": "genome_bam_flagstat", + "genome_bam_idxstats": "genome_bam_idxstats", + "transcriptome_bam": "transcriptome_bam", + "transcriptome_bam_index": "transcriptome_bam_index", + "transcriptome_bam_stats": "transcriptome_bam_stats", + "transcriptome_bam_flagstat": "transcriptome_bam_flagstat", + "transcriptome_bam_idxstats": "transcriptome_bam_idxstats", + "quant_out_dir": "quant_out_dir", + "quant_results_file": "quant_results_file", + "rsem_counts_gene": "rsem_counts_gene", + "rsem_counts_transcripts": "rsem_counts_transcripts", + "bam_genome_rsem": "bam_genome_rsem", + "bam_transcript_rsem": "bam_transcript_rsem" + ] + ) + + // Filter channels to get samples that passed STAR minimum mapping percentage + // TODO: Move to reporting or later step + | map { id, state -> + def percent_mapped = (!state.skip_alignment) ? getStarPercentMapped(state.star_multiqc) : 0.0 + def passed_mapping = (percent_mapped >= state.min_mapped_reads) ? true : false + [ id, state + [percent_mapped: percent_mapped, passed_mapping: passed_mapping] ] + } + + // Pseudo-alignment and quantification + | pseudo_alignment_and_quant.run ( + runIf: { id, state -> !state.skip_pseudo_alignment && state.passed_trimmed_reads }, + fromState: [ + "id": "id", + "fastq_1": "fastq_1", + "fastq_2": "fastq_2", + "strandedness": "strandedness", + "gtf": "gtf", + "transcript_fasta": "transcript_fasta", + "pseudo_aligner": "pseudo_aligner", + "salmon_index": "salmon_index", + "kallisto_index": "kallisto_index", + "extra_star_align_args": "extra_star_align_args", + "star_ignore_sjdbgtf": "star_ignore_sjdbgtf", + "seq_platform": "seq_platform", + "seq_center": "seq_center", + "with_umi": "with_umi", + "umi_dedup_stats": "umi_dedup_stats", + "gtf_group_features": "gtf_group_features", + "gtf_extra_attributes": "gtf_extra_attributes", + "lib_type": "salmon_quant_libtype", + "kallisto_quant_fragment_length": "kallisto_quant_fragment_length", + "kallisto_quant_fragment_length_sd": "kallisto_quant_fragment_length_sd" + ], + toState: [ + "pseudo_quant_out_dir": "quant_out_dir", + "pseudo_salmon_quant_results_file": "salmon_quant_results_file", + "pseudo_kallisto_quant_results_file": "kallisto_quant_results_file", + "pseudo_multiqc": "pseudo_multiqc" + ] + ) + + | map { id, state -> + def input = state.fastq_2 ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ] + def paired = input.size() == 2 + [ id, state + [ paired: paired ] ] + } + + // Post-processing + | post_processing.run ( + runIf: { id, state -> !state.skip_alignment && state.passed_trimmed_reads && state.passed_mapping }, + fromState: [ + "id": "id", + "paired": "paired", + "strandedness": "strandedness", + "fasta": "fasta", + "fai": "fai", + "gtf": "gtf", + "genome_bam": "genome_bam_sorted", + "chrom_sizes": "chrom_sizes", + "star_multiqc": "star_multiqc", + "extra_picard_args": "extra_picard_args", + "extra_stringtie_args": "extra_stringtie_args", + "stringtie_ignore_gtf": "stringtie_ignore_gtf", + "extra_bedtools_args": "extra_bedtools_args", + "bam_csi_index": "bam_csi_index", + "min_mapped_reads": "min_mapped_reads", + "with_umi": "with_umi", + "skip_qc": "skip_qc", + "skip_markduplicates": "skip_markduplicates", + "skip_stringtie": "skip_stringtie", + "skip_bigwig":"gencode" + ], + toState: [ + "genome_bam_sorted": "processed_genome_bam", + "genome_bam_index": "genome_bam_index", + "genome_bam_stats": "genome_bam_stats", + "genome_bam_flagstat": "genome_bam_flagstat", + "genome_bam_idxstats": "genome_bam_idxstats", + "markduplicates_metrics": "markduplicates_metrics", + "stringtie_transcript_gtf": "stringtie_transcript_gtf", + "stringtie_coverage_gtf": "stringtie_coverage_gtf", + "stringtie_abundance": "stringtie_abundance", + "stringtie_ballgown": "stringtie_ballgown", + "bedgraph_forward": "bedgraph_forward", + "bedgraph_reverse": "bedgraph_reverse", + "bigwig_forward": "bigwig_forward", + "bigwig_reverse": "bigwig_reverse" + ] + ) + + // Final QC + | quality_control.run ( + fromState: [ + "id": "id", + "paired": "paired", + "strandedness": "strandedness", + "skip_align": "skip_alignment", + "skip_pseudo_align": "skip_pseudo_alignment", + "skip_dupradar": "skip_dupradar", + "skip_qualimap": "skip_qualimap", + "skip_rseqc": "skip_rseqc", + "skip_multiqc": "skip_multiqc", + "skip_preseq": "skip_preseq", + "gtf": "gtf", + "num_trimmed_reads": "num_trimmed_reads", + "passed_trimmed_reads": "passed_trimmed_reads", + "passed_mapping": "passed_mapping", + "percent_mapped": "percent_mapped", + "genome_bam": "genome_bam_sorted", + "genome_bam_index": "genome_bam_index", + "salmon_multiqc": "salmon_multiqc", + "quant_results_file": "quant_results_file", + "rsem_multiqc": "rsem_multiqc", + "rsem_counts_gene": "rsem_counts_gene", + "rsem_counts_transcripts": "rsem_counts_transcripts", + "pseudo_multiqc": "pseudo_multiqc", + "pseudo_quant_out_dir": "pseudo_quant_out_dir", + "pseudo_salmon_quant_results_file": "pseudo_salmon_quant_results_file", + "pseudo_kallisto_quant_results_file": "pseudo_kallisto_quant_results_file", + "aligner": "aligner", + "pseudo_aligner": "pseudo_aligner", + "gene_bed": "gene_bed", + "extra_preseq_args": "extra_preseq_args", + "biotype": "biotype", + "skip_biotype_qc": "skip_biotype_qc", + "featurecounts_group_type": "featurecounts_group_type", + "featurecounts_feature_type": "featurecounts_feature_type", + "gencode": "gencode", + "skip_deseq2_qc": "skip_deseq2_qc", + "deseq2_vst": "deseq2_vst", + "multiqc_custom_config": "multiqc_custom_config", + "multiqc_title": "multiqc_title", + "multiqc_methods_description": "multiqc_methods_description", + "fastqc_zip_1": "fastqc_zip_1", + "fastqc_zip_2": "fastqc_zip_2", + "trim_log_1": "trim_log_1", + "trim_log_2": "trim_log_2", + "trim_zip_1": "trim_zip_1", + "trim_zip_2": "trim_zip_2", + "sortmerna_multiqc": "sortmerna_log", + "star_multiqc": "star_multiqc", + "genome_bam_stats": "genome_bam_stats", + "genome_bam_flagstat": "genome_bam_flagstat", + "genome_bam_idxstats": "genome_bam_idxstats", + "markduplicates_multiqc": "markduplicates_metrics", + "rseqc_modules": "rseqc_modules" + ], + toState: [ + "preseq_output": "preseq_output", + "bamstat_output": "bamstat_output", + "strandedness_output": "strandedness_output", + "inner_dist_output_stats": "inner_dist_output_stats", + "inner_dist_output_dist": "inner_dist_output_dist", + "inner_dist_output_freq": "inner_dist_output_freq", + "inner_dist_output_plot": "inner_dist_output_plot", + "inner_dist_output_plot_r": "inner_dist_output_plot_r", + "junction_annotation_output_log": "junction_annotation_output_log", + "junction_annotation_output_plot_r": "junction_annotation_output_plot_r", + "junction_annotation_output_junction_bed": "junction_annotation_output_junction_bed", + "junction_annotation_output_junction_interact": "junction_annotation_output_junction_interact", + "junction_annotation_output_junction_sheet": "junction_annotation_output_junction_sheet", + "junction_annotation_output_splice_events_plot": "junction_annotation_output_splice_events_plot", + "junction_annotation_output_splice_junctions_plot": "junction_annotation_output_splice_junctions_plot", + "junction_saturation_output_plot_r": "junction_saturation_output_plot_r", + "junction_saturation_output_plot": "junction_saturation_output_plot", + "read_distribution_output": "read_distribution_output", + "read_duplication_output_duplication_rate_plot_r": "read_duplication_output_duplication_rate_plot_r", + "read_duplication_output_duplication_rate_plot": "read_duplication_output_duplication_rate_plot", + "read_duplication_output_duplication_rate_mapping": "read_duplication_output_duplication_rate_mapping", + "read_duplication_output_duplication_rate_sequence": "read_duplication_output_duplication_rate_sequence", + "tin_output_summary": "tin_output_summary", + "tin_output_metrics": "tin_output_metrics", + "dupradar_output_dupmatrix": "dupradar_output_dupmatrix", + "dupradar_output_dup_intercept_mqc": "dupradar_output_dup_intercept_mqc", + "dupradar_output_duprate_exp_boxplot": "dupradar_output_duprate_exp_boxplot", + "dupradar_output_duprate_exp_densplot": "dupradar_output_duprate_exp_densplot", + "dupradar_output_duprate_exp_denscurve_mqc": "dupradar_output_duprate_exp_denscurve_mqc", + "dupradar_output_expression_histogram": "dupradar_output_expression_histogram", + "dupradar_output_intercept_slope": "dupradar_output_intercept_slope", + "qualimap_output_dir": "qualimap_output_dir", + "qualimap_output_pdf": "qualimap_output_pdf", + "featurecounts": "featurecounts", + "featurecounts_summary": "featurecounts_summary", + "featurecounts_multiqc": "featurecounts_multiqc", + "featurecounts_rrna_multiqc": "featurecounts_rrna_multiqc", + "tpm_gene": "tpm_gene", + "counts_gene": "counts_gene", + "counts_gene_length_scaled": "counts_gene_length_scaled", + "counts_gene_scaled": "counts_gene_scaled", + "tpm_transcript": "tpm_transcript", + "counts_transcript": "counts_transcript", + "qunat_merged_summarizedexperiment": "quant_merged_summarizedexperiment", + "deseq2_output": "deseq2_output", + "multiqc_report": "multiqc_report", + "multiqc_data": "multiqc_data", + "multiqc_plots": "multiqc_plots" + ] + ) + + | map { id, state -> + def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() } + [ id, mod_state ] + } + + | setState ( + [ + "output_fasta": "fasta", + "output_gtf": "gtf", + "output_transcript_fasta": "transcript_fasta", + "output_gene_bed": "gene_bed", + "output_bbsplit_index": "bbsplit_index", + "output_star_index": "star_index", + "output_salmon_index": "salmon_index", + "output_kallisto_index": "kallisto_index", "fastqc_html_1": "fastqc_html_1", "fastqc_html_2": "fastqc_html_2", "fastqc_zip_1": "fastqc_zip_1", "fastqc_zip_2": "fastqc_zip_2", - "fastq_1": "qc_output1", - "fastq_2": "qc_output2", + "output_fastq_1": "fastq_1", + "output_fastq_2": "fastq_2", "trim_log_1": "trim_log_1", "trim_log_2": "trim_log_2", "trim_zip_1": "trim_zip_1", "trim_zip_2": "trim_zip_2", "trim_html_1": "trim_html_1", "trim_html_2": "trim_html_2", - "passed_trimmed_reads": "passed_trimmed_reads", - "num_trimmed_reads": "num_trimmed_reads", "sortmerna_log": "sortmerna_log", - "salmon_quant_output": "salmon_quant_output", - "fastp_failed_trim": "failed_trim", - "fastp_failed_trim_unpaired1": "failed_trim_unpaired1", - "fastp_failed_trim_unpaired2": "failed_trim_unpaired2", - "fastp_trim_json": "trim_json", - "fastp_trim_html": "trim_html", - "fastp_trim_merged_out": "trim_merged_out" - ] - ) - - // Infer strandedness from Salmon pseudo-alignment results - | map { id, state -> - (state.strandedness == 'auto') ? - [ id, state + [strandedness: getSalmonInferredStrandedness(state.salmon_quant_output)] ] : - [id, state] - } - - // Filter FastQ files based on minimum trimmed read count after adapter trimming - | map { id, state -> - def input = state.fastq_2 ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ] - def num_reads = (state.skip_trimming) ? - state.min_trimmed_reads + 1 : - ( - (state.trimmer == "fastp") ? - getFastpReadsAfterFiltering(state.fastp_trim_json) : - ( - (!state.skip_trimming && input.size() == 2) ? - getTrimGaloreReadsAfterFiltering(state.trim_log_2) : - getTrimGaloreReadsAfterFiltering(state.trim_log_1) - ) - ) - def passed_trimmed_reads = - (state.skip_trimming || (num_reads >= state.min_trimmed_reads)) ? - true : - false - [ id, state + [num_trimmed_reads: num_reads, passed_trimmed_reads: passed_trimmed_reads] ] - } - - // Genome alignment and quantification - | genome_alignment_and_quant.run ( - runIf: { id, state -> !state.skip_alignment && state.passed_trimmed_reads }, - fromState: [ - "id": "id", - "fastq_1": "fastq_1", - "fastq_2": "fastq_2", - "strandedness": "strandedness", - "gtf": "gtf", - "transcript_fasta": "transcript_fasta", - "bam_csi_index": "bam_csi_index", - "aligner": "aligner", - "rsem_index": "rsem_index", - "star_index": "star_index", - "extra_star_align_args": "extra_star_align_args", - "star_ignore_sjdbgtf": "star_ignore_sjdbgtf", - "seq_platform": "seq_platform", - "seq_center": "seq_center", - "with_umi": "with_umi", - "umi_dedup_stats": "umi_dedup_stats", - "gtf_group_features": "gtf_group_features", - "gtf_extra_attributes": "gtf_extra_attributes", - "salmon_quant_libtype": "salmon_quant_libtype", - "salmon_index": "salmon_index", - "extra_rsem_calculate_expression_args": "extra_rsem_calculate_expression_args" - ], - toState: [ - "star_multiqc": "star_multiqc", - "rsem_multiqc": "rsem_multiqc", - "salmon_multiqc": "salmon_multiqc", + "star_log": "star_multiqc", "genome_bam_sorted": "genome_bam_sorted", "genome_bam_index": "genome_bam_index", "genome_bam_stats": "genome_bam_stats", @@ -231,162 +482,21 @@ workflow run_wf { "transcriptome_bam_stats": "transcriptome_bam_stats", "transcriptome_bam_flagstat": "transcriptome_bam_flagstat", "transcriptome_bam_idxstats": "transcriptome_bam_idxstats", - "quant_out_dir": "quant_out_dir", - "quant_results_file": "quant_results_file", - "rsem_counts_gene": "rsem_counts_gene", - "rsem_counts_transcripts": "rsem_counts_transcripts", - "bam_genome_rsem": "bam_genome_rsem", - "bam_transcript_rsem": "bam_transcript_rsem" - ] - ) - - // Filter channels to get samples that passed STAR minimum mapping percentage - | map { id, state -> - def percent_mapped = (!state.skip_alignment) ? getStarPercentMapped(state.star_multiqc) : 0.0 - def passed_mapping = (percent_mapped >= state.min_mapped_reads) ? true : false - [ id, state + [percent_mapped: percent_mapped, passed_mapping: passed_mapping] ] - } - - // Pseudo-alignment and quantification - | pseudo_alignment_and_quant.run ( - runIf: { id, state -> !state.skip_pseudo_alignment && state.passed_trimmed_reads }, - fromState: [ - "id": "id", - "fastq_1": "fastq_1", - "fastq_2": "fastq_2", - "strandedness": "strandedness", - "gtf": "gtf", - "transcript_fasta": "transcript_fasta", - "pseudo_aligner": "pseudo_aligner", - "salmon_index": "salmon_index", - "kallisto_index": "kallisto_index", - "extra_star_align_args": "extra_star_align_args", - "star_ignore_sjdbgtf": "star_ignore_sjdbgtf", - "seq_platform": "seq_platform", - "seq_center": "seq_center", - "with_umi": "with_umi", - "umi_dedup_stats": "umi_dedup_stats", - "gtf_group_features": "gtf_group_features", - "gtf_extra_attributes": "gtf_extra_attributes", - "lib_type": "salmon_quant_libtype", - "kallisto_quant_fragment_length": "kallisto_quant_fragment_length", - "kallisto_quant_fragment_length_sd": "kallisto_quant_fragment_length_sd" - ], - toState: [ - "pseudo_quant_out_dir": "quant_out_dir", - "pseudo_salmon_quant_results_file": "salmon_quant_results_file", - "pseudo_kallisto_quant_results_file": "kallisto_quant_results_file", - "pseudo_multiqc": "pseudo_multiqc" - ] - ) - - | map { id, state -> - def input = state.fastq_2 ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ] - def paired = input.size() == 2 - [ id, state + [ paired: paired ] ] - } - - // Post-processing - | post_processing.run ( - runIf: { id, state -> !state.skip_alignment && state.passed_trimmed_reads && state.passed_mapping }, - fromState: [ - "id": "id", - "paired": "paired", - "strandedness": "strandedness", - "fasta": "fasta", - "fai": "fai", - "gtf": "gtf", - "genome_bam": "genome_bam_sorted", - "chrom_sizes": "chrom_sizes", - "star_multiqc": "star_multiqc", - "extra_picard_args": "extra_picard_args", - "extra_stringtie_args": "extra_stringtie_args", - "stringtie_ignore_gtf": "stringtie_ignore_gtf", - "extra_bedtools_args": "extra_bedtools_args", - "bam_csi_index": "bam_csi_index", - "min_mapped_reads": "min_mapped_reads", - "with_umi": "with_umi", - "skip_qc": "skip_qc", - "skip_markduplicates": "skip_markduplicates", - "skip_stringtie": "skip_stringtie", - "skip_bigwig":"gencode" - ], - toState: [ - "genome_bam_sorted": "processed_genome_bam", - "genome_bam_index": "genome_bam_index", - "genome_bam_stats": "genome_bam_stats", - "genome_bam_flagstat": "genome_bam_flagstat", - "genome_bam_idxstats": "genome_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", "stringtie_ballgown": "stringtie_ballgown", + "featurecounts": "featurecounts", + "featurecounts_summary": "featurecounts_summary", + "featurecounts_multiqc": "featurecounts_multiqc", + "featurecounts_rrna_multiqc": "featurecounts_rrna_multiqc", "bedgraph_forward": "bedgraph_forward", "bedgraph_reverse": "bedgraph_reverse", "bigwig_forward": "bigwig_forward", - "bigwig_reverse": "bigwig_reverse" - ] - ) - - // Final QC - | quality_control.run ( - fromState: [ - "id": "id", - "paired": "paired", - "strandedness": "strandedness", - "skip_align": "skip_alignment", - "skip_pseudo_align": "skip_pseudo_alignment", - "skip_dupradar": "skip_dupradar", - "skip_qualimap": "skip_qualimap", - "skip_rseqc": "skip_rseqc", - "skip_multiqc": "skip_multiqc", - "skip_preseq": "skip_preseq", - "gtf": "gtf", - "num_trimmed_reads": "num_trimmed_reads", - "passed_trimmed_reads": "passed_trimmed_reads", - "passed_mapping": "passed_mapping", - "percent_mapped": "percent_mapped", - "genome_bam": "genome_bam_sorted", - "genome_bam_index": "genome_bam_index", - "salmon_multiqc": "salmon_multiqc", - "quant_results_file": "quant_results_file", - "rsem_multiqc": "rsem_multiqc", - "rsem_counts_gene": "rsem_counts_gene", - "rsem_counts_transcripts": "rsem_counts_transcripts", - "pseudo_multiqc": "pseudo_multiqc", - "pseudo_quant_out_dir": "pseudo_quant_out_dir", - "pseudo_salmon_quant_results_file": "pseudo_salmon_quant_results_file", - "pseudo_kallisto_quant_results_file": "pseudo_kallisto_quant_results_file", - "aligner": "aligner", - "pseudo_aligner": "pseudo_aligner", - "gene_bed": "gene_bed", - "extra_preseq_args": "extra_preseq_args", - "biotype": "biotype", - "skip_biotype_qc": "skip_biotype_qc", - "featurecounts_group_type": "featurecounts_group_type", - "featurecounts_feature_type": "featurecounts_feature_type", - "gencode": "gencode", - "skip_deseq2_qc": "skip_deseq2_qc", - "deseq2_vst": "deseq2_vst", - "multiqc_custom_config": "multiqc_custom_config", - "multiqc_title": "multiqc_title", - "multiqc_methods_description": "multiqc_methods_description", - "fastqc_zip_1": "fastqc_zip_1", - "fastqc_zip_2": "fastqc_zip_2", - "trim_log_1": "trim_log_1", - "trim_log_2": "trim_log_2", - "trim_zip_1": "trim_zip_1", - "trim_zip_2": "trim_zip_2", - "sortmerna_multiqc": "sortmerna_log", - "star_multiqc": "star_multiqc", - "genome_bam_stats": "genome_bam_stats", - "genome_bam_flagstat": "genome_bam_flagstat", - "genome_bam_idxstats": "genome_bam_idxstats", - "markduplicates_multiqc": "markduplicates_metrics", - "rseqc_modules": "rseqc_modules" - ], - toState: [ + "bigwig_reverse": "bigwig_reverse", "preseq_output": "preseq_output", "bamstat_output": "bamstat_output", "strandedness_output": "strandedness_output", @@ -419,140 +529,33 @@ workflow run_wf { "dupradar_output_expression_histogram": "dupradar_output_expression_histogram", "dupradar_output_intercept_slope": "dupradar_output_intercept_slope", "qualimap_output_dir": "qualimap_output_dir", - "qualimap_output_pdf": "qualimap_output_pdf", - "featurecounts": "featurecounts", - "featurecounts_summary": "featurecounts_summary", - "featurecounts_multiqc": "featurecounts_multiqc", - "featurecounts_rrna_multiqc": "featurecounts_rrna_multiqc", + "qualimap_output_pdf": "qualimap_output_pdf", "tpm_gene": "tpm_gene", "counts_gene": "counts_gene", "counts_gene_length_scaled": "counts_gene_length_scaled", "counts_gene_scaled": "counts_gene_scaled", "tpm_transcript": "tpm_transcript", "counts_transcript": "counts_transcript", - "qunat_merged_summarizedexperiment": "quant_merged_summarizedexperiment", + "quant_merged_summarizedexperiment": "quant_merged_summarizedexperiment", "deseq2_output": "deseq2_output", + "pseudo_tpm_gene": "pseudo_tpm_gene", + "pseudo_counts_gene": "pseudo_counts_gene", + "pseudo_counts_gene_length_scaled": "pseudo_counts_gene_length_scaled", + "pseudo_counts_gene_scaled": "pseudo_counts_gene_scaled", + "pseudo_tpm_transcript": "pseudo_tpm_transcript", + "pseudo_counts_transcript": "pseudo_counts_transcript", + "pseudo_lengths_gene": "pseudo_lengths_gene", + "pseudo_lengths_transcript": "pseudo_lengths_transcript", + "pseudo_quant_merged_summarizedexperiment": "pseudo_quant_merged_summarizedexperiment", + "deseq2_output_pseudo": "deseq2_output_pseudo", "multiqc_report": "multiqc_report", "multiqc_data": "multiqc_data", "multiqc_plots": "multiqc_plots" - ] - ) - - | map { id, state -> - def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() } - [ id, mod_state ] - } - - | setState ( - [ - "output_fasta": "fasta", - "output_gtf": "gtf", - "output_transcript_fasta": "transcript_fasta", - "output_gene_bed": "gene_bed", - "output_bbsplit_index": "bbsplit_index", - "output_star_index": "star_index", - "output_salmon_index": "salmon_index", - "output_kallisto_index": "kallisto_index", - "fastqc_html_1": "fastqc_html_1", - "fastqc_html_2": "fastqc_html_2", - "fastqc_zip_1": "fastqc_zip_1", - "fastqc_zip_2": "fastqc_zip_2", - "output_fastq_1": "fastq_1", - "output_fastq_2": "fastq_2", - "trim_log_1": "trim_log_1", - "trim_log_2": "trim_log_2", - "trim_zip_1": "trim_zip_1", - "trim_zip_2": "trim_zip_2", - "trim_html_1": "trim_html_1", - "trim_html_2": "trim_html_2", - "sortmerna_log": "sortmerna_log", - "star_log": "star_multiqc", - "genome_bam_sorted": "genome_bam_sorted", - "genome_bam_index": "genome_bam_index", - "genome_bam_stats": "genome_bam_stats", - "genome_bam_flagstat": "genome_bam_flagstat", - "genome_bam_idxstats": "genome_bam_idxstats", - "transcriptome_bam": "transcriptome_bam", - "transcriptome_bam_index": "transcriptome_bam_index", - "transcriptome_bam_stats": "transcriptome_bam_stats", - "transcriptome_bam_flagstat": "transcriptome_bam_flagstat", - "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", - "stringtie_ballgown": "stringtie_ballgown", - "featurecounts": "featurecounts", - "featurecounts_summary": "featurecounts_summary", - "featurecounts_multiqc": "featurecounts_multiqc", - "featurecounts_rrna_multiqc": "featurecounts_rrna_multiqc", - "bedgraph_forward": "bedgraph_forward", - "bedgraph_reverse": "bedgraph_reverse", - "bigwig_forward": "bigwig_forward", - "bigwig_reverse": "bigwig_reverse", - "preseq_output": "preseq_output", - "bamstat_output": "bamstat_output", - "strandedness_output": "strandedness_output", - "inner_dist_output_stats": "inner_dist_output_stats", - "inner_dist_output_dist": "inner_dist_output_dist", - "inner_dist_output_freq": "inner_dist_output_freq", - "inner_dist_output_plot": "inner_dist_output_plot", - "inner_dist_output_plot_r": "inner_dist_output_plot_r", - "junction_annotation_output_log": "junction_annotation_output_log", - "junction_annotation_output_plot_r": "junction_annotation_output_plot_r", - "junction_annotation_output_junction_bed": "junction_annotation_output_junction_bed", - "junction_annotation_output_junction_interact": "junction_annotation_output_junction_interact", - "junction_annotation_output_junction_sheet": "junction_annotation_output_junction_sheet", - "junction_annotation_output_splice_events_plot": "junction_annotation_output_splice_events_plot", - "junction_annotation_output_splice_junctions_plot": "junction_annotation_output_splice_junctions_plot", - "junction_saturation_output_plot_r": "junction_saturation_output_plot_r", - "junction_saturation_output_plot": "junction_saturation_output_plot", - "read_distribution_output": "read_distribution_output", - "read_duplication_output_duplication_rate_plot_r": "read_duplication_output_duplication_rate_plot_r", - "read_duplication_output_duplication_rate_plot": "read_duplication_output_duplication_rate_plot", - "read_duplication_output_duplication_rate_mapping": "read_duplication_output_duplication_rate_mapping", - "read_duplication_output_duplication_rate_sequence": "read_duplication_output_duplication_rate_sequence", - "tin_output_summary": "tin_output_summary", - "tin_output_metrics": "tin_output_metrics", - "dupradar_output_dupmatrix": "dupradar_output_dupmatrix", - "dupradar_output_dup_intercept_mqc": "dupradar_output_dup_intercept_mqc", - "dupradar_output_duprate_exp_boxplot": "dupradar_output_duprate_exp_boxplot", - "dupradar_output_duprate_exp_densplot": "dupradar_output_duprate_exp_densplot", - "dupradar_output_duprate_exp_denscurve_mqc": "dupradar_output_duprate_exp_denscurve_mqc", - "dupradar_output_expression_histogram": "dupradar_output_expression_histogram", - "dupradar_output_intercept_slope": "dupradar_output_intercept_slope", - "qualimap_output_dir": "qualimap_output_dir", - "qualimap_output_pdf": "qualimap_output_pdf", - "tpm_gene": "tpm_gene", - "counts_gene": "counts_gene", - "counts_gene_length_scaled": "counts_gene_length_scaled", - "counts_gene_scaled": "counts_gene_scaled", - "tpm_transcript": "tpm_transcript", - "counts_transcript": "counts_transcript", - "quant_merged_summarizedexperiment": "quant_merged_summarizedexperiment", - "deseq2_output": "deseq2_output", - "pseudo_tpm_gene": "pseudo_tpm_gene", - "pseudo_counts_gene": "pseudo_counts_gene", - "pseudo_counts_gene_length_scaled": "pseudo_counts_gene_length_scaled", - "pseudo_counts_gene_scaled": "pseudo_counts_gene_scaled", - "pseudo_tpm_transcript": "pseudo_tpm_transcript", - "pseudo_counts_transcript": "pseudo_counts_transcript", - "pseudo_lengths_gene": "pseudo_lengths_gene", - "pseudo_lengths_transcript": "pseudo_lengths_transcript", - "pseudo_quant_merged_summarizedexperiment": "pseudo_quant_merged_summarizedexperiment", - "deseq2_output_pseudo": "deseq2_output_pseudo", - "multiqc_report": "multiqc_report", - "multiqc_data": "multiqc_data", - "multiqc_plots": "multiqc_plots" - ] - ) - - output_ch = analysis_ch + ] + ) emit: - output_ch + analysis_ch } import nextflow.Nextflow diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/fastp/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/main/nextflow/fastp/.config.vsh.yaml index b53bd35..b114c3b 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/fastp/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/fastp/.config.vsh.yaml @@ -1083,9 +1083,9 @@ build_info: output: "target/nextflow/fastp" executable: "target/nextflow/fastp/main.nf" viash_version: "0.9.0" - git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9" - git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox" - git_tag: "v0.2.0-25-g065297b" + git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" + git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" + git_tag: "v0.2.0-26-ga13b57d" package_config: name: "biobox" version: "main" diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/fastp/main.nf b/target/dependencies/vsh/vsh/biobox/main/nextflow/fastp/main.nf index 8302aa1..9075708 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/fastp/main.nf +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/fastp/main.nf @@ -4023,9 +4023,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/fastp", "viash_version" : "0.9.0", - "git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9", - "git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-25-g065297b" + "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", + "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-26-ga13b57d" }, "package_config" : { "name" : "biobox", diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts/.config.vsh.yaml index 0b4a6e0..37865fe 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts/.config.vsh.yaml @@ -645,9 +645,9 @@ build_info: output: "target/nextflow/featurecounts" executable: "target/nextflow/featurecounts/main.nf" viash_version: "0.9.0" - git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9" - git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox" - git_tag: "v0.2.0-25-g065297b" + git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" + git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" + git_tag: "v0.2.0-26-ga13b57d" package_config: name: "biobox" version: "main" diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts/main.nf b/target/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts/main.nf index 042bf2b..6db06cc 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts/main.nf +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts/main.nf @@ -3549,9 +3549,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/featurecounts", "viash_version" : "0.9.0", - "git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9", - "git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-25-g065297b" + "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", + "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-26-ga13b57d" }, "package_config" : { "name" : "biobox", diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/gffread/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/main/nextflow/gffread/.config.vsh.yaml index a6b5707..90eb2f2 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/gffread/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/gffread/.config.vsh.yaml @@ -685,9 +685,9 @@ build_info: output: "target/nextflow/gffread" executable: "target/nextflow/gffread/main.nf" viash_version: "0.9.0" - git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9" - git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox" - git_tag: "v0.2.0-25-g065297b" + git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" + git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" + git_tag: "v0.2.0-26-ga13b57d" package_config: name: "biobox" version: "main" diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/gffread/main.nf b/target/dependencies/vsh/vsh/biobox/main/nextflow/gffread/main.nf index e0a1764..9c3fc68 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/gffread/main.nf +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/gffread/main.nf @@ -3606,9 +3606,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/gffread", "viash_version" : "0.9.0", - "git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9", - "git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-25-g065297b" + "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", + "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-26-ga13b57d" }, "package_config" : { "name" : "biobox", diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc/.config.vsh.yaml index 7d5d881..eddcbae 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc/.config.vsh.yaml @@ -456,9 +456,9 @@ build_info: output: "target/nextflow/multiqc" executable: "target/nextflow/multiqc/main.nf" viash_version: "0.9.0" - git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9" - git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox" - git_tag: "v0.2.0-25-g065297b" + git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" + git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" + git_tag: "v0.2.0-26-ga13b57d" package_config: name: "biobox" version: "main" diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc/main.nf b/target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc/main.nf index 026c331..9abc618 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc/main.nf +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc/main.nf @@ -3366,9 +3366,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/multiqc", "viash_version" : "0.9.0", - "git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9", - "git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-25-g065297b" + "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", + "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-26-ga13b57d" }, "package_config" : { "name" : "biobox", diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml index e7ab701..b77ed36 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml @@ -416,9 +416,9 @@ build_info: output: "target/nextflow/rsem/rsem_prepare_reference" executable: "target/nextflow/rsem/rsem_prepare_reference/main.nf" viash_version: "0.9.0" - git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9" - git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox" - git_tag: "v0.2.0-25-g065297b" + git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" + git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" + git_tag: "v0.2.0-26-ga13b57d" package_config: name: "biobox" version: "main" diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/main.nf b/target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/main.nf index 610b611..01da680 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/main.nf +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/main.nf @@ -3245,9 +3245,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/rsem/rsem_prepare_reference", "viash_version" : "0.9.0", - "git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9", - "git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-25-g065297b" + "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", + "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-26-ga13b57d" }, "package_config" : { "name" : "biobox", diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/.config.vsh.yaml index ee479fc..9426bd8 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/.config.vsh.yaml @@ -277,9 +277,9 @@ build_info: output: "target/nextflow/salmon/salmon_index" executable: "target/nextflow/salmon/salmon_index/main.nf" viash_version: "0.9.0" - git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9" - git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox" - git_tag: "v0.2.0-25-g065297b" + git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" + git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" + git_tag: "v0.2.0-26-ga13b57d" package_config: name: "biobox" version: "main" diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/main.nf b/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/main.nf index 69eec34..66caf72 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/main.nf +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/main.nf @@ -3129,9 +3129,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/salmon/salmon_index", "viash_version" : "0.9.0", - "git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9", - "git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-25-g065297b" + "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", + "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-26-ga13b57d" }, "package_config" : { "name" : "biobox", diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/.config.vsh.yaml index 1ca63e7..1f7058a 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/.config.vsh.yaml @@ -1173,9 +1173,9 @@ build_info: output: "target/nextflow/salmon/salmon_quant" executable: "target/nextflow/salmon/salmon_quant/main.nf" viash_version: "0.9.0" - git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9" - git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox" - git_tag: "v0.2.0-25-g065297b" + git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" + git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" + git_tag: "v0.2.0-26-ga13b57d" package_config: name: "biobox" version: "main" diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/main.nf b/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/main.nf index df9d30c..21999e3a 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/main.nf +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/main.nf @@ -3964,9 +3964,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/salmon/salmon_quant", "viash_version" : "0.9.0", - "git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9", - "git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-25-g065297b" + "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", + "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-26-ga13b57d" }, "package_config" : { "name" : "biobox", diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/.config.vsh.yaml index 249982e..4efc0e0 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/.config.vsh.yaml @@ -173,9 +173,9 @@ build_info: output: "target/nextflow/samtools/samtools_flagstat" executable: "target/nextflow/samtools/samtools_flagstat/main.nf" viash_version: "0.9.0" - git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9" - git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox" - git_tag: "v0.2.0-25-g065297b" + git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" + git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" + git_tag: "v0.2.0-26-ga13b57d" package_config: name: "biobox" version: "main" diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/main.nf b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/main.nf index 4c4395c..b637167 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/main.nf +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/main.nf @@ -3028,9 +3028,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_flagstat", "viash_version" : "0.9.0", - "git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9", - "git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-25-g065297b" + "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", + "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-26-ga13b57d" }, "package_config" : { "name" : "biobox", diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/.config.vsh.yaml index bbad56a..5bc8c43 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/.config.vsh.yaml @@ -183,9 +183,9 @@ build_info: output: "target/nextflow/samtools/samtools_idxstats" executable: "target/nextflow/samtools/samtools_idxstats/main.nf" viash_version: "0.9.0" - git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9" - git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox" - git_tag: "v0.2.0-25-g065297b" + git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" + git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" + git_tag: "v0.2.0-26-ga13b57d" package_config: name: "biobox" version: "main" diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/main.nf b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/main.nf index 60fb848..86aa0a2 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/main.nf +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/main.nf @@ -3040,9 +3040,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_idxstats", "viash_version" : "0.9.0", - "git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9", - "git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-25-g065297b" + "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", + "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-26-ga13b57d" }, "package_config" : { "name" : "biobox", diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index/.config.vsh.yaml index 6f0ef1b..7c6beaa 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index/.config.vsh.yaml @@ -189,9 +189,9 @@ build_info: output: "target/nextflow/samtools/samtools_index" executable: "target/nextflow/samtools/samtools_index/main.nf" viash_version: "0.9.0" - git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9" - git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox" - git_tag: "v0.2.0-25-g065297b" + git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" + git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" + git_tag: "v0.2.0-26-ga13b57d" package_config: name: "biobox" version: "main" diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index/main.nf b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index/main.nf index 7a857ef..210ff4b 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index/main.nf +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index/main.nf @@ -3053,9 +3053,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_index", "viash_version" : "0.9.0", - "git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9", - "git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-25-g065297b" + "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", + "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-26-ga13b57d" }, "package_config" : { "name" : "biobox", diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/.config.vsh.yaml index e6b54dd..4933b68 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/.config.vsh.yaml @@ -332,9 +332,9 @@ build_info: output: "target/nextflow/samtools/samtools_sort" executable: "target/nextflow/samtools/samtools_sort/main.nf" viash_version: "0.9.0" - git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9" - git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox" - git_tag: "v0.2.0-25-g065297b" + git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" + git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" + git_tag: "v0.2.0-26-ga13b57d" package_config: name: "biobox" version: "main" diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/main.nf b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/main.nf index b488127..b48f412 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/main.nf +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/main.nf @@ -3225,9 +3225,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_sort", "viash_version" : "0.9.0", - "git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9", - "git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-25-g065297b" + "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", + "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-26-ga13b57d" }, "package_config" : { "name" : "biobox", diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/.config.vsh.yaml index 8d001b6..90ed44a 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/.config.vsh.yaml @@ -401,9 +401,9 @@ build_info: output: "target/nextflow/samtools/samtools_stats" executable: "target/nextflow/samtools/samtools_stats/main.nf" viash_version: "0.9.0" - git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9" - git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox" - git_tag: "v0.2.0-25-g065297b" + git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" + git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" + git_tag: "v0.2.0-26-ga13b57d" package_config: name: "biobox" version: "main" diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/main.nf b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/main.nf index 4b5e55e..4faeaa1 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/main.nf +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/main.nf @@ -3295,9 +3295,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_stats", "viash_version" : "0.9.0", - "git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9", - "git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-25-g065297b" + "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", + "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-26-ga13b57d" }, "package_config" : { "name" : "biobox", diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads/.config.vsh.yaml index 6f32935..2723c12 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads/.config.vsh.yaml @@ -2663,9 +2663,9 @@ build_info: output: "target/nextflow/star/star_align_reads" executable: "target/nextflow/star/star_align_reads/main.nf" viash_version: "0.9.0" - git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9" - git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox" - git_tag: "v0.2.0-25-g065297b" + git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" + git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" + git_tag: "v0.2.0-26-ga13b57d" package_config: name: "biobox" version: "main" diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads/main.nf b/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads/main.nf index 616db3a..8057868 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads/main.nf +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads/main.nf @@ -5943,9 +5943,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/star/star_align_reads", "viash_version" : "0.9.0", - "git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9", - "git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-25-g065297b" + "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", + "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-26-ga13b57d" }, "package_config" : { "name" : "biobox", diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate/.config.vsh.yaml index 627bc7c..288d0cf 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate/.config.vsh.yaml @@ -333,9 +333,9 @@ build_info: output: "target/nextflow/star/star_genome_generate" executable: "target/nextflow/star/star_genome_generate/main.nf" viash_version: "0.9.0" - git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9" - git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox" - git_tag: "v0.2.0-25-g065297b" + git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" + git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" + git_tag: "v0.2.0-26-ga13b57d" package_config: name: "biobox" version: "main" diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate/main.nf b/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate/main.nf index 6f611a2..72211a4 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate/main.nf +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate/main.nf @@ -3195,9 +3195,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/star/star_genome_generate", "viash_version" : "0.9.0", - "git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9", - "git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-25-g065297b" + "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", + "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-26-ga13b57d" }, "package_config" : { "name" : "biobox", diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml index b9087e1..2a04ee4 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml @@ -434,9 +434,9 @@ build_info: output: "target/nextflow/umi_tools/umi_tools_extract" executable: "target/nextflow/umi_tools/umi_tools_extract/main.nf" viash_version: "0.9.0" - git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9" - git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox" - git_tag: "v0.2.0-25-g065297b" + git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" + git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" + git_tag: "v0.2.0-26-ga13b57d" package_config: name: "biobox" version: "main" diff --git a/target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/main.nf b/target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/main.nf index 89c8780..c392b78 100644 --- a/target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/main.nf +++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/main.nf @@ -3299,9 +3299,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/umi_tools/umi_tools_extract", "viash_version" : "0.9.0", - "git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9", - "git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-25-g065297b" + "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", + "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-26-ga13b57d" }, "package_config" : { "name" : "biobox", diff --git a/target/executable/bbmap_bbsplit/.config.vsh.yaml b/target/executable/bbmap_bbsplit/.config.vsh.yaml index 53e4405..91b92e8 100644 --- a/target/executable/bbmap_bbsplit/.config.vsh.yaml +++ b/target/executable/bbmap_bbsplit/.config.vsh.yaml @@ -246,8 +246,8 @@ build_info: output: "target/executable/bbmap_bbsplit" executable: "target/executable/bbmap_bbsplit/bbmap_bbsplit" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/bbmap_bbsplit/bbmap_bbsplit b/target/executable/bbmap_bbsplit/bbmap_bbsplit index 0690ed7..1d7a1dd 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="2024-11-18T16:13:12Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:13Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/bedtools_genomecov/.config.vsh.yaml b/target/executable/bedtools_genomecov/.config.vsh.yaml index 1f05257..62d1432 100644 --- a/target/executable/bedtools_genomecov/.config.vsh.yaml +++ b/target/executable/bedtools_genomecov/.config.vsh.yaml @@ -186,8 +186,8 @@ build_info: output: "target/executable/bedtools_genomecov" executable: "target/executable/bedtools_genomecov/bedtools_genomecov" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/bedtools_genomecov/bedtools_genomecov b/target/executable/bedtools_genomecov/bedtools_genomecov index effca96..e6a6b9f 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="2024-11-18T16:13:11Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:11Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/cat_additional_fasta/.config.vsh.yaml b/target/executable/cat_additional_fasta/.config.vsh.yaml index 15e9258..53f5fe5 100644 --- a/target/executable/cat_additional_fasta/.config.vsh.yaml +++ b/target/executable/cat_additional_fasta/.config.vsh.yaml @@ -190,8 +190,8 @@ build_info: output: "target/executable/cat_additional_fasta" executable: "target/executable/cat_additional_fasta/cat_additional_fasta" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/cat_additional_fasta/cat_additional_fasta b/target/executable/cat_additional_fasta/cat_additional_fasta index 0125678..9f0f250 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="2024-11-18T16:13:10Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:10Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/cat_fastq/.config.vsh.yaml b/target/executable/cat_fastq/.config.vsh.yaml index 8092edd..07d5059 100644 --- a/target/executable/cat_fastq/.config.vsh.yaml +++ b/target/executable/cat_fastq/.config.vsh.yaml @@ -177,8 +177,8 @@ build_info: output: "target/executable/cat_fastq" executable: "target/executable/cat_fastq/cat_fastq" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/cat_fastq/cat_fastq b/target/executable/cat_fastq/cat_fastq index 60afddc..47bc629 100755 --- a/target/executable/cat_fastq/cat_fastq +++ b/target/executable/cat_fastq/cat_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="2024-11-18T16:13:09Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:10Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/deseq2_qc/.config.vsh.yaml b/target/executable/deseq2_qc/.config.vsh.yaml index 8108cee..45ab699 100644 --- a/target/executable/deseq2_qc/.config.vsh.yaml +++ b/target/executable/deseq2_qc/.config.vsh.yaml @@ -245,8 +245,8 @@ build_info: output: "target/executable/deseq2_qc" executable: "target/executable/deseq2_qc/deseq2_qc" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/deseq2_qc/deseq2_qc b/target/executable/deseq2_qc/deseq2_qc index d3eaafa..c51e192 100755 --- a/target/executable/deseq2_qc/deseq2_qc +++ b/target/executable/deseq2_qc/deseq2_qc @@ -506,9 +506,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag Rscript -e 'remotes::install_cran(c("optparse", "ggplot2", "RColorBrewer", "pheatmap", "stringr", "matrixStats"), repos = "https://cran.rstudio.com")' LABEL org.opencontainers.image.description="Companion container for running component deseq2_qc" -LABEL org.opencontainers.image.created="2024-11-18T16:13:11Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:12Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/dupradar/.config.vsh.yaml b/target/executable/dupradar/.config.vsh.yaml index f0296e3..829c456 100644 --- a/target/executable/dupradar/.config.vsh.yaml +++ b/target/executable/dupradar/.config.vsh.yaml @@ -274,8 +274,8 @@ build_info: output: "target/executable/dupradar" executable: "target/executable/dupradar/dupradar" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/dupradar/dupradar b/target/executable/dupradar/dupradar index 235386e..3f4294b 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="2024-11-18T16:13:11Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:12Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/fastqc/.config.vsh.yaml b/target/executable/fastqc/.config.vsh.yaml index 7532254..8840568 100644 --- a/target/executable/fastqc/.config.vsh.yaml +++ b/target/executable/fastqc/.config.vsh.yaml @@ -206,8 +206,8 @@ build_info: output: "target/executable/fastqc" executable: "target/executable/fastqc/fastqc" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/fastqc/fastqc b/target/executable/fastqc/fastqc index 7e0f1fe..4899c4f 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="2024-11-18T16:13:14Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:14Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/fq_subsample/.config.vsh.yaml b/target/executable/fq_subsample/.config.vsh.yaml index 9f515b5..90f3c1a 100644 --- a/target/executable/fq_subsample/.config.vsh.yaml +++ b/target/executable/fq_subsample/.config.vsh.yaml @@ -185,8 +185,8 @@ build_info: output: "target/executable/fq_subsample" executable: "target/executable/fq_subsample/fq_subsample" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/fq_subsample/fq_subsample b/target/executable/fq_subsample/fq_subsample index f66121d..e89094c 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="2024-11-18T16:13:12Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:13Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/getchromsizes/.config.vsh.yaml b/target/executable/getchromsizes/.config.vsh.yaml index dfe4849..5382657 100644 --- a/target/executable/getchromsizes/.config.vsh.yaml +++ b/target/executable/getchromsizes/.config.vsh.yaml @@ -175,8 +175,8 @@ build_info: output: "target/executable/getchromsizes" executable: "target/executable/getchromsizes/getchromsizes" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/getchromsizes/getchromsizes b/target/executable/getchromsizes/getchromsizes index 686e078..3a7f330 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="2024-11-18T16:13:10Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:11Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/gtf2bed/.config.vsh.yaml b/target/executable/gtf2bed/.config.vsh.yaml index d954250..88d8523 100644 --- a/target/executable/gtf2bed/.config.vsh.yaml +++ b/target/executable/gtf2bed/.config.vsh.yaml @@ -153,8 +153,8 @@ build_info: output: "target/executable/gtf2bed" executable: "target/executable/gtf2bed/gtf2bed" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/gtf2bed/gtf2bed b/target/executable/gtf2bed/gtf2bed index 436fe06..43c1924 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="2024-11-18T16:13:12Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:12Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/gtf_filter/.config.vsh.yaml b/target/executable/gtf_filter/.config.vsh.yaml index 0f49378..9950d50 100644 --- a/target/executable/gtf_filter/.config.vsh.yaml +++ b/target/executable/gtf_filter/.config.vsh.yaml @@ -163,8 +163,8 @@ build_info: output: "target/executable/gtf_filter" executable: "target/executable/gtf_filter/gtf_filter" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/gtf_filter/gtf_filter b/target/executable/gtf_filter/gtf_filter index eaaa28f..d000deb 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="2024-11-18T16:13:10Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:11Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/gunzip/.config.vsh.yaml b/target/executable/gunzip/.config.vsh.yaml index 3ebf8d4..c093efe 100644 --- a/target/executable/gunzip/.config.vsh.yaml +++ b/target/executable/gunzip/.config.vsh.yaml @@ -152,8 +152,8 @@ build_info: output: "target/executable/gunzip" executable: "target/executable/gunzip/gunzip" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/gunzip/gunzip b/target/executable/gunzip/gunzip index 53032c5..ffada2b 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="2024-11-18T16:13:06Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:07Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/kallisto/kallisto_index/.config.vsh.yaml b/target/executable/kallisto/kallisto_index/.config.vsh.yaml index c96b360..8cf6286 100644 --- a/target/executable/kallisto/kallisto_index/.config.vsh.yaml +++ b/target/executable/kallisto/kallisto_index/.config.vsh.yaml @@ -163,8 +163,8 @@ build_info: output: "target/executable/kallisto/kallisto_index" executable: "target/executable/kallisto/kallisto_index/kallisto_index" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/kallisto/kallisto_index/kallisto_index b/target/executable/kallisto/kallisto_index/kallisto_index index 4bd62f0..a055752 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="2024-11-18T16:13:06Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:07Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml index 974ead8..16f50be 100644 --- a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml +++ b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml @@ -261,8 +261,8 @@ build_info: output: "target/executable/kallisto/kallisto_quant" executable: "target/executable/kallisto/kallisto_quant/kallisto_quant" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/kallisto/kallisto_quant/kallisto_quant b/target/executable/kallisto/kallisto_quant/kallisto_quant index 85fcda5..d0188b3 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="2024-11-18T16:13:07Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:07Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/multiqc_custom_biotype/.config.vsh.yaml b/target/executable/multiqc_custom_biotype/.config.vsh.yaml index c9c89aa..825fe2d 100644 --- a/target/executable/multiqc_custom_biotype/.config.vsh.yaml +++ b/target/executable/multiqc_custom_biotype/.config.vsh.yaml @@ -169,8 +169,8 @@ build_info: output: "target/executable/multiqc_custom_biotype" executable: "target/executable/multiqc_custom_biotype/multiqc_custom_biotype" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/multiqc_custom_biotype/multiqc_custom_biotype b/target/executable/multiqc_custom_biotype/multiqc_custom_biotype index 2bc932a..2d844cb 100755 --- a/target/executable/multiqc_custom_biotype/multiqc_custom_biotype +++ b/target/executable/multiqc_custom_biotype/multiqc_custom_biotype @@ -476,9 +476,9 @@ function ViashDockerfile { FROM python:latest ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component multiqc_custom_biotype" -LABEL org.opencontainers.image.created="2024-11-18T16:13:09Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:10Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/picard_markduplicates/.config.vsh.yaml b/target/executable/picard_markduplicates/.config.vsh.yaml index e1ea540..0a72d82 100644 --- a/target/executable/picard_markduplicates/.config.vsh.yaml +++ b/target/executable/picard_markduplicates/.config.vsh.yaml @@ -215,8 +215,8 @@ build_info: output: "target/executable/picard_markduplicates" executable: "target/executable/picard_markduplicates/picard_markduplicates" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/picard_markduplicates/picard_markduplicates b/target/executable/picard_markduplicates/picard_markduplicates index aacb1f5..e2930e1 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="2024-11-18T16:13:08Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:09Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/prepare_multiqc_input/.config.vsh.yaml b/target/executable/prepare_multiqc_input/.config.vsh.yaml index 8c7d766..5f4dfca 100644 --- a/target/executable/prepare_multiqc_input/.config.vsh.yaml +++ b/target/executable/prepare_multiqc_input/.config.vsh.yaml @@ -417,8 +417,8 @@ build_info: output: "target/executable/prepare_multiqc_input" executable: "target/executable/prepare_multiqc_input/prepare_multiqc_input" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/prepare_multiqc_input/prepare_multiqc_input b/target/executable/prepare_multiqc_input/prepare_multiqc_input index 0f6e0b5..26ad0f3 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="2024-11-18T16:13:04Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:05Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml b/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml index 06ef750..f2045b6 100644 --- a/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml +++ b/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml @@ -146,8 +146,8 @@ build_info: output: "target/executable/preprocess_transcripts_fasta" executable: "target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta b/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta index 35a9175..2499c32 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="2024-11-18T16:13:08Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:09Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/preseq_lcextrap/.config.vsh.yaml b/target/executable/preseq_lcextrap/.config.vsh.yaml index 946de61..9750805 100644 --- a/target/executable/preseq_lcextrap/.config.vsh.yaml +++ b/target/executable/preseq_lcextrap/.config.vsh.yaml @@ -199,8 +199,8 @@ build_info: output: "target/executable/preseq_lcextrap" executable: "target/executable/preseq_lcextrap/preseq_lcextrap" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/preseq_lcextrap/preseq_lcextrap b/target/executable/preseq_lcextrap/preseq_lcextrap index f8d3032..cb13a39 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="2024-11-18T16:13:08Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:08Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/qualimap/.config.vsh.yaml b/target/executable/qualimap/.config.vsh.yaml index a9b5e2e..a1e8c09 100644 --- a/target/executable/qualimap/.config.vsh.yaml +++ b/target/executable/qualimap/.config.vsh.yaml @@ -279,8 +279,8 @@ build_info: output: "target/executable/qualimap" executable: "target/executable/qualimap/qualimap" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/qualimap/qualimap b/target/executable/qualimap/qualimap index dd07738..78cb630 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="2024-11-18T16:13:06Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:06Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml b/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml index a457237..8bcbbcc 100644 --- a/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml +++ b/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml @@ -307,8 +307,8 @@ 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: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression b/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression index 0199e68..e40c5ab 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="2024-11-18T16:13:05Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:06Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml b/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml index 590a7f9..6ff9484 100644 --- a/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml +++ b/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml @@ -190,8 +190,8 @@ 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: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/rsem/rsem_merge_counts/rsem_merge_counts b/target/executable/rsem/rsem_merge_counts/rsem_merge_counts index bebe914..5ffbac9 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="2024-11-18T16:13:05Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:06Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml b/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml index 2d84715..eabb9ce 100644 --- a/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml @@ -171,8 +171,8 @@ build_info: output: "target/executable/rseqc/rseqc_bamstat" executable: "target/executable/rseqc/rseqc_bamstat/rseqc_bamstat" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat b/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat index 5f088a4..8666480 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="2024-11-18T16:13:10Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:10Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml b/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml index 173d944..8c91d03 100644 --- a/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml @@ -194,8 +194,8 @@ build_info: output: "target/executable/rseqc/rseqc_inferexperiment" executable: "target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment b/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment index ccc612b..0a6d25e 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="2024-11-18T16:13:11Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:12Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml b/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml index 9e899fc..c5b5fe6 100644 --- a/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml @@ -280,8 +280,8 @@ build_info: output: "target/executable/rseqc/rseqc_innerdistance" executable: "target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance b/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance index a4a0805..f67635f 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="2024-11-18T16:13:09Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:10Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml b/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml index b79c85b..f65e2da 100644 --- a/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml @@ -268,8 +268,8 @@ build_info: output: "target/executable/rseqc/rseqc_junctionannotation" executable: "target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation b/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation index 165fb59..4512dc3 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="2024-11-18T16:13:09Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:10Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml b/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml index b41fe60..21d3a60 100644 --- a/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml @@ -257,8 +257,8 @@ build_info: output: "target/executable/rseqc/rseqc_junctionsaturation" executable: "target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation b/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation index ab20ea6..f78515f 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="2024-11-18T16:13:10Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:11Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml b/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml index 99e1ae2..91e4e20 100644 --- a/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml @@ -170,8 +170,8 @@ build_info: output: "target/executable/rseqc/rseqc_readdistribution" executable: "target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution b/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution index 43f2ef0..debdf77 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="2024-11-18T16:13:10Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:11Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml b/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml index 8af64ef..deb6d29 100644 --- a/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml @@ -219,8 +219,8 @@ build_info: output: "target/executable/rseqc/rseqc_readduplication" executable: "target/executable/rseqc/rseqc_readduplication/rseqc_readduplication" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication b/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication index 620fac1..224d9df 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="2024-11-18T16:13:09Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:09Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_tin/.config.vsh.yaml b/target/executable/rseqc/rseqc_tin/.config.vsh.yaml index 652e5e3..9641f81 100644 --- a/target/executable/rseqc/rseqc_tin/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_tin/.config.vsh.yaml @@ -222,8 +222,8 @@ build_info: output: "target/executable/rseqc/rseqc_tin" executable: "target/executable/rseqc/rseqc_tin/rseqc_tin" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/rseqc/rseqc_tin/rseqc_tin b/target/executable/rseqc/rseqc_tin/rseqc_tin index 1e5d8cb..39dd10b 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="2024-11-18T16:13:10Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:11Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/sortmerna/.config.vsh.yaml b/target/executable/sortmerna/.config.vsh.yaml index 057f8f0..1a54f66 100644 --- a/target/executable/sortmerna/.config.vsh.yaml +++ b/target/executable/sortmerna/.config.vsh.yaml @@ -200,8 +200,8 @@ build_info: output: "target/executable/sortmerna" executable: "target/executable/sortmerna/sortmerna" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/sortmerna/sortmerna b/target/executable/sortmerna/sortmerna index bd29dc3..f7cfd9a 100755 --- a/target/executable/sortmerna/sortmerna +++ b/target/executable/sortmerna/sortmerna @@ -486,9 +486,9 @@ function ViashDockerfile { FROM quay.io/biocontainers/sortmerna:4.3.6--h9ee0642_0 ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component sortmerna" -LABEL org.opencontainers.image.created="2024-11-18T16:13:13Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:14Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/stringtie/.config.vsh.yaml b/target/executable/stringtie/.config.vsh.yaml index a35ec24..ef4a637 100644 --- a/target/executable/stringtie/.config.vsh.yaml +++ b/target/executable/stringtie/.config.vsh.yaml @@ -224,8 +224,8 @@ build_info: output: "target/executable/stringtie" executable: "target/executable/stringtie/stringtie" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/stringtie/stringtie b/target/executable/stringtie/stringtie index 6d4a2bd..d214b80 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="2024-11-18T16:13:14Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:15Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/summarizedexperiment/.config.vsh.yaml b/target/executable/summarizedexperiment/.config.vsh.yaml index d317a69..9133bc0 100644 --- a/target/executable/summarizedexperiment/.config.vsh.yaml +++ b/target/executable/summarizedexperiment/.config.vsh.yaml @@ -207,8 +207,8 @@ build_info: output: "target/executable/summarizedexperiment" executable: "target/executable/summarizedexperiment/summarizedexperiment" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/summarizedexperiment/summarizedexperiment b/target/executable/summarizedexperiment/summarizedexperiment index 324386c..9bda60a 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="2024-11-18T16:13:12Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:13Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/trimgalore/.config.vsh.yaml b/target/executable/trimgalore/.config.vsh.yaml index f993285..182b608 100644 --- a/target/executable/trimgalore/.config.vsh.yaml +++ b/target/executable/trimgalore/.config.vsh.yaml @@ -796,8 +796,8 @@ build_info: output: "target/executable/trimgalore" executable: "target/executable/trimgalore/trimgalore" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/trimgalore/trimgalore b/target/executable/trimgalore/trimgalore index 9b7fb37..2a5c83d 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="2024-11-18T16:13:13Z" +LABEL org.opencontainers.image.created="2024-11-27T16:55:13Z" LABEL org.opencontainers.image.source="https://github.com/FelixKrueger/TrimGalore" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/tx2gene/.config.vsh.yaml b/target/executable/tx2gene/.config.vsh.yaml index 074fd3f..f67651c 100644 --- a/target/executable/tx2gene/.config.vsh.yaml +++ b/target/executable/tx2gene/.config.vsh.yaml @@ -200,8 +200,8 @@ build_info: output: "target/executable/tx2gene" executable: "target/executable/tx2gene/tx2gene" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/tx2gene/tx2gene b/target/executable/tx2gene/tx2gene index 99edfb4..c6a12d2 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="2024-11-18T16:13:12Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:13Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/tximport/.config.vsh.yaml b/target/executable/tximport/.config.vsh.yaml index ec0a86c..89afadb 100644 --- a/target/executable/tximport/.config.vsh.yaml +++ b/target/executable/tximport/.config.vsh.yaml @@ -255,8 +255,8 @@ build_info: output: "target/executable/tximport" executable: "target/executable/tximport/tximport" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/tximport/tximport b/target/executable/tximport/tximport index 7cdac35..f6707db 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="2024-11-18T16:13:11Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:12Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/ucsc/bedclip/.config.vsh.yaml b/target/executable/ucsc/bedclip/.config.vsh.yaml index f1b11a4..4257dba 100644 --- a/target/executable/ucsc/bedclip/.config.vsh.yaml +++ b/target/executable/ucsc/bedclip/.config.vsh.yaml @@ -172,8 +172,8 @@ build_info: output: "target/executable/ucsc/bedclip" executable: "target/executable/ucsc/bedclip/bedclip" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/ucsc/bedclip/bedclip b/target/executable/ucsc/bedclip/bedclip index c6f4636..d2ac6d6 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="2024-11-18T16:13:11Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:12Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml b/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml index 8218961..8d43514 100644 --- a/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml +++ b/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml @@ -172,8 +172,8 @@ build_info: output: "target/executable/ucsc/bedgraphtobigwig" executable: "target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig b/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig index 812a934..4b5562e 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="2024-11-18T16:13:12Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:12Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/umitools/umitools_dedup/.config.vsh.yaml b/target/executable/umitools/umitools_dedup/.config.vsh.yaml index 157b36e..76b333e 100644 --- a/target/executable/umitools/umitools_dedup/.config.vsh.yaml +++ b/target/executable/umitools/umitools_dedup/.config.vsh.yaml @@ -203,8 +203,8 @@ build_info: output: "target/executable/umitools/umitools_dedup" executable: "target/executable/umitools/umitools_dedup/umitools_dedup" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/umitools/umitools_dedup/umitools_dedup b/target/executable/umitools/umitools_dedup/umitools_dedup index aac28a8..1c01d3e 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="2024-11-18T16:13:07Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:08Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/umitools/umitools_extract/.config.vsh.yaml b/target/executable/umitools/umitools_extract/.config.vsh.yaml index 1db7ba0..629d1d3 100644 --- a/target/executable/umitools/umitools_extract/.config.vsh.yaml +++ b/target/executable/umitools/umitools_extract/.config.vsh.yaml @@ -261,8 +261,8 @@ build_info: output: "target/executable/umitools/umitools_extract" executable: "target/executable/umitools/umitools_extract/umitools_extract" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/umitools/umitools_extract/umitools_extract b/target/executable/umitools/umitools_extract/umitools_extract index 77935f2..0034397 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="2024-11-18T16:13:07Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:08Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" VIASHDOCKER diff --git a/target/executable/umitools_prepareforquant/.config.vsh.yaml b/target/executable/umitools_prepareforquant/.config.vsh.yaml index c65670b..cfbaf63 100644 --- a/target/executable/umitools_prepareforquant/.config.vsh.yaml +++ b/target/executable/umitools_prepareforquant/.config.vsh.yaml @@ -164,8 +164,8 @@ build_info: output: "target/executable/umitools_prepareforquant" executable: "target/executable/umitools_prepareforquant/umitools_prepareforquant" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/executable/umitools_prepareforquant/umitools_prepareforquant b/target/executable/umitools_prepareforquant/umitools_prepareforquant index 23f0b97..62b788f 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="2024-11-18T16:13:13Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83" +LABEL org.opencontainers.image.created="2024-11-27T16:55:14Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611" LABEL org.opencontainers.image.version="add-labels" 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 5d4192a..e148174 100644 --- a/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml +++ b/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml @@ -611,8 +611,8 @@ 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: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads" - "target/dependencies/vsh/vsh/biobox/main/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 e26df75..1fdbd82 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 @@ -1349,6 +1349,8 @@ cat > "\$tempscript" << 'VIASHMAIN' // The following code has been auto-generated by Viash. //// VIASH END +// TODO: Improve logic of this wf, e.g. by splitting up in 2 subwfs +// TODO: See if this can be aligned with the pseudo-alignment branch of the logic workflow run_wf { take: input_ch diff --git a/target/executable/workflows/merge_quant_results/.config.vsh.yaml b/target/executable/workflows/merge_quant_results/.config.vsh.yaml index 9e04b75..7d9bb0e 100644 --- a/target/executable/workflows/merge_quant_results/.config.vsh.yaml +++ b/target/executable/workflows/merge_quant_results/.config.vsh.yaml @@ -286,8 +286,8 @@ 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: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@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 413e4fb..9f255f7 100644 --- a/target/executable/workflows/post_processing/.config.vsh.yaml +++ b/target/executable/workflows/post_processing/.config.vsh.yaml @@ -494,8 +494,8 @@ build_info: output: "target/executable/workflows/post_processing" executable: "target/executable/workflows/post_processing/post_processing" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/picard_markduplicates" - "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort" diff --git a/target/executable/workflows/pre_processing/.config.vsh.yaml b/target/executable/workflows/pre_processing/.config.vsh.yaml index 9ec8431..6927c5d 100644 --- a/target/executable/workflows/pre_processing/.config.vsh.yaml +++ b/target/executable/workflows/pre_processing/.config.vsh.yaml @@ -681,8 +681,8 @@ build_info: output: "target/executable/workflows/pre_processing" executable: "target/executable/workflows/pre_processing/pre_processing" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@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 db73ece..7f1432b 100644 --- a/target/executable/workflows/prepare_genome/.config.vsh.yaml +++ b/target/executable/workflows/prepare_genome/.config.vsh.yaml @@ -509,8 +509,8 @@ build_info: output: "target/executable/workflows/prepare_genome" executable: "target/executable/workflows/prepare_genome/prepare_genome" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/gunzip" - "target/dependencies/vsh/vsh/biobox/main/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 8719a30..21fe9c8 100644 --- a/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml +++ b/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml @@ -291,8 +291,8 @@ 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: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant" - "target/nextflow/kallisto/kallisto_quant" diff --git a/target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant b/target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant index aa0bc69..432a93e 100755 --- a/target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant +++ b/target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant @@ -800,6 +800,7 @@ cat > "\$tempscript" << 'VIASHMAIN' // The following code has been auto-generated by Viash. //// VIASH END +// TODO: See if the logic of this can be aligned with the STAR aligner logic workflow run_wf { take: input_ch diff --git a/target/executable/workflows/quality_control/.config.vsh.yaml b/target/executable/workflows/quality_control/.config.vsh.yaml index 9cf7d78..f23b927 100644 --- a/target/executable/workflows/quality_control/.config.vsh.yaml +++ b/target/executable/workflows/quality_control/.config.vsh.yaml @@ -1580,8 +1580,8 @@ build_info: output: "target/executable/workflows/quality_control" executable: "target/executable/workflows/quality_control/quality_control" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@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 a404397..bac339b 100755 --- a/target/executable/workflows/quality_control/quality_control +++ b/target/executable/workflows/quality_control/quality_control @@ -3597,6 +3597,7 @@ workflow run_wf { def skip_qc = list.collect { id, state -> state.skip_qc }.unique()[0] def skip_align = list.collect { id, state -> state.skip_align }.unique()[0] def skip_pseudo_align = list.collect { id, state -> state.skip_pseudo_align }.unique()[0] + // TODO: Are these checks necessary? def quant_results = list.collect { id, state -> (state.quant_results_file instanceof java.nio.file.Path && state.quant_results_file.exists()) ? state.quant_results_file : @@ -3895,6 +3896,7 @@ workflow run_wf { ) | niceView() // Get list of samples that failed trimming, mapping, and strand check for MultiQC report + // TODO: Refactor this to a process/step | map { id, state -> def fail_trimming_header = ["Sample", "Reads after trimming"] def fail_trimming_multiqc = "" @@ -4023,6 +4025,7 @@ workflow run_wf { | map { list -> [list[0], list[1] + list[2]] } | map { id, state -> + // TODO: Check this, necessary for setState def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() } [ id, mod_state ] } diff --git a/target/executable/workflows/rnaseq/.config.vsh.yaml b/target/executable/workflows/rnaseq/.config.vsh.yaml index c3dc51c..3ecc2ee 100644 --- a/target/executable/workflows/rnaseq/.config.vsh.yaml +++ b/target/executable/workflows/rnaseq/.config.vsh.yaml @@ -2090,8 +2090,8 @@ build_info: output: "target/executable/workflows/rnaseq" executable: "target/executable/workflows/rnaseq/rnaseq" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@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 c6ea7f9..37b51ec 100755 --- a/target/executable/workflows/rnaseq/rnaseq +++ b/target/executable/workflows/rnaseq/rnaseq @@ -4407,222 +4407,473 @@ workflow run_wf { main: reference_ch = input_ch - | map { id, state -> - def biotype = state.gencode ? "gene_type" : state.featurecounts_group_type - def filter_gtf = - ( - ( !state.skip_alignment && state.aligner) // Condition 1: Alignment is required and aligner is set - || ( !state.skip_pseudo_alignment && state.pseudo_aligner ) // Condition 2: Pseudoalignment is required and pseudoaligner is set - || ( !state.transcript_fasta ) // Condition 3: Transcript FASTA file is not provided - ) - && - ( !state.skip_gtf_filter ) // Condition 4: --skip_gtf_filter is not provided - [ id, state + [ biotype: biotype, filter_gtf: filter_gtf ] ] - } - - | toSortedList - - | map { list -> - [ "ref", - [ fasta: list.collect { id, state -> state.fasta }.unique()[0], - gtf: list.collect { id, state -> state.gtf }.unique()[0], - gff: list.collect { id, state -> state.gff }.unique()[0], - additional_fasta: list.collect { id, state -> state.additional_fasta }.unique()[0], - transcript_fasta:list.collect { id, state -> state.transcript_fasta }.unique()[0], - gene_bed: list.collect { id, state -> state.gene_bed }.unique()[0], - bbsplit_fasta_list: list.collect { id, state -> state.bbsplit_fasta_list }.unique()[0], - aligner: list.collect { id, state -> state.aligner }.unique()[0], - pseudo_aligner: list.collect { id, state -> state.pseudo_aligner }.unique()[0], - star_index: list.collect { id, state -> state.star_index }.unique()[0], - rsem_index: list.collect { id, state -> state.rsem_index }.unique()[0], - salmon_index: list.collect { id, state -> state.salmon_index }.unique()[0], - kallisto_index: list.collect { id, state -> state.kallisto_index }.unique()[0], - // splicesites: list.collect { id, state -> state.splicesites }.unique()[0], - // hisat2_index: list.collect { id, state -> state.hisat2_index }.unique()[0], - bbsplit_index: list.collect { id, state -> state.bbsplit_index }.unique()[0], - skip_bbsplit: list.collect { id, state -> state.skip_bbsplit }.unique()[0], - gencode: list.collect { id, state -> state.gencode }.unique()[0], - biotype: list.collect { id, state -> state.biotype }.unique()[0], - filter_gtf: list.collect { id, state -> state.filter_gtf }.unique()[0], - pseudo_aligner_kmer_size: list.collect { id, state -> state.pseudo_aligner_kmer_size }.unique()[0] ] - ] - } + | map { id, state -> + def biotype = state.gencode ? "gene_type" : state.featurecounts_group_type + def filter_gtf = + ( + ( !state.skip_alignment && state.aligner) // Condition 1: Alignment is required and aligner is set + || ( !state.skip_pseudo_alignment && state.pseudo_aligner ) // Condition 2: Pseudoalignment is required and pseudoaligner is set + || ( !state.transcript_fasta ) // Condition 3: Transcript FASTA file is not provided + ) + && + ( !state.skip_gtf_filter ) // Condition 4: --skip_gtf_filter is not provided + [ id, state + [ biotype: biotype, filter_gtf: filter_gtf ] ] + } + + | toSortedList + + | map { list -> + [ "ref", + [ fasta: list.collect { id, state -> state.fasta }.unique()[0], + gtf: list.collect { id, state -> state.gtf }.unique()[0], + gff: list.collect { id, state -> state.gff }.unique()[0], + additional_fasta: list.collect { id, state -> state.additional_fasta }.unique()[0], + transcript_fasta:list.collect { id, state -> state.transcript_fasta }.unique()[0], + gene_bed: list.collect { id, state -> state.gene_bed }.unique()[0], + bbsplit_fasta_list: list.collect { id, state -> state.bbsplit_fasta_list }.unique()[0], + aligner: list.collect { id, state -> state.aligner }.unique()[0], + pseudo_aligner: list.collect { id, state -> state.pseudo_aligner }.unique()[0], + star_index: list.collect { id, state -> state.star_index }.unique()[0], + rsem_index: list.collect { id, state -> state.rsem_index }.unique()[0], + salmon_index: list.collect { id, state -> state.salmon_index }.unique()[0], + kallisto_index: list.collect { id, state -> state.kallisto_index }.unique()[0], + // splicesites: list.collect { id, state -> state.splicesites }.unique()[0], + // hisat2_index: list.collect { id, state -> state.hisat2_index }.unique()[0], + bbsplit_index: list.collect { id, state -> state.bbsplit_index }.unique()[0], + skip_bbsplit: list.collect { id, state -> state.skip_bbsplit }.unique()[0], + gencode: list.collect { id, state -> state.gencode }.unique()[0], + biotype: list.collect { id, state -> state.biotype }.unique()[0], + filter_gtf: list.collect { id, state -> state.filter_gtf }.unique()[0], + pseudo_aligner_kmer_size: list.collect { id, state -> state.pseudo_aligner_kmer_size }.unique()[0] ] + ] + } - // prepare all the necessary files for reference genome - | prepare_genome.run ( - fromState: [ - "fasta": "fasta", - "gtf": "gtf", - "gff": "gff", - "additional_fasta": "additional_fasta", - "transcript_fasta": "transcript_fasta", - "gene_bed": "gene_bed", - "bbsplit_fasta_list": "bbsplit_fasta_list", - "star_index": "star_index", - "rsem_index": "rsem_index", - "salmon_index": "salmon_index", - "kallisto_index": "kallisto_index", - "pseudo_aligner_kmer_size": "pseudo_aligner_kmer_size", - // "splicesites": "splicesites", - // "hisat2_index": "hisat2_index", - "bbsplit_index": "bbsplit_index", - "skip_bbsplit": "skip_bbsplit", - "gencode": "gencode", - "biotype": "biotype", - "filter_gtf": "filter_gtf", - "aligner": "aligner", - "pseudo_aligner": "pseudo_aligner", - "skip_alignment": "skip_alignment" - ], - toState: [ - "fasta": "uncompressed_fasta", - "gtf": "gtf_uncompressed", - "transcript_fasta": "transcript_fasta_uncompressed", - "fai": "fai", - "chrom_sizes": "chrom_sizes", - "bbsplit_index": "bbsplit_index_uncompressed", - "star_index": "star_index_uncompressed", - "salmon_index": "salmon_index_uncompressed", - "kallisto_index": "kallisto_index_uncompressed", - "gene_bed": "gene_bed_uncompressed" - ] - ) + // prepare all the necessary files for reference genome + | prepare_genome.run ( + fromState: [ + "fasta": "fasta", + "gtf": "gtf", + "gff": "gff", + "additional_fasta": "additional_fasta", + "transcript_fasta": "transcript_fasta", + "gene_bed": "gene_bed", + "bbsplit_fasta_list": "bbsplit_fasta_list", + "star_index": "star_index", + "rsem_index": "rsem_index", + "salmon_index": "salmon_index", + "kallisto_index": "kallisto_index", + "pseudo_aligner_kmer_size": "pseudo_aligner_kmer_size", + // "splicesites": "splicesites", + // "hisat2_index": "hisat2_index", + "bbsplit_index": "bbsplit_index", + "skip_bbsplit": "skip_bbsplit", + "gencode": "gencode", + "biotype": "biotype", + "filter_gtf": "filter_gtf", + "aligner": "aligner", + "pseudo_aligner": "pseudo_aligner", + "skip_alignment": "skip_alignment" + ], + toState: [ + "fasta": "uncompressed_fasta", + "gtf": "gtf_uncompressed", + "transcript_fasta": "transcript_fasta_uncompressed", + "fai": "fai", + "chrom_sizes": "chrom_sizes", + "bbsplit_index": "bbsplit_index_uncompressed", + "star_index": "star_index_uncompressed", + "salmon_index": "salmon_index_uncompressed", + "kallisto_index": "kallisto_index_uncompressed", + "gene_bed": "gene_bed_uncompressed" + ] + ) - // Check if contigs in genome fasta file > 512 Mbp - | map { id, state -> - (isBelowMaxContigSize(state.fai)) ? [id, state] : [id, state + [bam_csi_index: true]] - } + // Check if contigs in genome fasta file > 512 Mbp + // TODO: check where this is required and move if necessary + | map { id, state -> + (isBelowMaxContigSize(state.fai)) ? [id, state] : [id, state + [bam_csi_index: true]] + } - | map { list -> list[1]} + // Pick out the state + | map { list -> list[1]} analysis_ch = input_ch - | combine(reference_ch) + | combine(reference_ch) - | map { list -> [list[0], list[1] + list[2]] } + | map { list -> [list[0], list[1] + list[2]] } - // Concatenate FastQ files from same sample if required - | cat_fastq.run ( - fromState: [ - "read_1": "fastq_1", - "read_2": "fastq_2" - ], - toState: [ - "fastq_1": "fastq_1", - "fastq_2": "fastq_2" - ] - ) + // Concatenate FastQ files from same sample if required + | cat_fastq.run ( + fromState: [ + "read_1": "fastq_1", + "read_2": "fastq_2" + ], + toState: [ + "fastq_1": "fastq_1", + "fastq_2": "fastq_2" + ] + ) - // Pre-process fastq files - | pre_processing.run ( - fromState: [ - "id": "id", - "fastq_1": "fastq_1", - "fastq_2": "fastq_2", - "umitools_bc_pattern": "umitools_bc_pattern", - "umitools_bc_pattern2": "umitools_bc_pattern2", - "strandedness": "strandedness", - "transcript_fasta": "transcript_fasta", - "gtf": "gtf", - "with_umi": "with_umi", - "bbsplit_index": "bbsplit_index", - "bbsplit_fasta_list": "bbsplit_fasta_list", - "bc_pattern": "bc_pattern", - "ribo_database_manifest": "ribo_database_manifest", - "salmon_index": "salmon_index", - "skip_qc": "skip_qc", - "skip_fastqc": "skip_fastqc", - "skip_skip_umi_extract": "skip_umi_extract", - "umi_discard_read": "umi_discard_read", - "skip_trimming": "skip_trimming", - "trimmer": "trimmer", - "skip_bbsplit": "skip_bbsplit", - "remove_ribo_rna": "remove_ribo_rna" - ], - toState: [ + // Pre-process fastq files + | pre_processing.run ( + fromState: [ + "id": "id", + "fastq_1": "fastq_1", + "fastq_2": "fastq_2", + "umitools_bc_pattern": "umitools_bc_pattern", + "umitools_bc_pattern2": "umitools_bc_pattern2", + "strandedness": "strandedness", + "transcript_fasta": "transcript_fasta", + "gtf": "gtf", + "with_umi": "with_umi", + "bbsplit_index": "bbsplit_index", + "bbsplit_fasta_list": "bbsplit_fasta_list", + "bc_pattern": "bc_pattern", + "ribo_database_manifest": "ribo_database_manifest", + "salmon_index": "salmon_index", + "skip_qc": "skip_qc", + "skip_fastqc": "skip_fastqc", + "skip_skip_umi_extract": "skip_umi_extract", + "umi_discard_read": "umi_discard_read", + "skip_trimming": "skip_trimming", + "trimmer": "trimmer", + "skip_bbsplit": "skip_bbsplit", + "remove_ribo_rna": "remove_ribo_rna" + ], + toState: [ + "fastqc_html_1": "fastqc_html_1", + "fastqc_html_2": "fastqc_html_2", + "fastqc_zip_1": "fastqc_zip_1", + "fastqc_zip_2": "fastqc_zip_2", + "fastq_1": "qc_output1", + "fastq_2": "qc_output2", + "trim_log_1": "trim_log_1", + "trim_log_2": "trim_log_2", + "trim_zip_1": "trim_zip_1", + "trim_zip_2": "trim_zip_2", + "trim_html_1": "trim_html_1", + "trim_html_2": "trim_html_2", + "passed_trimmed_reads": "passed_trimmed_reads", + "num_trimmed_reads": "num_trimmed_reads", + "sortmerna_log": "sortmerna_log", + "salmon_quant_output": "salmon_quant_output", + "fastp_failed_trim": "failed_trim", + "fastp_failed_trim_unpaired1": "failed_trim_unpaired1", + "fastp_failed_trim_unpaired2": "failed_trim_unpaired2", + "fastp_trim_json": "trim_json", + "fastp_trim_html": "trim_html", + "fastp_trim_merged_out": "trim_merged_out" + ] + ) + + // Infer strandedness from Salmon pseudo-alignment results + // TODO: Turn this into a workflow step and include as a dependency + | map { id, state -> + (state.strandedness == 'auto') ? + [ id, state + [strandedness: getSalmonInferredStrandedness(state.salmon_quant_output)] ] : + [id, state] + } + + // Filter FastQ files based on minimum trimmed read count after adapter trimming + // TODO: Turn this into a workflow step and include as a dependency + | map { id, state -> + def input = state.fastq_2 ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ] + def num_reads = (state.skip_trimming) ? + state.min_trimmed_reads + 1 : + ( + (state.trimmer == "fastp") ? + getFastpReadsAfterFiltering(state.fastp_trim_json) : + ( + (!state.skip_trimming && input.size() == 2) ? + getTrimGaloreReadsAfterFiltering(state.trim_log_2) : + getTrimGaloreReadsAfterFiltering(state.trim_log_1) + ) + ) + def passed_trimmed_reads = + (state.skip_trimming || (num_reads >= state.min_trimmed_reads)) ? + true : + false + [ id, state + [num_trimmed_reads: num_reads, passed_trimmed_reads: passed_trimmed_reads] ] + } + + // Genome alignment and quantification + | genome_alignment_and_quant.run ( + runIf: { id, state -> !state.skip_alignment && state.passed_trimmed_reads }, + fromState: [ + "id": "id", + "fastq_1": "fastq_1", + "fastq_2": "fastq_2", + "strandedness": "strandedness", + "gtf": "gtf", + "transcript_fasta": "transcript_fasta", + "bam_csi_index": "bam_csi_index", + "aligner": "aligner", + "rsem_index": "rsem_index", + "star_index": "star_index", + "extra_star_align_args": "extra_star_align_args", + "star_ignore_sjdbgtf": "star_ignore_sjdbgtf", + "seq_platform": "seq_platform", + "seq_center": "seq_center", + "with_umi": "with_umi", + "umi_dedup_stats": "umi_dedup_stats", + "gtf_group_features": "gtf_group_features", + "gtf_extra_attributes": "gtf_extra_attributes", + "salmon_quant_libtype": "salmon_quant_libtype", + "salmon_index": "salmon_index", + "extra_rsem_calculate_expression_args": "extra_rsem_calculate_expression_args" + ], + toState: [ + "star_multiqc": "star_multiqc", + "rsem_multiqc": "rsem_multiqc", + "salmon_multiqc": "salmon_multiqc", + "genome_bam_sorted": "genome_bam_sorted", + "genome_bam_index": "genome_bam_index", + "genome_bam_stats": "genome_bam_stats", + "genome_bam_flagstat": "genome_bam_flagstat", + "genome_bam_idxstats": "genome_bam_idxstats", + "transcriptome_bam": "transcriptome_bam", + "transcriptome_bam_index": "transcriptome_bam_index", + "transcriptome_bam_stats": "transcriptome_bam_stats", + "transcriptome_bam_flagstat": "transcriptome_bam_flagstat", + "transcriptome_bam_idxstats": "transcriptome_bam_idxstats", + "quant_out_dir": "quant_out_dir", + "quant_results_file": "quant_results_file", + "rsem_counts_gene": "rsem_counts_gene", + "rsem_counts_transcripts": "rsem_counts_transcripts", + "bam_genome_rsem": "bam_genome_rsem", + "bam_transcript_rsem": "bam_transcript_rsem" + ] + ) + + // Filter channels to get samples that passed STAR minimum mapping percentage + // TODO: Move to reporting or later step + | map { id, state -> + def percent_mapped = (!state.skip_alignment) ? getStarPercentMapped(state.star_multiqc) : 0.0 + def passed_mapping = (percent_mapped >= state.min_mapped_reads) ? true : false + [ id, state + [percent_mapped: percent_mapped, passed_mapping: passed_mapping] ] + } + + // Pseudo-alignment and quantification + | pseudo_alignment_and_quant.run ( + runIf: { id, state -> !state.skip_pseudo_alignment && state.passed_trimmed_reads }, + fromState: [ + "id": "id", + "fastq_1": "fastq_1", + "fastq_2": "fastq_2", + "strandedness": "strandedness", + "gtf": "gtf", + "transcript_fasta": "transcript_fasta", + "pseudo_aligner": "pseudo_aligner", + "salmon_index": "salmon_index", + "kallisto_index": "kallisto_index", + "extra_star_align_args": "extra_star_align_args", + "star_ignore_sjdbgtf": "star_ignore_sjdbgtf", + "seq_platform": "seq_platform", + "seq_center": "seq_center", + "with_umi": "with_umi", + "umi_dedup_stats": "umi_dedup_stats", + "gtf_group_features": "gtf_group_features", + "gtf_extra_attributes": "gtf_extra_attributes", + "lib_type": "salmon_quant_libtype", + "kallisto_quant_fragment_length": "kallisto_quant_fragment_length", + "kallisto_quant_fragment_length_sd": "kallisto_quant_fragment_length_sd" + ], + toState: [ + "pseudo_quant_out_dir": "quant_out_dir", + "pseudo_salmon_quant_results_file": "salmon_quant_results_file", + "pseudo_kallisto_quant_results_file": "kallisto_quant_results_file", + "pseudo_multiqc": "pseudo_multiqc" + ] + ) + + | map { id, state -> + def input = state.fastq_2 ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ] + def paired = input.size() == 2 + [ id, state + [ paired: paired ] ] + } + + // Post-processing + | post_processing.run ( + runIf: { id, state -> !state.skip_alignment && state.passed_trimmed_reads && state.passed_mapping }, + fromState: [ + "id": "id", + "paired": "paired", + "strandedness": "strandedness", + "fasta": "fasta", + "fai": "fai", + "gtf": "gtf", + "genome_bam": "genome_bam_sorted", + "chrom_sizes": "chrom_sizes", + "star_multiqc": "star_multiqc", + "extra_picard_args": "extra_picard_args", + "extra_stringtie_args": "extra_stringtie_args", + "stringtie_ignore_gtf": "stringtie_ignore_gtf", + "extra_bedtools_args": "extra_bedtools_args", + "bam_csi_index": "bam_csi_index", + "min_mapped_reads": "min_mapped_reads", + "with_umi": "with_umi", + "skip_qc": "skip_qc", + "skip_markduplicates": "skip_markduplicates", + "skip_stringtie": "skip_stringtie", + "skip_bigwig":"gencode" + ], + toState: [ + "genome_bam_sorted": "processed_genome_bam", + "genome_bam_index": "genome_bam_index", + "genome_bam_stats": "genome_bam_stats", + "genome_bam_flagstat": "genome_bam_flagstat", + "genome_bam_idxstats": "genome_bam_idxstats", + "markduplicates_metrics": "markduplicates_metrics", + "stringtie_transcript_gtf": "stringtie_transcript_gtf", + "stringtie_coverage_gtf": "stringtie_coverage_gtf", + "stringtie_abundance": "stringtie_abundance", + "stringtie_ballgown": "stringtie_ballgown", + "bedgraph_forward": "bedgraph_forward", + "bedgraph_reverse": "bedgraph_reverse", + "bigwig_forward": "bigwig_forward", + "bigwig_reverse": "bigwig_reverse" + ] + ) + + // Final QC + | quality_control.run ( + fromState: [ + "id": "id", + "paired": "paired", + "strandedness": "strandedness", + "skip_align": "skip_alignment", + "skip_pseudo_align": "skip_pseudo_alignment", + "skip_dupradar": "skip_dupradar", + "skip_qualimap": "skip_qualimap", + "skip_rseqc": "skip_rseqc", + "skip_multiqc": "skip_multiqc", + "skip_preseq": "skip_preseq", + "gtf": "gtf", + "num_trimmed_reads": "num_trimmed_reads", + "passed_trimmed_reads": "passed_trimmed_reads", + "passed_mapping": "passed_mapping", + "percent_mapped": "percent_mapped", + "genome_bam": "genome_bam_sorted", + "genome_bam_index": "genome_bam_index", + "salmon_multiqc": "salmon_multiqc", + "quant_results_file": "quant_results_file", + "rsem_multiqc": "rsem_multiqc", + "rsem_counts_gene": "rsem_counts_gene", + "rsem_counts_transcripts": "rsem_counts_transcripts", + "pseudo_multiqc": "pseudo_multiqc", + "pseudo_quant_out_dir": "pseudo_quant_out_dir", + "pseudo_salmon_quant_results_file": "pseudo_salmon_quant_results_file", + "pseudo_kallisto_quant_results_file": "pseudo_kallisto_quant_results_file", + "aligner": "aligner", + "pseudo_aligner": "pseudo_aligner", + "gene_bed": "gene_bed", + "extra_preseq_args": "extra_preseq_args", + "biotype": "biotype", + "skip_biotype_qc": "skip_biotype_qc", + "featurecounts_group_type": "featurecounts_group_type", + "featurecounts_feature_type": "featurecounts_feature_type", + "gencode": "gencode", + "skip_deseq2_qc": "skip_deseq2_qc", + "deseq2_vst": "deseq2_vst", + "multiqc_custom_config": "multiqc_custom_config", + "multiqc_title": "multiqc_title", + "multiqc_methods_description": "multiqc_methods_description", + "fastqc_zip_1": "fastqc_zip_1", + "fastqc_zip_2": "fastqc_zip_2", + "trim_log_1": "trim_log_1", + "trim_log_2": "trim_log_2", + "trim_zip_1": "trim_zip_1", + "trim_zip_2": "trim_zip_2", + "sortmerna_multiqc": "sortmerna_log", + "star_multiqc": "star_multiqc", + "genome_bam_stats": "genome_bam_stats", + "genome_bam_flagstat": "genome_bam_flagstat", + "genome_bam_idxstats": "genome_bam_idxstats", + "markduplicates_multiqc": "markduplicates_metrics", + "rseqc_modules": "rseqc_modules" + ], + toState: [ + "preseq_output": "preseq_output", + "bamstat_output": "bamstat_output", + "strandedness_output": "strandedness_output", + "inner_dist_output_stats": "inner_dist_output_stats", + "inner_dist_output_dist": "inner_dist_output_dist", + "inner_dist_output_freq": "inner_dist_output_freq", + "inner_dist_output_plot": "inner_dist_output_plot", + "inner_dist_output_plot_r": "inner_dist_output_plot_r", + "junction_annotation_output_log": "junction_annotation_output_log", + "junction_annotation_output_plot_r": "junction_annotation_output_plot_r", + "junction_annotation_output_junction_bed": "junction_annotation_output_junction_bed", + "junction_annotation_output_junction_interact": "junction_annotation_output_junction_interact", + "junction_annotation_output_junction_sheet": "junction_annotation_output_junction_sheet", + "junction_annotation_output_splice_events_plot": "junction_annotation_output_splice_events_plot", + "junction_annotation_output_splice_junctions_plot": "junction_annotation_output_splice_junctions_plot", + "junction_saturation_output_plot_r": "junction_saturation_output_plot_r", + "junction_saturation_output_plot": "junction_saturation_output_plot", + "read_distribution_output": "read_distribution_output", + "read_duplication_output_duplication_rate_plot_r": "read_duplication_output_duplication_rate_plot_r", + "read_duplication_output_duplication_rate_plot": "read_duplication_output_duplication_rate_plot", + "read_duplication_output_duplication_rate_mapping": "read_duplication_output_duplication_rate_mapping", + "read_duplication_output_duplication_rate_sequence": "read_duplication_output_duplication_rate_sequence", + "tin_output_summary": "tin_output_summary", + "tin_output_metrics": "tin_output_metrics", + "dupradar_output_dupmatrix": "dupradar_output_dupmatrix", + "dupradar_output_dup_intercept_mqc": "dupradar_output_dup_intercept_mqc", + "dupradar_output_duprate_exp_boxplot": "dupradar_output_duprate_exp_boxplot", + "dupradar_output_duprate_exp_densplot": "dupradar_output_duprate_exp_densplot", + "dupradar_output_duprate_exp_denscurve_mqc": "dupradar_output_duprate_exp_denscurve_mqc", + "dupradar_output_expression_histogram": "dupradar_output_expression_histogram", + "dupradar_output_intercept_slope": "dupradar_output_intercept_slope", + "qualimap_output_dir": "qualimap_output_dir", + "qualimap_output_pdf": "qualimap_output_pdf", + "featurecounts": "featurecounts", + "featurecounts_summary": "featurecounts_summary", + "featurecounts_multiqc": "featurecounts_multiqc", + "featurecounts_rrna_multiqc": "featurecounts_rrna_multiqc", + "tpm_gene": "tpm_gene", + "counts_gene": "counts_gene", + "counts_gene_length_scaled": "counts_gene_length_scaled", + "counts_gene_scaled": "counts_gene_scaled", + "tpm_transcript": "tpm_transcript", + "counts_transcript": "counts_transcript", + "qunat_merged_summarizedexperiment": "quant_merged_summarizedexperiment", + "deseq2_output": "deseq2_output", + "multiqc_report": "multiqc_report", + "multiqc_data": "multiqc_data", + "multiqc_plots": "multiqc_plots" + ] + ) + + | map { id, state -> + def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() } + [ id, mod_state ] + } + + | setState ( + [ + "output_fasta": "fasta", + "output_gtf": "gtf", + "output_transcript_fasta": "transcript_fasta", + "output_gene_bed": "gene_bed", + "output_bbsplit_index": "bbsplit_index", + "output_star_index": "star_index", + "output_salmon_index": "salmon_index", + "output_kallisto_index": "kallisto_index", "fastqc_html_1": "fastqc_html_1", "fastqc_html_2": "fastqc_html_2", "fastqc_zip_1": "fastqc_zip_1", "fastqc_zip_2": "fastqc_zip_2", - "fastq_1": "qc_output1", - "fastq_2": "qc_output2", + "output_fastq_1": "fastq_1", + "output_fastq_2": "fastq_2", "trim_log_1": "trim_log_1", "trim_log_2": "trim_log_2", "trim_zip_1": "trim_zip_1", "trim_zip_2": "trim_zip_2", "trim_html_1": "trim_html_1", "trim_html_2": "trim_html_2", - "passed_trimmed_reads": "passed_trimmed_reads", - "num_trimmed_reads": "num_trimmed_reads", "sortmerna_log": "sortmerna_log", - "salmon_quant_output": "salmon_quant_output", - "fastp_failed_trim": "failed_trim", - "fastp_failed_trim_unpaired1": "failed_trim_unpaired1", - "fastp_failed_trim_unpaired2": "failed_trim_unpaired2", - "fastp_trim_json": "trim_json", - "fastp_trim_html": "trim_html", - "fastp_trim_merged_out": "trim_merged_out" - ] - ) - - // Infer strandedness from Salmon pseudo-alignment results - | map { id, state -> - (state.strandedness == 'auto') ? - [ id, state + [strandedness: getSalmonInferredStrandedness(state.salmon_quant_output)] ] : - [id, state] - } - - // Filter FastQ files based on minimum trimmed read count after adapter trimming - | map { id, state -> - def input = state.fastq_2 ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ] - def num_reads = (state.skip_trimming) ? - state.min_trimmed_reads + 1 : - ( - (state.trimmer == "fastp") ? - getFastpReadsAfterFiltering(state.fastp_trim_json) : - ( - (!state.skip_trimming && input.size() == 2) ? - getTrimGaloreReadsAfterFiltering(state.trim_log_2) : - getTrimGaloreReadsAfterFiltering(state.trim_log_1) - ) - ) - def passed_trimmed_reads = - (state.skip_trimming || (num_reads >= state.min_trimmed_reads)) ? - true : - false - [ id, state + [num_trimmed_reads: num_reads, passed_trimmed_reads: passed_trimmed_reads] ] - } - - // Genome alignment and quantification - | genome_alignment_and_quant.run ( - runIf: { id, state -> !state.skip_alignment && state.passed_trimmed_reads }, - fromState: [ - "id": "id", - "fastq_1": "fastq_1", - "fastq_2": "fastq_2", - "strandedness": "strandedness", - "gtf": "gtf", - "transcript_fasta": "transcript_fasta", - "bam_csi_index": "bam_csi_index", - "aligner": "aligner", - "rsem_index": "rsem_index", - "star_index": "star_index", - "extra_star_align_args": "extra_star_align_args", - "star_ignore_sjdbgtf": "star_ignore_sjdbgtf", - "seq_platform": "seq_platform", - "seq_center": "seq_center", - "with_umi": "with_umi", - "umi_dedup_stats": "umi_dedup_stats", - "gtf_group_features": "gtf_group_features", - "gtf_extra_attributes": "gtf_extra_attributes", - "salmon_quant_libtype": "salmon_quant_libtype", - "salmon_index": "salmon_index", - "extra_rsem_calculate_expression_args": "extra_rsem_calculate_expression_args" - ], - toState: [ - "star_multiqc": "star_multiqc", - "rsem_multiqc": "rsem_multiqc", - "salmon_multiqc": "salmon_multiqc", + "star_log": "star_multiqc", "genome_bam_sorted": "genome_bam_sorted", "genome_bam_index": "genome_bam_index", "genome_bam_stats": "genome_bam_stats", @@ -4633,162 +4884,21 @@ workflow run_wf { "transcriptome_bam_stats": "transcriptome_bam_stats", "transcriptome_bam_flagstat": "transcriptome_bam_flagstat", "transcriptome_bam_idxstats": "transcriptome_bam_idxstats", - "quant_out_dir": "quant_out_dir", - "quant_results_file": "quant_results_file", - "rsem_counts_gene": "rsem_counts_gene", - "rsem_counts_transcripts": "rsem_counts_transcripts", - "bam_genome_rsem": "bam_genome_rsem", - "bam_transcript_rsem": "bam_transcript_rsem" - ] - ) - - // Filter channels to get samples that passed STAR minimum mapping percentage - | map { id, state -> - def percent_mapped = (!state.skip_alignment) ? getStarPercentMapped(state.star_multiqc) : 0.0 - def passed_mapping = (percent_mapped >= state.min_mapped_reads) ? true : false - [ id, state + [percent_mapped: percent_mapped, passed_mapping: passed_mapping] ] - } - - // Pseudo-alignment and quantification - | pseudo_alignment_and_quant.run ( - runIf: { id, state -> !state.skip_pseudo_alignment && state.passed_trimmed_reads }, - fromState: [ - "id": "id", - "fastq_1": "fastq_1", - "fastq_2": "fastq_2", - "strandedness": "strandedness", - "gtf": "gtf", - "transcript_fasta": "transcript_fasta", - "pseudo_aligner": "pseudo_aligner", - "salmon_index": "salmon_index", - "kallisto_index": "kallisto_index", - "extra_star_align_args": "extra_star_align_args", - "star_ignore_sjdbgtf": "star_ignore_sjdbgtf", - "seq_platform": "seq_platform", - "seq_center": "seq_center", - "with_umi": "with_umi", - "umi_dedup_stats": "umi_dedup_stats", - "gtf_group_features": "gtf_group_features", - "gtf_extra_attributes": "gtf_extra_attributes", - "lib_type": "salmon_quant_libtype", - "kallisto_quant_fragment_length": "kallisto_quant_fragment_length", - "kallisto_quant_fragment_length_sd": "kallisto_quant_fragment_length_sd" - ], - toState: [ - "pseudo_quant_out_dir": "quant_out_dir", - "pseudo_salmon_quant_results_file": "salmon_quant_results_file", - "pseudo_kallisto_quant_results_file": "kallisto_quant_results_file", - "pseudo_multiqc": "pseudo_multiqc" - ] - ) - - | map { id, state -> - def input = state.fastq_2 ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ] - def paired = input.size() == 2 - [ id, state + [ paired: paired ] ] - } - - // Post-processing - | post_processing.run ( - runIf: { id, state -> !state.skip_alignment && state.passed_trimmed_reads && state.passed_mapping }, - fromState: [ - "id": "id", - "paired": "paired", - "strandedness": "strandedness", - "fasta": "fasta", - "fai": "fai", - "gtf": "gtf", - "genome_bam": "genome_bam_sorted", - "chrom_sizes": "chrom_sizes", - "star_multiqc": "star_multiqc", - "extra_picard_args": "extra_picard_args", - "extra_stringtie_args": "extra_stringtie_args", - "stringtie_ignore_gtf": "stringtie_ignore_gtf", - "extra_bedtools_args": "extra_bedtools_args", - "bam_csi_index": "bam_csi_index", - "min_mapped_reads": "min_mapped_reads", - "with_umi": "with_umi", - "skip_qc": "skip_qc", - "skip_markduplicates": "skip_markduplicates", - "skip_stringtie": "skip_stringtie", - "skip_bigwig":"gencode" - ], - toState: [ - "genome_bam_sorted": "processed_genome_bam", - "genome_bam_index": "genome_bam_index", - "genome_bam_stats": "genome_bam_stats", - "genome_bam_flagstat": "genome_bam_flagstat", - "genome_bam_idxstats": "genome_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", "stringtie_ballgown": "stringtie_ballgown", + "featurecounts": "featurecounts", + "featurecounts_summary": "featurecounts_summary", + "featurecounts_multiqc": "featurecounts_multiqc", + "featurecounts_rrna_multiqc": "featurecounts_rrna_multiqc", "bedgraph_forward": "bedgraph_forward", "bedgraph_reverse": "bedgraph_reverse", "bigwig_forward": "bigwig_forward", - "bigwig_reverse": "bigwig_reverse" - ] - ) - - // Final QC - | quality_control.run ( - fromState: [ - "id": "id", - "paired": "paired", - "strandedness": "strandedness", - "skip_align": "skip_alignment", - "skip_pseudo_align": "skip_pseudo_alignment", - "skip_dupradar": "skip_dupradar", - "skip_qualimap": "skip_qualimap", - "skip_rseqc": "skip_rseqc", - "skip_multiqc": "skip_multiqc", - "skip_preseq": "skip_preseq", - "gtf": "gtf", - "num_trimmed_reads": "num_trimmed_reads", - "passed_trimmed_reads": "passed_trimmed_reads", - "passed_mapping": "passed_mapping", - "percent_mapped": "percent_mapped", - "genome_bam": "genome_bam_sorted", - "genome_bam_index": "genome_bam_index", - "salmon_multiqc": "salmon_multiqc", - "quant_results_file": "quant_results_file", - "rsem_multiqc": "rsem_multiqc", - "rsem_counts_gene": "rsem_counts_gene", - "rsem_counts_transcripts": "rsem_counts_transcripts", - "pseudo_multiqc": "pseudo_multiqc", - "pseudo_quant_out_dir": "pseudo_quant_out_dir", - "pseudo_salmon_quant_results_file": "pseudo_salmon_quant_results_file", - "pseudo_kallisto_quant_results_file": "pseudo_kallisto_quant_results_file", - "aligner": "aligner", - "pseudo_aligner": "pseudo_aligner", - "gene_bed": "gene_bed", - "extra_preseq_args": "extra_preseq_args", - "biotype": "biotype", - "skip_biotype_qc": "skip_biotype_qc", - "featurecounts_group_type": "featurecounts_group_type", - "featurecounts_feature_type": "featurecounts_feature_type", - "gencode": "gencode", - "skip_deseq2_qc": "skip_deseq2_qc", - "deseq2_vst": "deseq2_vst", - "multiqc_custom_config": "multiqc_custom_config", - "multiqc_title": "multiqc_title", - "multiqc_methods_description": "multiqc_methods_description", - "fastqc_zip_1": "fastqc_zip_1", - "fastqc_zip_2": "fastqc_zip_2", - "trim_log_1": "trim_log_1", - "trim_log_2": "trim_log_2", - "trim_zip_1": "trim_zip_1", - "trim_zip_2": "trim_zip_2", - "sortmerna_multiqc": "sortmerna_log", - "star_multiqc": "star_multiqc", - "genome_bam_stats": "genome_bam_stats", - "genome_bam_flagstat": "genome_bam_flagstat", - "genome_bam_idxstats": "genome_bam_idxstats", - "markduplicates_multiqc": "markduplicates_metrics", - "rseqc_modules": "rseqc_modules" - ], - toState: [ + "bigwig_reverse": "bigwig_reverse", "preseq_output": "preseq_output", "bamstat_output": "bamstat_output", "strandedness_output": "strandedness_output", @@ -4821,140 +4931,33 @@ workflow run_wf { "dupradar_output_expression_histogram": "dupradar_output_expression_histogram", "dupradar_output_intercept_slope": "dupradar_output_intercept_slope", "qualimap_output_dir": "qualimap_output_dir", - "qualimap_output_pdf": "qualimap_output_pdf", - "featurecounts": "featurecounts", - "featurecounts_summary": "featurecounts_summary", - "featurecounts_multiqc": "featurecounts_multiqc", - "featurecounts_rrna_multiqc": "featurecounts_rrna_multiqc", + "qualimap_output_pdf": "qualimap_output_pdf", "tpm_gene": "tpm_gene", "counts_gene": "counts_gene", "counts_gene_length_scaled": "counts_gene_length_scaled", "counts_gene_scaled": "counts_gene_scaled", "tpm_transcript": "tpm_transcript", "counts_transcript": "counts_transcript", - "qunat_merged_summarizedexperiment": "quant_merged_summarizedexperiment", + "quant_merged_summarizedexperiment": "quant_merged_summarizedexperiment", "deseq2_output": "deseq2_output", + "pseudo_tpm_gene": "pseudo_tpm_gene", + "pseudo_counts_gene": "pseudo_counts_gene", + "pseudo_counts_gene_length_scaled": "pseudo_counts_gene_length_scaled", + "pseudo_counts_gene_scaled": "pseudo_counts_gene_scaled", + "pseudo_tpm_transcript": "pseudo_tpm_transcript", + "pseudo_counts_transcript": "pseudo_counts_transcript", + "pseudo_lengths_gene": "pseudo_lengths_gene", + "pseudo_lengths_transcript": "pseudo_lengths_transcript", + "pseudo_quant_merged_summarizedexperiment": "pseudo_quant_merged_summarizedexperiment", + "deseq2_output_pseudo": "deseq2_output_pseudo", "multiqc_report": "multiqc_report", "multiqc_data": "multiqc_data", "multiqc_plots": "multiqc_plots" - ] - ) - - | map { id, state -> - def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() } - [ id, mod_state ] - } - - | setState ( - [ - "output_fasta": "fasta", - "output_gtf": "gtf", - "output_transcript_fasta": "transcript_fasta", - "output_gene_bed": "gene_bed", - "output_bbsplit_index": "bbsplit_index", - "output_star_index": "star_index", - "output_salmon_index": "salmon_index", - "output_kallisto_index": "kallisto_index", - "fastqc_html_1": "fastqc_html_1", - "fastqc_html_2": "fastqc_html_2", - "fastqc_zip_1": "fastqc_zip_1", - "fastqc_zip_2": "fastqc_zip_2", - "output_fastq_1": "fastq_1", - "output_fastq_2": "fastq_2", - "trim_log_1": "trim_log_1", - "trim_log_2": "trim_log_2", - "trim_zip_1": "trim_zip_1", - "trim_zip_2": "trim_zip_2", - "trim_html_1": "trim_html_1", - "trim_html_2": "trim_html_2", - "sortmerna_log": "sortmerna_log", - "star_log": "star_multiqc", - "genome_bam_sorted": "genome_bam_sorted", - "genome_bam_index": "genome_bam_index", - "genome_bam_stats": "genome_bam_stats", - "genome_bam_flagstat": "genome_bam_flagstat", - "genome_bam_idxstats": "genome_bam_idxstats", - "transcriptome_bam": "transcriptome_bam", - "transcriptome_bam_index": "transcriptome_bam_index", - "transcriptome_bam_stats": "transcriptome_bam_stats", - "transcriptome_bam_flagstat": "transcriptome_bam_flagstat", - "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", - "stringtie_ballgown": "stringtie_ballgown", - "featurecounts": "featurecounts", - "featurecounts_summary": "featurecounts_summary", - "featurecounts_multiqc": "featurecounts_multiqc", - "featurecounts_rrna_multiqc": "featurecounts_rrna_multiqc", - "bedgraph_forward": "bedgraph_forward", - "bedgraph_reverse": "bedgraph_reverse", - "bigwig_forward": "bigwig_forward", - "bigwig_reverse": "bigwig_reverse", - "preseq_output": "preseq_output", - "bamstat_output": "bamstat_output", - "strandedness_output": "strandedness_output", - "inner_dist_output_stats": "inner_dist_output_stats", - "inner_dist_output_dist": "inner_dist_output_dist", - "inner_dist_output_freq": "inner_dist_output_freq", - "inner_dist_output_plot": "inner_dist_output_plot", - "inner_dist_output_plot_r": "inner_dist_output_plot_r", - "junction_annotation_output_log": "junction_annotation_output_log", - "junction_annotation_output_plot_r": "junction_annotation_output_plot_r", - "junction_annotation_output_junction_bed": "junction_annotation_output_junction_bed", - "junction_annotation_output_junction_interact": "junction_annotation_output_junction_interact", - "junction_annotation_output_junction_sheet": "junction_annotation_output_junction_sheet", - "junction_annotation_output_splice_events_plot": "junction_annotation_output_splice_events_plot", - "junction_annotation_output_splice_junctions_plot": "junction_annotation_output_splice_junctions_plot", - "junction_saturation_output_plot_r": "junction_saturation_output_plot_r", - "junction_saturation_output_plot": "junction_saturation_output_plot", - "read_distribution_output": "read_distribution_output", - "read_duplication_output_duplication_rate_plot_r": "read_duplication_output_duplication_rate_plot_r", - "read_duplication_output_duplication_rate_plot": "read_duplication_output_duplication_rate_plot", - "read_duplication_output_duplication_rate_mapping": "read_duplication_output_duplication_rate_mapping", - "read_duplication_output_duplication_rate_sequence": "read_duplication_output_duplication_rate_sequence", - "tin_output_summary": "tin_output_summary", - "tin_output_metrics": "tin_output_metrics", - "dupradar_output_dupmatrix": "dupradar_output_dupmatrix", - "dupradar_output_dup_intercept_mqc": "dupradar_output_dup_intercept_mqc", - "dupradar_output_duprate_exp_boxplot": "dupradar_output_duprate_exp_boxplot", - "dupradar_output_duprate_exp_densplot": "dupradar_output_duprate_exp_densplot", - "dupradar_output_duprate_exp_denscurve_mqc": "dupradar_output_duprate_exp_denscurve_mqc", - "dupradar_output_expression_histogram": "dupradar_output_expression_histogram", - "dupradar_output_intercept_slope": "dupradar_output_intercept_slope", - "qualimap_output_dir": "qualimap_output_dir", - "qualimap_output_pdf": "qualimap_output_pdf", - "tpm_gene": "tpm_gene", - "counts_gene": "counts_gene", - "counts_gene_length_scaled": "counts_gene_length_scaled", - "counts_gene_scaled": "counts_gene_scaled", - "tpm_transcript": "tpm_transcript", - "counts_transcript": "counts_transcript", - "quant_merged_summarizedexperiment": "quant_merged_summarizedexperiment", - "deseq2_output": "deseq2_output", - "pseudo_tpm_gene": "pseudo_tpm_gene", - "pseudo_counts_gene": "pseudo_counts_gene", - "pseudo_counts_gene_length_scaled": "pseudo_counts_gene_length_scaled", - "pseudo_counts_gene_scaled": "pseudo_counts_gene_scaled", - "pseudo_tpm_transcript": "pseudo_tpm_transcript", - "pseudo_counts_transcript": "pseudo_counts_transcript", - "pseudo_lengths_gene": "pseudo_lengths_gene", - "pseudo_lengths_transcript": "pseudo_lengths_transcript", - "pseudo_quant_merged_summarizedexperiment": "pseudo_quant_merged_summarizedexperiment", - "deseq2_output_pseudo": "deseq2_output_pseudo", - "multiqc_report": "multiqc_report", - "multiqc_data": "multiqc_data", - "multiqc_plots": "multiqc_plots" - ] - ) - - output_ch = analysis_ch + ] + ) emit: - output_ch + analysis_ch } import nextflow.Nextflow diff --git a/target/nextflow/bbmap_bbsplit/.config.vsh.yaml b/target/nextflow/bbmap_bbsplit/.config.vsh.yaml index ba27800..125e6e1 100644 --- a/target/nextflow/bbmap_bbsplit/.config.vsh.yaml +++ b/target/nextflow/bbmap_bbsplit/.config.vsh.yaml @@ -246,8 +246,8 @@ build_info: output: "target/nextflow/bbmap_bbsplit" executable: "target/nextflow/bbmap_bbsplit/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/bbmap_bbsplit/main.nf b/target/nextflow/bbmap_bbsplit/main.nf index 4db13c2..e28ffc6 100644 --- a/target/nextflow/bbmap_bbsplit/main.nf +++ b/target/nextflow/bbmap_bbsplit/main.nf @@ -3116,8 +3116,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/bbmap_bbsplit", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/bbmap_bbsplit/nextflow_schema.json b/target/nextflow/bbmap_bbsplit/nextflow_schema.json index d2c006d..450686b 100644 --- a/target/nextflow/bbmap_bbsplit/nextflow_schema.json +++ b/target/nextflow/bbmap_bbsplit/nextflow_schema.json @@ -30,7 +30,7 @@ "description": "Type: `boolean`, default: `false`. Paired fastq files or not?", "help_text": "Type: `boolean`, default: `false`. Paired fastq files or not?" , - "default": "False" + "default":false } @@ -101,7 +101,7 @@ "description": "Type: `file`, default: `$id.$key.fastq_1.fastq`. Output file for read 1", "help_text": "Type: `file`, default: `$id.$key.fastq_1.fastq`. Output file for read 1." , - "default": "$id.$key.fastq_1.fastq" + "default":"$id.$key.fastq_1.fastq" } @@ -112,7 +112,7 @@ "description": "Type: `file`, default: `$id.$key.fastq_2.fastq`. Output file for read 2", "help_text": "Type: `file`, default: `$id.$key.fastq_2.fastq`. Output file for read 2." , - "default": "$id.$key.fastq_2.fastq" + "default":"$id.$key.fastq_2.fastq" } @@ -123,7 +123,7 @@ "description": "Type: `file`, default: `$id.$key.bbsplit_index.bbsplit_index`. Directory with index files", "help_text": "Type: `file`, default: `$id.$key.bbsplit_index.bbsplit_index`. Directory with index files" , - "default": "$id.$key.bbsplit_index.bbsplit_index" + "default":"$id.$key.bbsplit_index.bbsplit_index" } diff --git a/target/nextflow/bedtools_genomecov/.config.vsh.yaml b/target/nextflow/bedtools_genomecov/.config.vsh.yaml index b771d23..066af61 100644 --- a/target/nextflow/bedtools_genomecov/.config.vsh.yaml +++ b/target/nextflow/bedtools_genomecov/.config.vsh.yaml @@ -186,8 +186,8 @@ build_info: output: "target/nextflow/bedtools_genomecov" executable: "target/nextflow/bedtools_genomecov/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/bedtools_genomecov/main.nf b/target/nextflow/bedtools_genomecov/main.nf index 2e1e947..3edb508 100644 --- a/target/nextflow/bedtools_genomecov/main.nf +++ b/target/nextflow/bedtools_genomecov/main.nf @@ -3043,8 +3043,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/bedtools_genomecov", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/bedtools_genomecov/nextflow_schema.json b/target/nextflow/bedtools_genomecov/nextflow_schema.json index 58ca8b7..311b6f8 100644 --- a/target/nextflow/bedtools_genomecov/nextflow_schema.json +++ b/target/nextflow/bedtools_genomecov/nextflow_schema.json @@ -42,7 +42,7 @@ "description": "Type: `string`, default: ``. ", "help_text": "Type: `string`, default: ``. " , - "default": "" + "default":"" } @@ -63,7 +63,7 @@ "description": "Type: `file`, default: `$id.$key.bedgraph_forward.bedgraph`. ", "help_text": "Type: `file`, default: `$id.$key.bedgraph_forward.bedgraph`. " , - "default": "$id.$key.bedgraph_forward.bedgraph" + "default":"$id.$key.bedgraph_forward.bedgraph" } @@ -74,7 +74,7 @@ "description": "Type: `file`, default: `$id.$key.bedgraph_reverse.bedgraph`. ", "help_text": "Type: `file`, default: `$id.$key.bedgraph_reverse.bedgraph`. " , - "default": "$id.$key.bedgraph_reverse.bedgraph" + "default":"$id.$key.bedgraph_reverse.bedgraph" } diff --git a/target/nextflow/cat_additional_fasta/.config.vsh.yaml b/target/nextflow/cat_additional_fasta/.config.vsh.yaml index e7fee86..a9fe71d 100644 --- a/target/nextflow/cat_additional_fasta/.config.vsh.yaml +++ b/target/nextflow/cat_additional_fasta/.config.vsh.yaml @@ -190,8 +190,8 @@ build_info: output: "target/nextflow/cat_additional_fasta" executable: "target/nextflow/cat_additional_fasta/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/cat_additional_fasta/main.nf b/target/nextflow/cat_additional_fasta/main.nf index 9d9d051..b278b14 100644 --- a/target/nextflow/cat_additional_fasta/main.nf +++ b/target/nextflow/cat_additional_fasta/main.nf @@ -3044,8 +3044,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/cat_additional_fasta", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/cat_additional_fasta/nextflow_schema.json b/target/nextflow/cat_additional_fasta/nextflow_schema.json index 43c1747..61a5eee 100644 --- a/target/nextflow/cat_additional_fasta/nextflow_schema.json +++ b/target/nextflow/cat_additional_fasta/nextflow_schema.json @@ -70,7 +70,7 @@ "description": "Type: `file`, default: `$id.$key.fasta_output.fasta_output`. Concatenated FASTA file", "help_text": "Type: `file`, default: `$id.$key.fasta_output.fasta_output`. Concatenated FASTA file." , - "default": "$id.$key.fasta_output.fasta_output" + "default":"$id.$key.fasta_output.fasta_output" } @@ -81,7 +81,7 @@ "description": "Type: `file`, default: `$id.$key.gtf_output.gtf_output`. Concatenated GTF file", "help_text": "Type: `file`, default: `$id.$key.gtf_output.gtf_output`. Concatenated GTF file." , - "default": "$id.$key.gtf_output.gtf_output" + "default":"$id.$key.gtf_output.gtf_output" } diff --git a/target/nextflow/cat_fastq/.config.vsh.yaml b/target/nextflow/cat_fastq/.config.vsh.yaml index 3173e21..6d279bd 100644 --- a/target/nextflow/cat_fastq/.config.vsh.yaml +++ b/target/nextflow/cat_fastq/.config.vsh.yaml @@ -177,8 +177,8 @@ build_info: output: "target/nextflow/cat_fastq" executable: "target/nextflow/cat_fastq/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/cat_fastq/main.nf b/target/nextflow/cat_fastq/main.nf index f3cefa4..7e0a456 100644 --- a/target/nextflow/cat_fastq/main.nf +++ b/target/nextflow/cat_fastq/main.nf @@ -3035,8 +3035,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/cat_fastq", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/cat_fastq/nextflow_schema.json b/target/nextflow/cat_fastq/nextflow_schema.json index 800cc2b..af6d77a 100644 --- a/target/nextflow/cat_fastq/nextflow_schema.json +++ b/target/nextflow/cat_fastq/nextflow_schema.json @@ -50,7 +50,7 @@ "description": "Type: `file`, default: `$id.$key.fastq_1.fastq`. Concatenated read 1 fastq", "help_text": "Type: `file`, default: `$id.$key.fastq_1.fastq`. Concatenated read 1 fastq" , - "default": "$id.$key.fastq_1.fastq" + "default":"$id.$key.fastq_1.fastq" } @@ -61,7 +61,7 @@ "description": "Type: `file`, default: `$id.$key.fastq_2.fastq`. Concatenated read 2 fastq", "help_text": "Type: `file`, default: `$id.$key.fastq_2.fastq`. Concatenated read 2 fastq" , - "default": "$id.$key.fastq_2.fastq" + "default":"$id.$key.fastq_2.fastq" } diff --git a/target/nextflow/deseq2_qc/.config.vsh.yaml b/target/nextflow/deseq2_qc/.config.vsh.yaml index e07c71c..5c8681d 100644 --- a/target/nextflow/deseq2_qc/.config.vsh.yaml +++ b/target/nextflow/deseq2_qc/.config.vsh.yaml @@ -245,8 +245,8 @@ build_info: output: "target/nextflow/deseq2_qc" executable: "target/nextflow/deseq2_qc/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/deseq2_qc/main.nf b/target/nextflow/deseq2_qc/main.nf index f2518ad..8d3c52d 100644 --- a/target/nextflow/deseq2_qc/main.nf +++ b/target/nextflow/deseq2_qc/main.nf @@ -3116,8 +3116,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/deseq2_qc", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/deseq2_qc/nextflow_schema.json b/target/nextflow/deseq2_qc/nextflow_schema.json index 8bd6fa4..828a82f 100644 --- a/target/nextflow/deseq2_qc/nextflow_schema.json +++ b/target/nextflow/deseq2_qc/nextflow_schema.json @@ -30,7 +30,7 @@ "description": "Type: `boolean`, default: `false`. Use vst transformation instead of rlog with ", "help_text": "Type: `boolean`, default: `false`. Use vst transformation instead of rlog with .DESeq2" , - "default": "False" + "default":false } @@ -41,7 +41,7 @@ "description": "Type: `integer`, default: `3`. First column containing sample count data", "help_text": "Type: `integer`, default: `3`. First column containing sample count data." , - "default": "3" + "default":3 } @@ -52,7 +52,7 @@ "description": "Type: `integer`, default: `1`. Column containing identifiers to be used", "help_text": "Type: `integer`, default: `1`. Column containing identifiers to be used." , - "default": "1" + "default":1 } @@ -63,7 +63,7 @@ "description": "Type: `string`, default: ``. Suffix to remove after sample name in columns e", "help_text": "Type: `string`, default: ``. Suffix to remove after sample name in columns e.g. \u0027.rmDup.bam\u0027 if \u0027DRUG_R1.rmDup.bam\u0027." , - "default": "" + "default":"" } @@ -74,7 +74,7 @@ "description": "Type: `string`, default: `deseq2`. Output prefix", "help_text": "Type: `string`, default: `deseq2`. Output prefix" , - "default": "deseq2" + "default":"deseq2" } @@ -105,7 +105,7 @@ "description": "Type: `file`, default: `$id.$key.outdir.outdir`. ", "help_text": "Type: `file`, default: `$id.$key.outdir.outdir`. " , - "default": "$id.$key.outdir.outdir" + "default":"$id.$key.outdir.outdir" } @@ -116,7 +116,7 @@ "description": "Type: `file`, default: `$id.$key.pca_multiqc.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.pca_multiqc.tsv`. " , - "default": "$id.$key.pca_multiqc.tsv" + "default":"$id.$key.pca_multiqc.tsv" } @@ -127,7 +127,7 @@ "description": "Type: `file`, default: `$id.$key.sample_dists_multiqc.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.sample_dists_multiqc.tsv`. " , - "default": "$id.$key.sample_dists_multiqc.tsv" + "default":"$id.$key.sample_dists_multiqc.tsv" } diff --git a/target/nextflow/dupradar/.config.vsh.yaml b/target/nextflow/dupradar/.config.vsh.yaml index 4c6a208..c8bbc7a 100644 --- a/target/nextflow/dupradar/.config.vsh.yaml +++ b/target/nextflow/dupradar/.config.vsh.yaml @@ -274,8 +274,8 @@ build_info: output: "target/nextflow/dupradar" executable: "target/nextflow/dupradar/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/dupradar/main.nf b/target/nextflow/dupradar/main.nf index c152cb9..61ad5a7 100644 --- a/target/nextflow/dupradar/main.nf +++ b/target/nextflow/dupradar/main.nf @@ -3148,8 +3148,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/dupradar", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/dupradar/nextflow_schema.json b/target/nextflow/dupradar/nextflow_schema.json index cd113eb..d5c3ad3 100644 --- a/target/nextflow/dupradar/nextflow_schema.json +++ b/target/nextflow/dupradar/nextflow_schema.json @@ -82,7 +82,7 @@ "description": "Type: `file`, default: `$id.$key.output_dupmatrix.txt`. path to output file (txt) of duplicate tag counts", "help_text": "Type: `file`, default: `$id.$key.output_dupmatrix.txt`. path to output file (txt) of duplicate tag counts" , - "default": "$id.$key.output_dupmatrix.txt" + "default":"$id.$key.output_dupmatrix.txt" } @@ -93,7 +93,7 @@ "description": "Type: `file`, default: `$id.$key.output_dup_intercept_mqc.txt`. path to output file (txt) of multiqc intercept value DupRadar", "help_text": "Type: `file`, default: `$id.$key.output_dup_intercept_mqc.txt`. path to output file (txt) of multiqc intercept value DupRadar" , - "default": "$id.$key.output_dup_intercept_mqc.txt" + "default":"$id.$key.output_dup_intercept_mqc.txt" } @@ -104,7 +104,7 @@ "description": "Type: `file`, default: `$id.$key.output_duprate_exp_boxplot.pdf`. path to output file (pdf) of distribution of expression box plot", "help_text": "Type: `file`, default: `$id.$key.output_duprate_exp_boxplot.pdf`. path to output file (pdf) of distribution of expression box plot" , - "default": "$id.$key.output_duprate_exp_boxplot.pdf" + "default":"$id.$key.output_duprate_exp_boxplot.pdf" } @@ -115,7 +115,7 @@ "description": "Type: `file`, default: `$id.$key.output_duprate_exp_densplot.pdf`. path to output file (pdf) of 2D density scatter plot of duplicate tag counts", "help_text": "Type: `file`, default: `$id.$key.output_duprate_exp_densplot.pdf`. path to output file (pdf) of 2D density scatter plot of duplicate tag counts" , - "default": "$id.$key.output_duprate_exp_densplot.pdf" + "default":"$id.$key.output_duprate_exp_densplot.pdf" } @@ -126,7 +126,7 @@ "description": "Type: `file`, default: `$id.$key.output_duprate_exp_denscurve_mqc.txt`. path to output file (pdf) of density curve of gene duplication multiqc", "help_text": "Type: `file`, default: `$id.$key.output_duprate_exp_denscurve_mqc.txt`. path to output file (pdf) of density curve of gene duplication multiqc" , - "default": "$id.$key.output_duprate_exp_denscurve_mqc.txt" + "default":"$id.$key.output_duprate_exp_denscurve_mqc.txt" } @@ -137,7 +137,7 @@ "description": "Type: `file`, default: `$id.$key.output_expression_histogram.pdf`. path to output file (pdf) of distribution of RPK values per gene histogram", "help_text": "Type: `file`, default: `$id.$key.output_expression_histogram.pdf`. path to output file (pdf) of distribution of RPK values per gene histogram" , - "default": "$id.$key.output_expression_histogram.pdf" + "default":"$id.$key.output_expression_histogram.pdf" } @@ -148,7 +148,7 @@ "description": "Type: `file`, default: `$id.$key.output_intercept_slope.txt`. output file (txt) with progression of duplication rate value", "help_text": "Type: `file`, default: `$id.$key.output_intercept_slope.txt`. output file (txt) with progression of duplication rate value" , - "default": "$id.$key.output_intercept_slope.txt" + "default":"$id.$key.output_intercept_slope.txt" } diff --git a/target/nextflow/fastqc/.config.vsh.yaml b/target/nextflow/fastqc/.config.vsh.yaml index 74a0cf8..0ee51d8 100644 --- a/target/nextflow/fastqc/.config.vsh.yaml +++ b/target/nextflow/fastqc/.config.vsh.yaml @@ -206,8 +206,8 @@ build_info: output: "target/nextflow/fastqc" executable: "target/nextflow/fastqc/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/fastqc/main.nf b/target/nextflow/fastqc/main.nf index 9973e90..9361364 100644 --- a/target/nextflow/fastqc/main.nf +++ b/target/nextflow/fastqc/main.nf @@ -3068,8 +3068,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/fastqc", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/fastqc/nextflow_schema.json b/target/nextflow/fastqc/nextflow_schema.json index 593cc46..868796b 100644 --- a/target/nextflow/fastqc/nextflow_schema.json +++ b/target/nextflow/fastqc/nextflow_schema.json @@ -20,7 +20,7 @@ "description": "Type: `boolean`, default: `false`. Paired fastq files or not?", "help_text": "Type: `boolean`, default: `false`. Paired fastq files or not?" , - "default": "False" + "default":false } @@ -51,7 +51,7 @@ "description": "Type: `file`, default: `$id.$key.fastqc_html_1.html`. FastQC HTML report for read 1", "help_text": "Type: `file`, default: `$id.$key.fastqc_html_1.html`. FastQC HTML report for read 1." , - "default": "$id.$key.fastqc_html_1.html" + "default":"$id.$key.fastqc_html_1.html" } @@ -62,7 +62,7 @@ "description": "Type: `file`, default: `$id.$key.fastqc_html_2.html`. FastQC HTML report for read 2", "help_text": "Type: `file`, default: `$id.$key.fastqc_html_2.html`. FastQC HTML report for read 2." , - "default": "$id.$key.fastqc_html_2.html" + "default":"$id.$key.fastqc_html_2.html" } @@ -73,7 +73,7 @@ "description": "Type: `file`, default: `$id.$key.fastqc_zip_1.zip`. FastQC report archive for read 1", "help_text": "Type: `file`, default: `$id.$key.fastqc_zip_1.zip`. FastQC report archive for read 1." , - "default": "$id.$key.fastqc_zip_1.zip" + "default":"$id.$key.fastqc_zip_1.zip" } @@ -84,7 +84,7 @@ "description": "Type: `file`, default: `$id.$key.fastqc_zip_2.zip`. FastQC report archive for read 2", "help_text": "Type: `file`, default: `$id.$key.fastqc_zip_2.zip`. FastQC report archive for read 2." , - "default": "$id.$key.fastqc_zip_2.zip" + "default":"$id.$key.fastqc_zip_2.zip" } diff --git a/target/nextflow/fq_subsample/.config.vsh.yaml b/target/nextflow/fq_subsample/.config.vsh.yaml index e79acc3..4f4c929 100644 --- a/target/nextflow/fq_subsample/.config.vsh.yaml +++ b/target/nextflow/fq_subsample/.config.vsh.yaml @@ -185,8 +185,8 @@ build_info: output: "target/nextflow/fq_subsample" executable: "target/nextflow/fq_subsample/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/fq_subsample/main.nf b/target/nextflow/fq_subsample/main.nf index 6c972cf..4280473 100644 --- a/target/nextflow/fq_subsample/main.nf +++ b/target/nextflow/fq_subsample/main.nf @@ -3039,8 +3039,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/fq_subsample", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/fq_subsample/nextflow_schema.json b/target/nextflow/fq_subsample/nextflow_schema.json index 920835a..0a22405 100644 --- a/target/nextflow/fq_subsample/nextflow_schema.json +++ b/target/nextflow/fq_subsample/nextflow_schema.json @@ -30,7 +30,7 @@ "description": "Type: `string`, default: ``. Extra arguments to pass to fq subsample", "help_text": "Type: `string`, default: ``. Extra arguments to pass to fq subsample" , - "default": "" + "default":"" } @@ -51,7 +51,7 @@ "description": "Type: `file`, default: `$id.$key.output_1.fastq`. Sampled read 1 fastq files", "help_text": "Type: `file`, default: `$id.$key.output_1.fastq`. Sampled read 1 fastq files" , - "default": "$id.$key.output_1.fastq" + "default":"$id.$key.output_1.fastq" } @@ -62,7 +62,7 @@ "description": "Type: `file`, default: `$id.$key.output_2.fastq`. Sampled read 2 fastq files", "help_text": "Type: `file`, default: `$id.$key.output_2.fastq`. Sampled read 2 fastq files" , - "default": "$id.$key.output_2.fastq" + "default":"$id.$key.output_2.fastq" } diff --git a/target/nextflow/getchromsizes/.config.vsh.yaml b/target/nextflow/getchromsizes/.config.vsh.yaml index ca9ec0b..18fccec 100644 --- a/target/nextflow/getchromsizes/.config.vsh.yaml +++ b/target/nextflow/getchromsizes/.config.vsh.yaml @@ -175,8 +175,8 @@ build_info: output: "target/nextflow/getchromsizes" executable: "target/nextflow/getchromsizes/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/getchromsizes/main.nf b/target/nextflow/getchromsizes/main.nf index a54973c..80d23f5 100644 --- a/target/nextflow/getchromsizes/main.nf +++ b/target/nextflow/getchromsizes/main.nf @@ -3025,8 +3025,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/getchromsizes", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/getchromsizes/nextflow_schema.json b/target/nextflow/getchromsizes/nextflow_schema.json index da770aa..f6a05b2 100644 --- a/target/nextflow/getchromsizes/nextflow_schema.json +++ b/target/nextflow/getchromsizes/nextflow_schema.json @@ -40,7 +40,7 @@ "description": "Type: `file`, default: `$id.$key.sizes.sizes`. File containing chromosome lengths", "help_text": "Type: `file`, default: `$id.$key.sizes.sizes`. File containing chromosome lengths" , - "default": "$id.$key.sizes.sizes" + "default":"$id.$key.sizes.sizes" } @@ -51,7 +51,7 @@ "description": "Type: `file`, default: `$id.$key.fai.fai`. FASTA index file", "help_text": "Type: `file`, default: `$id.$key.fai.fai`. FASTA index file" , - "default": "$id.$key.fai.fai" + "default":"$id.$key.fai.fai" } @@ -62,7 +62,7 @@ "description": "Type: `file`, default: `$id.$key.gzi.gzi`. Optional gzip index file for compressed inputs", "help_text": "Type: `file`, default: `$id.$key.gzi.gzi`. Optional gzip index file for compressed inputs" , - "default": "$id.$key.gzi.gzi" + "default":"$id.$key.gzi.gzi" } diff --git a/target/nextflow/gtf2bed/.config.vsh.yaml b/target/nextflow/gtf2bed/.config.vsh.yaml index 71d0d9b..be1798e 100644 --- a/target/nextflow/gtf2bed/.config.vsh.yaml +++ b/target/nextflow/gtf2bed/.config.vsh.yaml @@ -153,8 +153,8 @@ build_info: output: "target/nextflow/gtf2bed" executable: "target/nextflow/gtf2bed/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/gtf2bed/main.nf b/target/nextflow/gtf2bed/main.nf index fa4b8a5..c70aa5e 100644 --- a/target/nextflow/gtf2bed/main.nf +++ b/target/nextflow/gtf2bed/main.nf @@ -3007,8 +3007,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/gtf2bed", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/gtf2bed/nextflow_schema.json b/target/nextflow/gtf2bed/nextflow_schema.json index a151d8e..ae24eac 100644 --- a/target/nextflow/gtf2bed/nextflow_schema.json +++ b/target/nextflow/gtf2bed/nextflow_schema.json @@ -40,7 +40,7 @@ "description": "Type: `file`, required, default: `$id.$key.bed_output.bed_output`. BED file resulting from the conversion of the GTF input file", "help_text": "Type: `file`, required, default: `$id.$key.bed_output.bed_output`. BED file resulting from the conversion of the GTF input file." , - "default": "$id.$key.bed_output.bed_output" + "default":"$id.$key.bed_output.bed_output" } diff --git a/target/nextflow/gtf_filter/.config.vsh.yaml b/target/nextflow/gtf_filter/.config.vsh.yaml index 46ad108..c39fa92 100644 --- a/target/nextflow/gtf_filter/.config.vsh.yaml +++ b/target/nextflow/gtf_filter/.config.vsh.yaml @@ -163,8 +163,8 @@ build_info: output: "target/nextflow/gtf_filter" executable: "target/nextflow/gtf_filter/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/gtf_filter/main.nf b/target/nextflow/gtf_filter/main.nf index 8f6f09e..7e1eb3f 100644 --- a/target/nextflow/gtf_filter/main.nf +++ b/target/nextflow/gtf_filter/main.nf @@ -3015,8 +3015,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/gtf_filter", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/gtf_filter/nextflow_schema.json b/target/nextflow/gtf_filter/nextflow_schema.json index aaf4b67..ded4692 100644 --- a/target/nextflow/gtf_filter/nextflow_schema.json +++ b/target/nextflow/gtf_filter/nextflow_schema.json @@ -40,7 +40,7 @@ "description": "Type: `boolean_true`, default: `false`. Skip checking for transcript IDs in the GTF file", "help_text": "Type: `boolean_true`, default: `false`. Skip checking for transcript IDs in the GTF file." , - "default": "False" + "default":false } @@ -61,7 +61,7 @@ "description": "Type: `file`, default: `$id.$key.filtered_gtf.filtered_gtf`. Filtered GTF file containing only sequences in the FASTA file", "help_text": "Type: `file`, default: `$id.$key.filtered_gtf.filtered_gtf`. Filtered GTF file containing only sequences in the FASTA file" , - "default": "$id.$key.filtered_gtf.filtered_gtf" + "default":"$id.$key.filtered_gtf.filtered_gtf" } diff --git a/target/nextflow/gunzip/.config.vsh.yaml b/target/nextflow/gunzip/.config.vsh.yaml index 6454718..e7ae9b9 100644 --- a/target/nextflow/gunzip/.config.vsh.yaml +++ b/target/nextflow/gunzip/.config.vsh.yaml @@ -152,8 +152,8 @@ build_info: output: "target/nextflow/gunzip" executable: "target/nextflow/gunzip/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/gunzip/main.nf b/target/nextflow/gunzip/main.nf index 45ded41..6b3d2e0 100644 --- a/target/nextflow/gunzip/main.nf +++ b/target/nextflow/gunzip/main.nf @@ -3004,8 +3004,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/gunzip", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/gunzip/nextflow_schema.json b/target/nextflow/gunzip/nextflow_schema.json index d1639ae..19860ae 100644 --- a/target/nextflow/gunzip/nextflow_schema.json +++ b/target/nextflow/gunzip/nextflow_schema.json @@ -40,7 +40,7 @@ "description": "Type: `file`, required, default: `$id.$key.output.output`. Decompressed file", "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Decompressed file." , - "default": "$id.$key.output.output" + "default":"$id.$key.output.output" } diff --git a/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml b/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml index 908766a..2d43afd 100644 --- a/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml +++ b/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml @@ -163,8 +163,8 @@ build_info: output: "target/nextflow/kallisto/kallisto_index" executable: "target/nextflow/kallisto/kallisto_index/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/kallisto/kallisto_index/main.nf b/target/nextflow/kallisto/kallisto_index/main.nf index 5ca5690..fd3286c 100644 --- a/target/nextflow/kallisto/kallisto_index/main.nf +++ b/target/nextflow/kallisto/kallisto_index/main.nf @@ -3014,8 +3014,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/kallisto/kallisto_index", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/kallisto/kallisto_index/nextflow_schema.json b/target/nextflow/kallisto/kallisto_index/nextflow_schema.json index c2651b0..837bc7c 100644 --- a/target/nextflow/kallisto/kallisto_index/nextflow_schema.json +++ b/target/nextflow/kallisto/kallisto_index/nextflow_schema.json @@ -50,7 +50,7 @@ "description": "Type: `file`, default: `$id.$key.kallisto_index.kallisto_index`. ", "help_text": "Type: `file`, default: `$id.$key.kallisto_index.kallisto_index`. " , - "default": "$id.$key.kallisto_index.kallisto_index" + "default":"$id.$key.kallisto_index.kallisto_index" } diff --git a/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml b/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml index 44aad38..437868a 100644 --- a/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml +++ b/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml @@ -261,8 +261,8 @@ build_info: output: "target/nextflow/kallisto/kallisto_quant" executable: "target/nextflow/kallisto/kallisto_quant/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/kallisto/kallisto_quant/main.nf b/target/nextflow/kallisto/kallisto_quant/main.nf index 0c5979d..bdc3eff 100644 --- a/target/nextflow/kallisto/kallisto_quant/main.nf +++ b/target/nextflow/kallisto/kallisto_quant/main.nf @@ -3126,8 +3126,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/kallisto/kallisto_quant", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/kallisto/kallisto_quant/nextflow_schema.json b/target/nextflow/kallisto/kallisto_quant/nextflow_schema.json index 91ca2a2..14f0600 100644 --- a/target/nextflow/kallisto/kallisto_quant/nextflow_schema.json +++ b/target/nextflow/kallisto/kallisto_quant/nextflow_schema.json @@ -110,7 +110,7 @@ "description": "Type: `file`, default: `$id.$key.output.kallisto_quant_results`. Kallisto quant results", "help_text": "Type: `file`, default: `$id.$key.output.kallisto_quant_results`. Kallisto quant results" , - "default": "$id.$key.output.kallisto_quant_results" + "default":"$id.$key.output.kallisto_quant_results" } @@ -121,7 +121,7 @@ "description": "Type: `file`, default: `$id.$key.log.txt`. File containing log information from running kallisto quant", "help_text": "Type: `file`, default: `$id.$key.log.txt`. File containing log information from running kallisto quant" , - "default": "$id.$key.log.txt" + "default":"$id.$key.log.txt" } @@ -132,7 +132,7 @@ "description": "Type: `file`, default: `$id.$key.run_info.json`. A json file containing information about the run", "help_text": "Type: `file`, default: `$id.$key.run_info.json`. A json file containing information about the run" , - "default": "$id.$key.run_info.json" + "default":"$id.$key.run_info.json" } @@ -143,7 +143,7 @@ "description": "Type: `file`, default: `$id.$key.quant_results_file.tsv`. TSV file containing abundance estimates from Kallisto", "help_text": "Type: `file`, default: `$id.$key.quant_results_file.tsv`. TSV file containing abundance estimates from Kallisto" , - "default": "$id.$key.quant_results_file.tsv" + "default":"$id.$key.quant_results_file.tsv" } diff --git a/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml b/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml index 5498a20..a4ca1d5 100644 --- a/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml +++ b/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml @@ -169,8 +169,8 @@ build_info: output: "target/nextflow/multiqc_custom_biotype" executable: "target/nextflow/multiqc_custom_biotype/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/multiqc_custom_biotype/main.nf b/target/nextflow/multiqc_custom_biotype/main.nf index 0eebb32..d2347e5 100644 --- a/target/nextflow/multiqc_custom_biotype/main.nf +++ b/target/nextflow/multiqc_custom_biotype/main.nf @@ -3017,8 +3017,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/multiqc_custom_biotype", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/multiqc_custom_biotype/nextflow_schema.json b/target/nextflow/multiqc_custom_biotype/nextflow_schema.json index 9124ba9..73e6582 100644 --- a/target/nextflow/multiqc_custom_biotype/nextflow_schema.json +++ b/target/nextflow/multiqc_custom_biotype/nextflow_schema.json @@ -30,7 +30,7 @@ "description": "Type: `string`, default: `$id`. Sample name", "help_text": "Type: `string`, default: `$id`. Sample name" , - "default": "$id" + "default":"$id" } @@ -41,7 +41,7 @@ "description": "Type: `string`, default: `rRNA`. Features to count", "help_text": "Type: `string`, default: `rRNA`. Features to count" , - "default": "rRNA" + "default":"rRNA" } @@ -62,7 +62,7 @@ "description": "Type: `file`, default: `$id.$key.featurecounts_multiqc.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.featurecounts_multiqc.tsv`. " , - "default": "$id.$key.featurecounts_multiqc.tsv" + "default":"$id.$key.featurecounts_multiqc.tsv" } @@ -73,7 +73,7 @@ "description": "Type: `file`, default: `$id.$key.featurecounts_rrna_multiqc.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.featurecounts_rrna_multiqc.tsv`. " , - "default": "$id.$key.featurecounts_rrna_multiqc.tsv" + "default":"$id.$key.featurecounts_rrna_multiqc.tsv" } diff --git a/target/nextflow/picard_markduplicates/.config.vsh.yaml b/target/nextflow/picard_markduplicates/.config.vsh.yaml index e5a8684..d67ee5a 100644 --- a/target/nextflow/picard_markduplicates/.config.vsh.yaml +++ b/target/nextflow/picard_markduplicates/.config.vsh.yaml @@ -215,8 +215,8 @@ build_info: output: "target/nextflow/picard_markduplicates" executable: "target/nextflow/picard_markduplicates/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/picard_markduplicates/main.nf b/target/nextflow/picard_markduplicates/main.nf index 4f1857d..470cf19 100644 --- a/target/nextflow/picard_markduplicates/main.nf +++ b/target/nextflow/picard_markduplicates/main.nf @@ -3075,8 +3075,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/picard_markduplicates", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/picard_markduplicates/nextflow_schema.json b/target/nextflow/picard_markduplicates/nextflow_schema.json index d5be121..7195d87 100644 --- a/target/nextflow/picard_markduplicates/nextflow_schema.json +++ b/target/nextflow/picard_markduplicates/nextflow_schema.json @@ -50,7 +50,7 @@ "description": "Type: `string`, default: `--ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp`. Additional argument to be passed to Picard MarkDuplicates", "help_text": "Type: `string`, default: `--ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp`. Additional argument to be passed to Picard MarkDuplicates" , - "default": "--ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp" + "default":"--ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp" } @@ -71,7 +71,7 @@ "description": "Type: `file`, default: `$id.$key.output_bam.bam`. BAM file with duplicate reads marked/removed", "help_text": "Type: `file`, default: `$id.$key.output_bam.bam`. BAM file with duplicate reads marked/removed" , - "default": "$id.$key.output_bam.bam" + "default":"$id.$key.output_bam.bam" } @@ -82,7 +82,7 @@ "description": "Type: `file`, default: `$id.$key.bai.bai`. An optional BAM index file", "help_text": "Type: `file`, default: `$id.$key.bai.bai`. An optional BAM index file. If desired, --CREATE_INDEX must be passed as a flag" , - "default": "$id.$key.bai.bai" + "default":"$id.$key.bai.bai" } @@ -93,7 +93,7 @@ "description": "Type: `file`, default: `$id.$key.metrics.txt`. Duplicate metrics file generated by picard", "help_text": "Type: `file`, default: `$id.$key.metrics.txt`. Duplicate metrics file generated by picard" , - "default": "$id.$key.metrics.txt" + "default":"$id.$key.metrics.txt" } diff --git a/target/nextflow/prepare_multiqc_input/.config.vsh.yaml b/target/nextflow/prepare_multiqc_input/.config.vsh.yaml index 2f61ba0..0524b22 100644 --- a/target/nextflow/prepare_multiqc_input/.config.vsh.yaml +++ b/target/nextflow/prepare_multiqc_input/.config.vsh.yaml @@ -417,8 +417,8 @@ build_info: output: "target/nextflow/prepare_multiqc_input" executable: "target/nextflow/prepare_multiqc_input/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/prepare_multiqc_input/main.nf b/target/nextflow/prepare_multiqc_input/main.nf index 84608a4..43467ba 100644 --- a/target/nextflow/prepare_multiqc_input/main.nf +++ b/target/nextflow/prepare_multiqc_input/main.nf @@ -3289,8 +3289,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/prepare_multiqc_input", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/prepare_multiqc_input/nextflow_schema.json b/target/nextflow/prepare_multiqc_input/nextflow_schema.json index 612c807..cbe5fba 100644 --- a/target/nextflow/prepare_multiqc_input/nextflow_schema.json +++ b/target/nextflow/prepare_multiqc_input/nextflow_schema.json @@ -360,7 +360,7 @@ "description": "Type: `file`, default: `$id.$key.output.output`. ", "help_text": "Type: `file`, default: `$id.$key.output.output`. " , - "default": "$id.$key.output.output" + "default":"$id.$key.output.output" } diff --git a/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml b/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml index d3578ae..b0014b0 100644 --- a/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml +++ b/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml @@ -146,8 +146,8 @@ build_info: output: "target/nextflow/preprocess_transcripts_fasta" executable: "target/nextflow/preprocess_transcripts_fasta/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/preprocess_transcripts_fasta/main.nf b/target/nextflow/preprocess_transcripts_fasta/main.nf index 8279b12..87ab371 100644 --- a/target/nextflow/preprocess_transcripts_fasta/main.nf +++ b/target/nextflow/preprocess_transcripts_fasta/main.nf @@ -2994,8 +2994,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/preprocess_transcripts_fasta", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/preprocess_transcripts_fasta/nextflow_schema.json b/target/nextflow/preprocess_transcripts_fasta/nextflow_schema.json index 0ae0e4f..5015eae 100644 --- a/target/nextflow/preprocess_transcripts_fasta/nextflow_schema.json +++ b/target/nextflow/preprocess_transcripts_fasta/nextflow_schema.json @@ -40,7 +40,7 @@ "description": "Type: `file`, required, default: `$id.$key.output.output`. Path of processed output FASTA file", "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Path of processed output FASTA file." , - "default": "$id.$key.output.output" + "default":"$id.$key.output.output" } diff --git a/target/nextflow/preseq_lcextrap/.config.vsh.yaml b/target/nextflow/preseq_lcextrap/.config.vsh.yaml index 5a10de7..1baf8b6 100644 --- a/target/nextflow/preseq_lcextrap/.config.vsh.yaml +++ b/target/nextflow/preseq_lcextrap/.config.vsh.yaml @@ -199,8 +199,8 @@ build_info: output: "target/nextflow/preseq_lcextrap" executable: "target/nextflow/preseq_lcextrap/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/preseq_lcextrap/main.nf b/target/nextflow/preseq_lcextrap/main.nf index ff56332..e734dd3 100644 --- a/target/nextflow/preseq_lcextrap/main.nf +++ b/target/nextflow/preseq_lcextrap/main.nf @@ -3047,8 +3047,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/preseq_lcextrap", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/preseq_lcextrap/nextflow_schema.json b/target/nextflow/preseq_lcextrap/nextflow_schema.json index 886d4e3..776bf27 100644 --- a/target/nextflow/preseq_lcextrap/nextflow_schema.json +++ b/target/nextflow/preseq_lcextrap/nextflow_schema.json @@ -60,7 +60,7 @@ "description": "Type: `file`, default: `$id.$key.output.txt`. ", "help_text": "Type: `file`, default: `$id.$key.output.txt`. " , - "default": "$id.$key.output.txt" + "default":"$id.$key.output.txt" } diff --git a/target/nextflow/qualimap/.config.vsh.yaml b/target/nextflow/qualimap/.config.vsh.yaml index a40fd62..fc2d63d 100644 --- a/target/nextflow/qualimap/.config.vsh.yaml +++ b/target/nextflow/qualimap/.config.vsh.yaml @@ -279,8 +279,8 @@ build_info: output: "target/nextflow/qualimap" executable: "target/nextflow/qualimap/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/qualimap/main.nf b/target/nextflow/qualimap/main.nf index e080f30..829c329 100644 --- a/target/nextflow/qualimap/main.nf +++ b/target/nextflow/qualimap/main.nf @@ -3156,8 +3156,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/qualimap", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/qualimap/nextflow_schema.json b/target/nextflow/qualimap/nextflow_schema.json index 73d681d..8defe51 100644 --- a/target/nextflow/qualimap/nextflow_schema.json +++ b/target/nextflow/qualimap/nextflow_schema.json @@ -50,7 +50,7 @@ "description": "Type: `file`, default: `$id.$key.output_dir.qualimap_output`. path to output directory for raw data and report", "help_text": "Type: `file`, default: `$id.$key.output_dir.qualimap_output`. path to output directory for raw data and report." , - "default": "$id.$key.output_dir.qualimap_output" + "default":"$id.$key.output_dir.qualimap_output" } @@ -61,7 +61,7 @@ "description": "Type: `file`, default: `$id.$key.output_pdf.pdf`. path to output file for pdf report", "help_text": "Type: `file`, default: `$id.$key.output_pdf.pdf`. path to output file for pdf report." , - "default": "$id.$key.output_pdf.pdf" + "default":"$id.$key.output_pdf.pdf" } @@ -72,7 +72,7 @@ "description": "Type: `string`, default: `html`. Format of the output report (PDF or HTML, default is HTML)", "help_text": "Type: `string`, default: `html`. Format of the output report (PDF or HTML, default is HTML)" , - "default": "html" + "default":"html" } @@ -93,7 +93,7 @@ "description": "Type: `integer`, default: `100`. Number of upstream/downstream nucleotide bases to compute 5\u0027-3\u0027 bias (default = 100)", "help_text": "Type: `integer`, default: `100`. Number of upstream/downstream nucleotide bases to compute 5\u0027-3\u0027 bias (default = 100)." , - "default": "100" + "default":100 } @@ -104,7 +104,7 @@ "description": "Type: `integer`, default: `1000`. Number of top highly expressed transcripts to compute 5\u0027-3\u0027 bias (default = 1000)", "help_text": "Type: `integer`, default: `1000`. Number of top highly expressed transcripts to compute 5\u0027-3\u0027 bias (default = 1000)." , - "default": "1000" + "default":1000 } @@ -115,7 +115,7 @@ "description": "Type: `string`, default: `uniquely-mapped-reads`. Counting algorithm (uniquely-mapped-reads (default) or proportional)", "help_text": "Type: `string`, default: `uniquely-mapped-reads`. Counting algorithm (uniquely-mapped-reads (default) or proportional)." , - "default": "uniquely-mapped-reads" + "default":"uniquely-mapped-reads" } @@ -128,7 +128,7 @@ "enum": ["non-strand-specific", "strand-specific-reverse", "strand-specific-forward"] , - "default": "non-strand-specific" + "default":"non-strand-specific" } @@ -139,7 +139,7 @@ "description": "Type: `boolean_true`, default: `false`. Setting this flag for paired-end experiments will result in counting fragments instead of reads", "help_text": "Type: `boolean_true`, default: `false`. Setting this flag for paired-end experiments will result in counting fragments instead of reads." , - "default": "False" + "default":false } @@ -150,7 +150,7 @@ "description": "Type: `boolean_true`, default: `false`. Setting this flag indicates that the input file is already sorted by name", "help_text": "Type: `boolean_true`, default: `false`. Setting this flag indicates that the input file is already sorted by name. If flag is not set, additional sorting by name will be performed. Only requiredfor paired-end analysis." , - "default": "False" + "default":false } @@ -161,7 +161,7 @@ "description": "Type: `string`, default: `4G`. maximum Java heap memory size, default = 4G", "help_text": "Type: `string`, default: `4G`. maximum Java heap memory size, default = 4G." , - "default": "4G" + "default":"4G" } diff --git a/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml b/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml index 53fe94f..1e99496 100644 --- a/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml +++ b/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml @@ -307,8 +307,8 @@ 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: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/rsem/rsem_calculate_expression/main.nf b/target/nextflow/rsem/rsem_calculate_expression/main.nf index d5ca56d..ea84ac2 100644 --- a/target/nextflow/rsem/rsem_calculate_expression/main.nf +++ b/target/nextflow/rsem/rsem_calculate_expression/main.nf @@ -3175,8 +3175,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rsem/rsem_calculate_expression", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/rsem/rsem_calculate_expression/nextflow_schema.json b/target/nextflow/rsem/rsem_calculate_expression/nextflow_schema.json index a6b77fb..81d4502 100644 --- a/target/nextflow/rsem/rsem_calculate_expression/nextflow_schema.json +++ b/target/nextflow/rsem/rsem_calculate_expression/nextflow_schema.json @@ -92,7 +92,7 @@ "description": "Type: `file`, default: `$id.$key.counts_gene.results`, example: `sample.genes.results`. Expression counts on gene level", "help_text": "Type: `file`, default: `$id.$key.counts_gene.results`, example: `sample.genes.results`. Expression counts on gene level" , - "default": "$id.$key.counts_gene.results" + "default":"$id.$key.counts_gene.results" } @@ -103,7 +103,7 @@ "description": "Type: `file`, default: `$id.$key.counts_transcripts.results`, example: `sample.isoforms.results`. Expression counts on transcript level", "help_text": "Type: `file`, default: `$id.$key.counts_transcripts.results`, example: `sample.isoforms.results`. Expression counts on transcript level" , - "default": "$id.$key.counts_transcripts.results" + "default":"$id.$key.counts_transcripts.results" } @@ -114,7 +114,7 @@ "description": "Type: `file`, default: `$id.$key.stat.stat`, example: `sample.stat`. RSEM statistics", "help_text": "Type: `file`, default: `$id.$key.stat.stat`, example: `sample.stat`. RSEM statistics" , - "default": "$id.$key.stat.stat" + "default":"$id.$key.stat.stat" } @@ -125,7 +125,7 @@ "description": "Type: `file`, default: `$id.$key.logs.log`, example: `sample.log`. RSEM logs", "help_text": "Type: `file`, default: `$id.$key.logs.log`, example: `sample.log`. RSEM logs" , - "default": "$id.$key.logs.log" + "default":"$id.$key.logs.log" } @@ -136,7 +136,7 @@ "description": "Type: `file`, default: `$id.$key.bam_star.bam`, example: `sample.STAR.genome.bam`. BAM file generated by STAR (optional)", "help_text": "Type: `file`, default: `$id.$key.bam_star.bam`, example: `sample.STAR.genome.bam`. BAM file generated by STAR (optional)" , - "default": "$id.$key.bam_star.bam" + "default":"$id.$key.bam_star.bam" } @@ -147,7 +147,7 @@ "description": "Type: `file`, default: `$id.$key.bam_genome.bam`, example: `sample.genome.bam`. Genome BAM file (optional)", "help_text": "Type: `file`, default: `$id.$key.bam_genome.bam`, example: `sample.genome.bam`. Genome BAM file (optional)" , - "default": "$id.$key.bam_genome.bam" + "default":"$id.$key.bam_genome.bam" } @@ -158,7 +158,7 @@ "description": "Type: `file`, default: `$id.$key.bam_transcript.bam`, example: `sample.transcript.bam`. Transcript BAM file (optional)", "help_text": "Type: `file`, default: `$id.$key.bam_transcript.bam`, example: `sample.transcript.bam`. Transcript BAM file (optional)" , - "default": "$id.$key.bam_transcript.bam" + "default":"$id.$key.bam_transcript.bam" } diff --git a/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml b/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml index b813fba..f5f9750 100644 --- a/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml +++ b/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml @@ -190,8 +190,8 @@ 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: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/rsem/rsem_merge_counts/main.nf b/target/nextflow/rsem/rsem_merge_counts/main.nf index 7ac2b72..c860161 100644 --- a/target/nextflow/rsem/rsem_merge_counts/main.nf +++ b/target/nextflow/rsem/rsem_merge_counts/main.nf @@ -3040,8 +3040,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rsem/rsem_merge_counts", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/rsem/rsem_merge_counts/nextflow_schema.json b/target/nextflow/rsem/rsem_merge_counts/nextflow_schema.json index 6d8506c..2ec8321 100644 --- a/target/nextflow/rsem/rsem_merge_counts/nextflow_schema.json +++ b/target/nextflow/rsem/rsem_merge_counts/nextflow_schema.json @@ -50,7 +50,7 @@ "description": "Type: `file`, default: `$id.$key.merged_gene_counts.tsv`. File containing gene counts across all samples", "help_text": "Type: `file`, default: `$id.$key.merged_gene_counts.tsv`. File containing gene counts across all samples." , - "default": "$id.$key.merged_gene_counts.tsv" + "default":"$id.$key.merged_gene_counts.tsv" } @@ -61,7 +61,7 @@ "description": "Type: `file`, default: `$id.$key.merged_gene_tpm.tsv`. File containing gene TPM across all samples", "help_text": "Type: `file`, default: `$id.$key.merged_gene_tpm.tsv`. File containing gene TPM across all samples." , - "default": "$id.$key.merged_gene_tpm.tsv" + "default":"$id.$key.merged_gene_tpm.tsv" } @@ -72,7 +72,7 @@ "description": "Type: `file`, default: `$id.$key.merged_transcript_counts.tsv`. File containing transcript counts across all samples", "help_text": "Type: `file`, default: `$id.$key.merged_transcript_counts.tsv`. File containing transcript counts across all samples." , - "default": "$id.$key.merged_transcript_counts.tsv" + "default":"$id.$key.merged_transcript_counts.tsv" } @@ -83,7 +83,7 @@ "description": "Type: `file`, default: `$id.$key.merged_transcript_tpm.tsv`. File containing transcript TPM across all samples", "help_text": "Type: `file`, default: `$id.$key.merged_transcript_tpm.tsv`. File containing transcript TPM across all samples." , - "default": "$id.$key.merged_transcript_tpm.tsv" + "default":"$id.$key.merged_transcript_tpm.tsv" } diff --git a/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml index c9cabf0..65b6bb7 100644 --- a/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml @@ -171,8 +171,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_bamstat" executable: "target/nextflow/rseqc/rseqc_bamstat/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/rseqc/rseqc_bamstat/main.nf b/target/nextflow/rseqc/rseqc_bamstat/main.nf index d2749dd..75c41f1 100644 --- a/target/nextflow/rseqc/rseqc_bamstat/main.nf +++ b/target/nextflow/rseqc/rseqc_bamstat/main.nf @@ -3028,8 +3028,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_bamstat", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/rseqc/rseqc_bamstat/nextflow_schema.json b/target/nextflow/rseqc/rseqc_bamstat/nextflow_schema.json index ccd0e05..10fcdfd 100644 --- a/target/nextflow/rseqc/rseqc_bamstat/nextflow_schema.json +++ b/target/nextflow/rseqc/rseqc_bamstat/nextflow_schema.json @@ -30,7 +30,7 @@ "description": "Type: `integer`, default: `30`. Minimum mapping quality (phred scaled) to determine uniquely mapped reads, default=30", "help_text": "Type: `integer`, default: `30`. Minimum mapping quality (phred scaled) to determine uniquely mapped reads, default=30." , - "default": "30" + "default":30 } @@ -51,7 +51,7 @@ "description": "Type: `file`, default: `$id.$key.output.txt`. output file (txt) with mapping quality statistics", "help_text": "Type: `file`, default: `$id.$key.output.txt`. output file (txt) with mapping quality statistics" , - "default": "$id.$key.output.txt" + "default":"$id.$key.output.txt" } diff --git a/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml index 0e6ee56..18bb632 100644 --- a/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml @@ -194,8 +194,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_inferexperiment" executable: "target/nextflow/rseqc/rseqc_inferexperiment/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/rseqc/rseqc_inferexperiment/main.nf b/target/nextflow/rseqc/rseqc_inferexperiment/main.nf index ec6944d..83040de 100644 --- a/target/nextflow/rseqc/rseqc_inferexperiment/main.nf +++ b/target/nextflow/rseqc/rseqc_inferexperiment/main.nf @@ -3056,8 +3056,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_inferexperiment", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/rseqc/rseqc_inferexperiment/nextflow_schema.json b/target/nextflow/rseqc/rseqc_inferexperiment/nextflow_schema.json index d3c717a..2334e9c 100644 --- a/target/nextflow/rseqc/rseqc_inferexperiment/nextflow_schema.json +++ b/target/nextflow/rseqc/rseqc_inferexperiment/nextflow_schema.json @@ -40,7 +40,7 @@ "description": "Type: `integer`, default: `200000`. Numer of reads sampled from SAM/BAM file, default = 200000", "help_text": "Type: `integer`, default: `200000`. Numer of reads sampled from SAM/BAM file, default = 200000." , - "default": "200000" + "default":200000 } @@ -51,7 +51,7 @@ "description": "Type: `integer`, default: `30`. Minimum mapping quality (phred scaled) to determine uniquely mapped reads, default=30", "help_text": "Type: `integer`, default: `30`. Minimum mapping quality (phred scaled) to determine uniquely mapped reads, default=30." , - "default": "30" + "default":30 } @@ -72,7 +72,7 @@ "description": "Type: `file`, default: `$id.$key.output.txt`. output file (txt) of strandness report", "help_text": "Type: `file`, default: `$id.$key.output.txt`. output file (txt) of strandness report" , - "default": "$id.$key.output.txt" + "default":"$id.$key.output.txt" } diff --git a/target/nextflow/rseqc/rseqc_innerdistance/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_innerdistance/.config.vsh.yaml index 2ebcf18..e8922c4 100644 --- a/target/nextflow/rseqc/rseqc_innerdistance/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_innerdistance/.config.vsh.yaml @@ -280,8 +280,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_innerdistance" executable: "target/nextflow/rseqc/rseqc_innerdistance/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/rseqc/rseqc_innerdistance/main.nf b/target/nextflow/rseqc/rseqc_innerdistance/main.nf index 920e794..30d5620 100644 --- a/target/nextflow/rseqc/rseqc_innerdistance/main.nf +++ b/target/nextflow/rseqc/rseqc_innerdistance/main.nf @@ -3149,8 +3149,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_innerdistance", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/rseqc/rseqc_innerdistance/nextflow_schema.json b/target/nextflow/rseqc/rseqc_innerdistance/nextflow_schema.json index 933a44f..85f21e3 100644 --- a/target/nextflow/rseqc/rseqc_innerdistance/nextflow_schema.json +++ b/target/nextflow/rseqc/rseqc_innerdistance/nextflow_schema.json @@ -40,7 +40,7 @@ "description": "Type: `integer`, default: `200000`. Numer of reads sampled from SAM/BAM file, default = 200000", "help_text": "Type: `integer`, default: `200000`. Numer of reads sampled from SAM/BAM file, default = 200000." , - "default": "200000" + "default":200000 } @@ -51,7 +51,7 @@ "description": "Type: `integer`, default: `30`. Minimum mapping quality (phred scaled) to determine uniquely mapped reads, default=30", "help_text": "Type: `integer`, default: `30`. Minimum mapping quality (phred scaled) to determine uniquely mapped reads, default=30." , - "default": "30" + "default":30 } @@ -62,7 +62,7 @@ "description": "Type: `integer`, default: `-250`. Lower bound of inner distance (bp)", "help_text": "Type: `integer`, default: `-250`. Lower bound of inner distance (bp). This option is used for ploting histograme, default=-250." , - "default": "-250" + "default":-250 } @@ -73,7 +73,7 @@ "description": "Type: `integer`, default: `250`. Upper bound of inner distance (bp)", "help_text": "Type: `integer`, default: `250`. Upper bound of inner distance (bp). This option is used for ploting histograme, default=250." , - "default": "250" + "default":250 } @@ -84,7 +84,7 @@ "description": "Type: `integer`, default: `5`. Step size (bp) of histograme", "help_text": "Type: `integer`, default: `5`. Step size (bp) of histograme. This option is used for plotting histogram, default=5." , - "default": "5" + "default":5 } @@ -105,7 +105,7 @@ "description": "Type: `file`, default: `$id.$key.output_stats.stats`. output file (txt) with summary statistics of inner distances of paired reads", "help_text": "Type: `file`, default: `$id.$key.output_stats.stats`. output file (txt) with summary statistics of inner distances of paired reads" , - "default": "$id.$key.output_stats.stats" + "default":"$id.$key.output_stats.stats" } @@ -116,7 +116,7 @@ "description": "Type: `file`, default: `$id.$key.output_dist.txt`. output file (txt) with inner distances of all paired reads", "help_text": "Type: `file`, default: `$id.$key.output_dist.txt`. output file (txt) with inner distances of all paired reads" , - "default": "$id.$key.output_dist.txt" + "default":"$id.$key.output_dist.txt" } @@ -127,7 +127,7 @@ "description": "Type: `file`, default: `$id.$key.output_freq.txt`. output file (txt) with frequencies of inner distances of all paired reads", "help_text": "Type: `file`, default: `$id.$key.output_freq.txt`. output file (txt) with frequencies of inner distances of all paired reads" , - "default": "$id.$key.output_freq.txt" + "default":"$id.$key.output_freq.txt" } @@ -138,7 +138,7 @@ "description": "Type: `file`, default: `$id.$key.output_plot.pdf`. output file (pdf) with histogram plot of of inner distances of all paired reads", "help_text": "Type: `file`, default: `$id.$key.output_plot.pdf`. output file (pdf) with histogram plot of of inner distances of all paired reads" , - "default": "$id.$key.output_plot.pdf" + "default":"$id.$key.output_plot.pdf" } @@ -149,7 +149,7 @@ "description": "Type: `file`, default: `$id.$key.output_plot_r.r`. output file (R) with script of histogram plot of of inner distances of all paired reads", "help_text": "Type: `file`, default: `$id.$key.output_plot_r.r`. output file (R) with script of histogram plot of of inner distances of all paired reads" , - "default": "$id.$key.output_plot_r.r" + "default":"$id.$key.output_plot_r.r" } diff --git a/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml index 4c70bba..0fca7a2 100644 --- a/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml @@ -268,8 +268,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_junctionannotation" executable: "target/nextflow/rseqc/rseqc_junctionannotation/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/rseqc/rseqc_junctionannotation/main.nf b/target/nextflow/rseqc/rseqc_junctionannotation/main.nf index 23e607c..b3f71e5 100644 --- a/target/nextflow/rseqc/rseqc_junctionannotation/main.nf +++ b/target/nextflow/rseqc/rseqc_junctionannotation/main.nf @@ -3140,8 +3140,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_junctionannotation", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/rseqc/rseqc_junctionannotation/nextflow_schema.json b/target/nextflow/rseqc/rseqc_junctionannotation/nextflow_schema.json index dfbfdb9..d5d5891 100644 --- a/target/nextflow/rseqc/rseqc_junctionannotation/nextflow_schema.json +++ b/target/nextflow/rseqc/rseqc_junctionannotation/nextflow_schema.json @@ -40,7 +40,7 @@ "description": "Type: `integer`, default: `30`. Minimum mapping quality (phred scaled) to determine uniquely mapped reads, default=30", "help_text": "Type: `integer`, default: `30`. Minimum mapping quality (phred scaled) to determine uniquely mapped reads, default=30." , - "default": "30" + "default":30 } @@ -51,7 +51,7 @@ "description": "Type: `integer`, default: `50`. Minimum intron length (bp), default = 50", "help_text": "Type: `integer`, default: `50`. Minimum intron length (bp), default = 50." , - "default": "50" + "default":50 } @@ -72,7 +72,7 @@ "description": "Type: `file`, default: `$id.$key.output_log.log`. output log of junction annotation script", "help_text": "Type: `file`, default: `$id.$key.output_log.log`. output log of junction annotation script" , - "default": "$id.$key.output_log.log" + "default":"$id.$key.output_log.log" } @@ -83,7 +83,7 @@ "description": "Type: `file`, default: `$id.$key.output_plot_r.r`. r script to generate splice_junction and splice_events plot", "help_text": "Type: `file`, default: `$id.$key.output_plot_r.r`. r script to generate splice_junction and splice_events plot" , - "default": "$id.$key.output_plot_r.r" + "default":"$id.$key.output_plot_r.r" } @@ -94,7 +94,7 @@ "description": "Type: `file`, default: `$id.$key.output_junction_bed.bed`. junction annotation file (bed format)", "help_text": "Type: `file`, default: `$id.$key.output_junction_bed.bed`. junction annotation file (bed format)" , - "default": "$id.$key.output_junction_bed.bed" + "default":"$id.$key.output_junction_bed.bed" } @@ -105,7 +105,7 @@ "description": "Type: `file`, default: `$id.$key.output_junction_interact.bed`. interact file (bed format) of junctions", "help_text": "Type: `file`, default: `$id.$key.output_junction_interact.bed`. interact file (bed format) of junctions. Can be uploaded to UCSC genome browser or converted to bigInteract (using bedToBigBed program) for visualization." , - "default": "$id.$key.output_junction_interact.bed" + "default":"$id.$key.output_junction_interact.bed" } @@ -116,7 +116,7 @@ "description": "Type: `file`, default: `$id.$key.output_junction_sheet.xls`. junction annotation file (xls format)", "help_text": "Type: `file`, default: `$id.$key.output_junction_sheet.xls`. junction annotation file (xls format)" , - "default": "$id.$key.output_junction_sheet.xls" + "default":"$id.$key.output_junction_sheet.xls" } @@ -127,7 +127,7 @@ "description": "Type: `file`, default: `$id.$key.output_splice_events_plot.pdf`. plot of splice events (pdf)", "help_text": "Type: `file`, default: `$id.$key.output_splice_events_plot.pdf`. plot of splice events (pdf)" , - "default": "$id.$key.output_splice_events_plot.pdf" + "default":"$id.$key.output_splice_events_plot.pdf" } @@ -138,7 +138,7 @@ "description": "Type: `file`, default: `$id.$key.output_splice_junctions_plot.pdf`. plot of junctions (pdf)", "help_text": "Type: `file`, default: `$id.$key.output_splice_junctions_plot.pdf`. plot of junctions (pdf)" , - "default": "$id.$key.output_splice_junctions_plot.pdf" + "default":"$id.$key.output_splice_junctions_plot.pdf" } diff --git a/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml index 80b499c..c2e007a 100644 --- a/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml @@ -257,8 +257,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_junctionsaturation" executable: "target/nextflow/rseqc/rseqc_junctionsaturation/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf b/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf index 128cfde..50eb1cf 100644 --- a/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf +++ b/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf @@ -3125,8 +3125,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_junctionsaturation", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/rseqc/rseqc_junctionsaturation/nextflow_schema.json b/target/nextflow/rseqc/rseqc_junctionsaturation/nextflow_schema.json index b593c4c..f1e6368 100644 --- a/target/nextflow/rseqc/rseqc_junctionsaturation/nextflow_schema.json +++ b/target/nextflow/rseqc/rseqc_junctionsaturation/nextflow_schema.json @@ -40,7 +40,7 @@ "description": "Type: `integer`, default: `5`. Sampling starts from this percentile, must be an integer between 0 and 100, default =5", "help_text": "Type: `integer`, default: `5`. Sampling starts from this percentile, must be an integer between 0 and 100, default =5." , - "default": "5" + "default":5 } @@ -51,7 +51,7 @@ "description": "Type: `integer`, default: `100`. Sampling ends at this percentile, must be an integer between 0 and 100, default =5", "help_text": "Type: `integer`, default: `100`. Sampling ends at this percentile, must be an integer between 0 and 100, default =5." , - "default": "100" + "default":100 } @@ -62,7 +62,7 @@ "description": "Type: `integer`, default: `5`. Sampling frequency in %", "help_text": "Type: `integer`, default: `5`. Sampling frequency in %. Smaller value means more sampling times. Must be an integer between 0 and 100, default = 5." , - "default": "5" + "default":5 } @@ -73,7 +73,7 @@ "description": "Type: `integer`, default: `50`. Minimum intron length (bp), default = 50", "help_text": "Type: `integer`, default: `50`. Minimum intron length (bp), default = 50." , - "default": "50" + "default":50 } @@ -84,7 +84,7 @@ "description": "Type: `integer`, default: `1`. Minimum number of supporting reads to call a junction, default = 1", "help_text": "Type: `integer`, default: `1`. Minimum number of supporting reads to call a junction, default = 1." , - "default": "1" + "default":1 } @@ -95,7 +95,7 @@ "description": "Type: `integer`, default: `30`. Minimum mapping quality (phred scaled) to determine uniquely mapped reads, default=30", "help_text": "Type: `integer`, default: `30`. Minimum mapping quality (phred scaled) to determine uniquely mapped reads, default=30." , - "default": "30" + "default":30 } @@ -116,7 +116,7 @@ "description": "Type: `file`, default: `$id.$key.output_plot_r.r`. r script to generate junction_saturation_plot plot", "help_text": "Type: `file`, default: `$id.$key.output_plot_r.r`. r script to generate junction_saturation_plot plot" , - "default": "$id.$key.output_plot_r.r" + "default":"$id.$key.output_plot_r.r" } @@ -127,7 +127,7 @@ "description": "Type: `file`, default: `$id.$key.output_plot.pdf`. plot of junction saturation (pdf)", "help_text": "Type: `file`, default: `$id.$key.output_plot.pdf`. plot of junction saturation (pdf)" , - "default": "$id.$key.output_plot.pdf" + "default":"$id.$key.output_plot.pdf" } diff --git a/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml index f1cd15c..ea5c4e0 100644 --- a/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml @@ -170,8 +170,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_readdistribution" executable: "target/nextflow/rseqc/rseqc_readdistribution/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/rseqc/rseqc_readdistribution/main.nf b/target/nextflow/rseqc/rseqc_readdistribution/main.nf index 6c30a48..1207bfb 100644 --- a/target/nextflow/rseqc/rseqc_readdistribution/main.nf +++ b/target/nextflow/rseqc/rseqc_readdistribution/main.nf @@ -3029,8 +3029,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_readdistribution", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/rseqc/rseqc_readdistribution/nextflow_schema.json b/target/nextflow/rseqc/rseqc_readdistribution/nextflow_schema.json index 0fda1f4..f53d310 100644 --- a/target/nextflow/rseqc/rseqc_readdistribution/nextflow_schema.json +++ b/target/nextflow/rseqc/rseqc_readdistribution/nextflow_schema.json @@ -50,7 +50,7 @@ "description": "Type: `file`, default: `$id.$key.output.txt`. output file (txt) of read distribution analysis", "help_text": "Type: `file`, default: `$id.$key.output.txt`. output file (txt) of read distribution analysis." , - "default": "$id.$key.output.txt" + "default":"$id.$key.output.txt" } diff --git a/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml index 5d0c43d..6308ef8 100644 --- a/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml @@ -219,8 +219,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_readduplication" executable: "target/nextflow/rseqc/rseqc_readduplication/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/rseqc/rseqc_readduplication/main.nf b/target/nextflow/rseqc/rseqc_readduplication/main.nf index 5d3c925..e8f5247 100644 --- a/target/nextflow/rseqc/rseqc_readduplication/main.nf +++ b/target/nextflow/rseqc/rseqc_readduplication/main.nf @@ -3083,8 +3083,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_readduplication", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/rseqc/rseqc_readduplication/nextflow_schema.json b/target/nextflow/rseqc/rseqc_readduplication/nextflow_schema.json index 509fc4f..9dbcbb6 100644 --- a/target/nextflow/rseqc/rseqc_readduplication/nextflow_schema.json +++ b/target/nextflow/rseqc/rseqc_readduplication/nextflow_schema.json @@ -30,7 +30,7 @@ "description": "Type: `integer`, default: `500`. Upper limit of reads\u0027 occurence", "help_text": "Type: `integer`, default: `500`. Upper limit of reads\u0027 occurence. Only used for plotting, default = 500 (times)." , - "default": "500" + "default":500 } @@ -41,7 +41,7 @@ "description": "Type: `integer`, default: `30`. Minimum mapping quality (phred scaled) to determine uniquely mapped reads, default=30", "help_text": "Type: `integer`, default: `30`. Minimum mapping quality (phred scaled) to determine uniquely mapped reads, default=30." , - "default": "30" + "default":30 } @@ -62,7 +62,7 @@ "description": "Type: `file`, default: `$id.$key.output_duplication_rate_plot_r.r`. R script for generating duplication rate plot", "help_text": "Type: `file`, default: `$id.$key.output_duplication_rate_plot_r.r`. R script for generating duplication rate plot" , - "default": "$id.$key.output_duplication_rate_plot_r.r" + "default":"$id.$key.output_duplication_rate_plot_r.r" } @@ -73,7 +73,7 @@ "description": "Type: `file`, default: `$id.$key.output_duplication_rate_plot.pdf`. duplication rate plot (pdf)", "help_text": "Type: `file`, default: `$id.$key.output_duplication_rate_plot.pdf`. duplication rate plot (pdf)" , - "default": "$id.$key.output_duplication_rate_plot.pdf" + "default":"$id.$key.output_duplication_rate_plot.pdf" } @@ -84,7 +84,7 @@ "description": "Type: `file`, default: `$id.$key.output_duplication_rate_mapping.xls`. Summary of mapping-based read duplication", "help_text": "Type: `file`, default: `$id.$key.output_duplication_rate_mapping.xls`. Summary of mapping-based read duplication" , - "default": "$id.$key.output_duplication_rate_mapping.xls" + "default":"$id.$key.output_duplication_rate_mapping.xls" } @@ -95,7 +95,7 @@ "description": "Type: `file`, default: `$id.$key.output_duplication_rate_sequence.xls`. Summary of sequencing-based read duplication", "help_text": "Type: `file`, default: `$id.$key.output_duplication_rate_sequence.xls`. Summary of sequencing-based read duplication" , - "default": "$id.$key.output_duplication_rate_sequence.xls" + "default":"$id.$key.output_duplication_rate_sequence.xls" } diff --git a/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml index 9eba589..7062492 100644 --- a/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml @@ -222,8 +222,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_tin" executable: "target/nextflow/rseqc/rseqc_tin/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/rseqc/rseqc_tin/main.nf b/target/nextflow/rseqc/rseqc_tin/main.nf index 8b0ff52..b0bc894 100644 --- a/target/nextflow/rseqc/rseqc_tin/main.nf +++ b/target/nextflow/rseqc/rseqc_tin/main.nf @@ -3088,8 +3088,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_tin", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/rseqc/rseqc_tin/nextflow_schema.json b/target/nextflow/rseqc/rseqc_tin/nextflow_schema.json index 6f63e35..0039ad0 100644 --- a/target/nextflow/rseqc/rseqc_tin/nextflow_schema.json +++ b/target/nextflow/rseqc/rseqc_tin/nextflow_schema.json @@ -50,7 +50,7 @@ "description": "Type: `integer`, default: `10`. Minimum number of reads mapped to a transcript, default = 10", "help_text": "Type: `integer`, default: `10`. Minimum number of reads mapped to a transcript, default = 10." , - "default": "10" + "default":10 } @@ -61,7 +61,7 @@ "description": "Type: `integer`, default: `100`. Number of equal-spaced nucleotide positions picked from mRNA", "help_text": "Type: `integer`, default: `100`. Number of equal-spaced nucleotide positions picked from mRNA. Note, if this number is larger than the length of mRNA (L), it will be halved until it\u0027s smaller than L (default = 100)" , - "default": "100" + "default":100 } @@ -72,7 +72,7 @@ "description": "Type: `boolean_true`, default: `false`. Set flag to subtract background noise (estimated from intronic reads)", "help_text": "Type: `boolean_true`, default: `false`. Set flag to subtract background noise (estimated from intronic reads). Only use this option if there are substantial intronic reads." , - "default": "False" + "default":false } @@ -93,7 +93,7 @@ "description": "Type: `file`, default: `$id.$key.output_tin_summary.txt`. summary statistics (txt) of calculated TIN metrics", "help_text": "Type: `file`, default: `$id.$key.output_tin_summary.txt`. summary statistics (txt) of calculated TIN metrics" , - "default": "$id.$key.output_tin_summary.txt" + "default":"$id.$key.output_tin_summary.txt" } @@ -104,7 +104,7 @@ "description": "Type: `file`, default: `$id.$key.output_tin.xls`. file with TIN metrics (xls)", "help_text": "Type: `file`, default: `$id.$key.output_tin.xls`. file with TIN metrics (xls)" , - "default": "$id.$key.output_tin.xls" + "default":"$id.$key.output_tin.xls" } diff --git a/target/nextflow/sortmerna/.config.vsh.yaml b/target/nextflow/sortmerna/.config.vsh.yaml index 9674560..602d31e 100644 --- a/target/nextflow/sortmerna/.config.vsh.yaml +++ b/target/nextflow/sortmerna/.config.vsh.yaml @@ -200,8 +200,8 @@ build_info: output: "target/nextflow/sortmerna" executable: "target/nextflow/sortmerna/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/sortmerna/main.nf b/target/nextflow/sortmerna/main.nf index 1f1d677..b556e70 100644 --- a/target/nextflow/sortmerna/main.nf +++ b/target/nextflow/sortmerna/main.nf @@ -3054,8 +3054,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/sortmerna", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/sortmerna/nextflow_schema.json b/target/nextflow/sortmerna/nextflow_schema.json index 7b8a6bb..c7fb0fe 100644 --- a/target/nextflow/sortmerna/nextflow_schema.json +++ b/target/nextflow/sortmerna/nextflow_schema.json @@ -60,7 +60,7 @@ "description": "Type: `file`, default: `$id.$key.sortmerna_log.log`. Sortmerna log file", "help_text": "Type: `file`, default: `$id.$key.sortmerna_log.log`. Sortmerna log file." , - "default": "$id.$key.sortmerna_log.log" + "default":"$id.$key.sortmerna_log.log" } @@ -71,7 +71,7 @@ "description": "Type: `file`, required, default: `$id.$key.fastq_1.gz`. Output file for read 1", "help_text": "Type: `file`, required, default: `$id.$key.fastq_1.gz`. Output file for read 1." , - "default": "$id.$key.fastq_1.gz" + "default":"$id.$key.fastq_1.gz" } @@ -82,7 +82,7 @@ "description": "Type: `file`, default: `$id.$key.fastq_2.gz`. Output file for read 2", "help_text": "Type: `file`, default: `$id.$key.fastq_2.gz`. Output file for read 2." , - "default": "$id.$key.fastq_2.gz" + "default":"$id.$key.fastq_2.gz" } diff --git a/target/nextflow/stringtie/.config.vsh.yaml b/target/nextflow/stringtie/.config.vsh.yaml index c76604f..ebba84d 100644 --- a/target/nextflow/stringtie/.config.vsh.yaml +++ b/target/nextflow/stringtie/.config.vsh.yaml @@ -224,8 +224,8 @@ build_info: output: "target/nextflow/stringtie" executable: "target/nextflow/stringtie/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/stringtie/main.nf b/target/nextflow/stringtie/main.nf index 65234cd..4885618 100644 --- a/target/nextflow/stringtie/main.nf +++ b/target/nextflow/stringtie/main.nf @@ -3085,8 +3085,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/stringtie", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/stringtie/nextflow_schema.json b/target/nextflow/stringtie/nextflow_schema.json index 460e522..aeb01f6 100644 --- a/target/nextflow/stringtie/nextflow_schema.json +++ b/target/nextflow/stringtie/nextflow_schema.json @@ -80,7 +80,7 @@ "description": "Type: `file`, default: `$id.$key.transcript_gtf.gtf`. ", "help_text": "Type: `file`, default: `$id.$key.transcript_gtf.gtf`. " , - "default": "$id.$key.transcript_gtf.gtf" + "default":"$id.$key.transcript_gtf.gtf" } @@ -91,7 +91,7 @@ "description": "Type: `file`, default: `$id.$key.coverage_gtf.gtf`. ", "help_text": "Type: `file`, default: `$id.$key.coverage_gtf.gtf`. " , - "default": "$id.$key.coverage_gtf.gtf" + "default":"$id.$key.coverage_gtf.gtf" } @@ -102,7 +102,7 @@ "description": "Type: `file`, default: `$id.$key.abundance.txt`. ", "help_text": "Type: `file`, default: `$id.$key.abundance.txt`. " , - "default": "$id.$key.abundance.txt" + "default":"$id.$key.abundance.txt" } @@ -113,7 +113,7 @@ "description": "Type: `file`, default: `$id.$key.ballgown.ballgown`. for running ballgown", "help_text": "Type: `file`, default: `$id.$key.ballgown.ballgown`. for running ballgown" , - "default": "$id.$key.ballgown.ballgown" + "default":"$id.$key.ballgown.ballgown" } diff --git a/target/nextflow/summarizedexperiment/.config.vsh.yaml b/target/nextflow/summarizedexperiment/.config.vsh.yaml index e7ef378..417b974 100644 --- a/target/nextflow/summarizedexperiment/.config.vsh.yaml +++ b/target/nextflow/summarizedexperiment/.config.vsh.yaml @@ -207,8 +207,8 @@ build_info: output: "target/nextflow/summarizedexperiment" executable: "target/nextflow/summarizedexperiment/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/summarizedexperiment/main.nf b/target/nextflow/summarizedexperiment/main.nf index 24acaa4..19e90be 100644 --- a/target/nextflow/summarizedexperiment/main.nf +++ b/target/nextflow/summarizedexperiment/main.nf @@ -3066,8 +3066,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/summarizedexperiment", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/summarizedexperiment/nextflow_schema.json b/target/nextflow/summarizedexperiment/nextflow_schema.json index 9d76a55..fb1515b 100644 --- a/target/nextflow/summarizedexperiment/nextflow_schema.json +++ b/target/nextflow/summarizedexperiment/nextflow_schema.json @@ -100,7 +100,7 @@ "description": "Type: `file`, default: `$id.$key.output.output`. ", "help_text": "Type: `file`, default: `$id.$key.output.output`. " , - "default": "$id.$key.output.output" + "default":"$id.$key.output.output" } diff --git a/target/nextflow/trimgalore/.config.vsh.yaml b/target/nextflow/trimgalore/.config.vsh.yaml index b1e8cce..2788be7 100644 --- a/target/nextflow/trimgalore/.config.vsh.yaml +++ b/target/nextflow/trimgalore/.config.vsh.yaml @@ -796,8 +796,8 @@ build_info: output: "target/nextflow/trimgalore" executable: "target/nextflow/trimgalore/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/trimgalore/main.nf b/target/nextflow/trimgalore/main.nf index e23297c..2fb7088 100644 --- a/target/nextflow/trimgalore/main.nf +++ b/target/nextflow/trimgalore/main.nf @@ -3588,8 +3588,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/trimgalore", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/trimgalore/nextflow_schema.json b/target/nextflow/trimgalore/nextflow_schema.json index feb3442..76bc6ff 100644 --- a/target/nextflow/trimgalore/nextflow_schema.json +++ b/target/nextflow/trimgalore/nextflow_schema.json @@ -490,7 +490,7 @@ "description": "Type: `file`, default: `$id.$key.output_dir.output_dir`. If specified all output will be written to this directory instead of the current directory", "help_text": "Type: `file`, default: `$id.$key.output_dir.output_dir`. If specified all output will be written to this directory instead of the current directory." , - "default": "$id.$key.output_dir.output_dir" + "default":"$id.$key.output_dir.output_dir" } @@ -501,7 +501,7 @@ "description": "Type: `file`, default: `$id.$key.trimmed_r1.gz`, example: `read_1.fastq.gz`. Output file for read 1", "help_text": "Type: `file`, default: `$id.$key.trimmed_r1.gz`, example: `read_1.fastq.gz`. Output file for read 1. Only works when 1 file (single-end) or 2 files (paired-end) are specified, but not for longer lists." , - "default": "$id.$key.trimmed_r1.gz" + "default":"$id.$key.trimmed_r1.gz" } @@ -512,7 +512,7 @@ "description": "Type: `file`, default: `$id.$key.trimmed_r2.gz`, example: `read_2.fastq.gz`. Output file for read 2", "help_text": "Type: `file`, default: `$id.$key.trimmed_r2.gz`, example: `read_2.fastq.gz`. Output file for read 2. Only works when 1 file (single-end) or 2 files (paired-end) are specified, but not for longer lists." , - "default": "$id.$key.trimmed_r2.gz" + "default":"$id.$key.trimmed_r2.gz" } @@ -523,7 +523,7 @@ "description": "Type: `file`, default: `$id.$key.trimming_report_r1.txt`, example: `read_1.trimming_report.txt`. Trimming report for read 1", "help_text": "Type: `file`, default: `$id.$key.trimming_report_r1.txt`, example: `read_1.trimming_report.txt`. Trimming report for read 1. Only works when 1 file (single-end) or 2 files (paired-end) are specified, but not for longer lists." , - "default": "$id.$key.trimming_report_r1.txt" + "default":"$id.$key.trimming_report_r1.txt" } @@ -534,7 +534,7 @@ "description": "Type: `file`, default: `$id.$key.trimming_report_r2.txt`, example: `read_2.trimming_report.txt`. Trimming report for read 1", "help_text": "Type: `file`, default: `$id.$key.trimming_report_r2.txt`, example: `read_2.trimming_report.txt`. Trimming report for read 1. Only works when 1 file (single-end) or 2 files (paired-end) are specified, but not for longer lists." , - "default": "$id.$key.trimming_report_r2.txt" + "default":"$id.$key.trimming_report_r2.txt" } @@ -545,7 +545,7 @@ "description": "Type: `file`, default: `$id.$key.trimmed_fastqc_html_1.html`, example: `read_1.fastqc.html`. FastQC report for trimmed (single-end) reads (or read 1 for paired-end)", "help_text": "Type: `file`, default: `$id.$key.trimmed_fastqc_html_1.html`, example: `read_1.fastqc.html`. FastQC report for trimmed (single-end) reads (or read 1 for paired-end). Only works when 1 file (single-end) or 2 files (paired-end) are specified, but not for longer lists." , - "default": "$id.$key.trimmed_fastqc_html_1.html" + "default":"$id.$key.trimmed_fastqc_html_1.html" } @@ -556,7 +556,7 @@ "description": "Type: `file`, default: `$id.$key.trimmed_fastqc_html_2.html`, example: `read_2.fastqc.html`. FastQC report for trimmed reads (read2 for paired-end)", "help_text": "Type: `file`, default: `$id.$key.trimmed_fastqc_html_2.html`, example: `read_2.fastqc.html`. FastQC report for trimmed reads (read2 for paired-end). Only works when 1 file (single-end) or 2 files (paired-end) are specified, but not for longer lists." , - "default": "$id.$key.trimmed_fastqc_html_2.html" + "default":"$id.$key.trimmed_fastqc_html_2.html" } @@ -567,7 +567,7 @@ "description": "Type: `file`, default: `$id.$key.trimmed_fastqc_zip_1.zip`, example: `read_1.fastqc.zip`. FastQC results for trimmed (single-end) reads (or read 1 for paired-end)", "help_text": "Type: `file`, default: `$id.$key.trimmed_fastqc_zip_1.zip`, example: `read_1.fastqc.zip`. FastQC results for trimmed (single-end) reads (or read 1 for paired-end). Only works when 1 file (single-end) or 2 files (paired-end) are specified, but not for longer lists." , - "default": "$id.$key.trimmed_fastqc_zip_1.zip" + "default":"$id.$key.trimmed_fastqc_zip_1.zip" } @@ -578,7 +578,7 @@ "description": "Type: `file`, default: `$id.$key.trimmed_fastqc_zip_2.zip`, example: `read_2.fastqc.zip`. FastQC results for trimmed reads (read2 for paired-end)", "help_text": "Type: `file`, default: `$id.$key.trimmed_fastqc_zip_2.zip`, example: `read_2.fastqc.zip`. FastQC results for trimmed reads (read2 for paired-end). Only works when 1 file (single-end) or 2 files (paired-end) are specified, but not for longer lists." , - "default": "$id.$key.trimmed_fastqc_zip_2.zip" + "default":"$id.$key.trimmed_fastqc_zip_2.zip" } @@ -589,7 +589,7 @@ "description": "Type: `file`, default: `$id.$key.unpaired_r1.fastq`, example: `unpaired_read_1.fastq`. Output file for unpired read 1", "help_text": "Type: `file`, default: `$id.$key.unpaired_r1.fastq`, example: `unpaired_read_1.fastq`. Output file for unpired read 1. Only works when 1 file (single-end) or 2 files (paired-end) are specified, but not for longer lists." , - "default": "$id.$key.unpaired_r1.fastq" + "default":"$id.$key.unpaired_r1.fastq" } @@ -600,7 +600,7 @@ "description": "Type: `file`, default: `$id.$key.unpaired_r2.fastq`, example: `unpaired_read_2.fastq`. Output file for unpaired read 2", "help_text": "Type: `file`, default: `$id.$key.unpaired_r2.fastq`, example: `unpaired_read_2.fastq`. Output file for unpaired read 2. Only works when 1 file (single-end) or 2 files (paired-end) are specified, but not for longer lists." , - "default": "$id.$key.unpaired_r2.fastq" + "default":"$id.$key.unpaired_r2.fastq" } diff --git a/target/nextflow/tx2gene/.config.vsh.yaml b/target/nextflow/tx2gene/.config.vsh.yaml index d03dac4..efaa570 100644 --- a/target/nextflow/tx2gene/.config.vsh.yaml +++ b/target/nextflow/tx2gene/.config.vsh.yaml @@ -200,8 +200,8 @@ build_info: output: "target/nextflow/tx2gene" executable: "target/nextflow/tx2gene/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/tx2gene/main.nf b/target/nextflow/tx2gene/main.nf index f087e1d..359cdfc 100644 --- a/target/nextflow/tx2gene/main.nf +++ b/target/nextflow/tx2gene/main.nf @@ -3061,8 +3061,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/tx2gene", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/tx2gene/nextflow_schema.json b/target/nextflow/tx2gene/nextflow_schema.json index 4c65bfd..18d9966 100644 --- a/target/nextflow/tx2gene/nextflow_schema.json +++ b/target/nextflow/tx2gene/nextflow_schema.json @@ -40,7 +40,7 @@ "description": "Type: `string`, default: `gene_name`. ", "help_text": "Type: `string`, default: `gene_name`. " , - "default": "gene_name" + "default":"gene_name" } @@ -51,7 +51,7 @@ "description": "Type: `string`, default: `gene_id`. ", "help_text": "Type: `string`, default: `gene_id`. " , - "default": "gene_id" + "default":"gene_id" } @@ -84,7 +84,7 @@ "description": "Type: `file`, default: `$id.$key.tsv.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.tsv.tsv`. " , - "default": "$id.$key.tsv.tsv" + "default":"$id.$key.tsv.tsv" } @@ -95,7 +95,7 @@ "description": "Type: `file`, default: `$id.$key.updated_versions.yml`. ", "help_text": "Type: `file`, default: `$id.$key.updated_versions.yml`. " , - "default": "$id.$key.updated_versions.yml" + "default":"$id.$key.updated_versions.yml" } diff --git a/target/nextflow/tximport/.config.vsh.yaml b/target/nextflow/tximport/.config.vsh.yaml index c7bf9a9..09b60ac 100644 --- a/target/nextflow/tximport/.config.vsh.yaml +++ b/target/nextflow/tximport/.config.vsh.yaml @@ -255,8 +255,8 @@ build_info: output: "target/nextflow/tximport" executable: "target/nextflow/tximport/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/tximport/main.nf b/target/nextflow/tximport/main.nf index 7a0ca37..8f87c4b 100644 --- a/target/nextflow/tximport/main.nf +++ b/target/nextflow/tximport/main.nf @@ -3126,8 +3126,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/tximport", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/tximport/nextflow_schema.json b/target/nextflow/tximport/nextflow_schema.json index 6bd4ddf..20043f4 100644 --- a/target/nextflow/tximport/nextflow_schema.json +++ b/target/nextflow/tximport/nextflow_schema.json @@ -62,7 +62,7 @@ "description": "Type: `file`, default: `$id.$key.tpm_gene.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.tpm_gene.tsv`. " , - "default": "$id.$key.tpm_gene.tsv" + "default":"$id.$key.tpm_gene.tsv" } @@ -73,7 +73,7 @@ "description": "Type: `file`, default: `$id.$key.counts_gene.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.counts_gene.tsv`. " , - "default": "$id.$key.counts_gene.tsv" + "default":"$id.$key.counts_gene.tsv" } @@ -84,7 +84,7 @@ "description": "Type: `file`, default: `$id.$key.counts_gene_length_scaled.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.counts_gene_length_scaled.tsv`. " , - "default": "$id.$key.counts_gene_length_scaled.tsv" + "default":"$id.$key.counts_gene_length_scaled.tsv" } @@ -95,7 +95,7 @@ "description": "Type: `file`, default: `$id.$key.counts_gene_scaled.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.counts_gene_scaled.tsv`. " , - "default": "$id.$key.counts_gene_scaled.tsv" + "default":"$id.$key.counts_gene_scaled.tsv" } @@ -106,7 +106,7 @@ "description": "Type: `file`, default: `$id.$key.lengths_gene.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.lengths_gene.tsv`. " , - "default": "$id.$key.lengths_gene.tsv" + "default":"$id.$key.lengths_gene.tsv" } @@ -117,7 +117,7 @@ "description": "Type: `file`, default: `$id.$key.tpm_transcript.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.tpm_transcript.tsv`. " , - "default": "$id.$key.tpm_transcript.tsv" + "default":"$id.$key.tpm_transcript.tsv" } @@ -128,7 +128,7 @@ "description": "Type: `file`, default: `$id.$key.counts_transcript.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.counts_transcript.tsv`. " , - "default": "$id.$key.counts_transcript.tsv" + "default":"$id.$key.counts_transcript.tsv" } @@ -139,7 +139,7 @@ "description": "Type: `file`, default: `$id.$key.lengths_transcript.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.lengths_transcript.tsv`. " , - "default": "$id.$key.lengths_transcript.tsv" + "default":"$id.$key.lengths_transcript.tsv" } diff --git a/target/nextflow/ucsc/bedclip/.config.vsh.yaml b/target/nextflow/ucsc/bedclip/.config.vsh.yaml index 232a7b5..11e8be2 100644 --- a/target/nextflow/ucsc/bedclip/.config.vsh.yaml +++ b/target/nextflow/ucsc/bedclip/.config.vsh.yaml @@ -172,8 +172,8 @@ build_info: output: "target/nextflow/ucsc/bedclip" executable: "target/nextflow/ucsc/bedclip/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/ucsc/bedclip/main.nf b/target/nextflow/ucsc/bedclip/main.nf index 31aa3f7..b77a76a 100644 --- a/target/nextflow/ucsc/bedclip/main.nf +++ b/target/nextflow/ucsc/bedclip/main.nf @@ -3030,8 +3030,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/ucsc/bedclip", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/ucsc/bedclip/nextflow_schema.json b/target/nextflow/ucsc/bedclip/nextflow_schema.json index 3455b54..456033f 100644 --- a/target/nextflow/ucsc/bedclip/nextflow_schema.json +++ b/target/nextflow/ucsc/bedclip/nextflow_schema.json @@ -50,7 +50,7 @@ "description": "Type: `file`, default: `$id.$key.output_bedgraph.bedgraph`. bedGraph file after clipping", "help_text": "Type: `file`, default: `$id.$key.output_bedgraph.bedgraph`. bedGraph file after clipping" , - "default": "$id.$key.output_bedgraph.bedgraph" + "default":"$id.$key.output_bedgraph.bedgraph" } diff --git a/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml b/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml index bf0d824..c0258e5 100644 --- a/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml +++ b/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml @@ -172,8 +172,8 @@ build_info: output: "target/nextflow/ucsc/bedgraphtobigwig" executable: "target/nextflow/ucsc/bedgraphtobigwig/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/ucsc/bedgraphtobigwig/main.nf b/target/nextflow/ucsc/bedgraphtobigwig/main.nf index 952f55d..39b6c2b 100644 --- a/target/nextflow/ucsc/bedgraphtobigwig/main.nf +++ b/target/nextflow/ucsc/bedgraphtobigwig/main.nf @@ -3030,8 +3030,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/ucsc/bedgraphtobigwig", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/ucsc/bedgraphtobigwig/nextflow_schema.json b/target/nextflow/ucsc/bedgraphtobigwig/nextflow_schema.json index 468353f..1798946 100644 --- a/target/nextflow/ucsc/bedgraphtobigwig/nextflow_schema.json +++ b/target/nextflow/ucsc/bedgraphtobigwig/nextflow_schema.json @@ -50,7 +50,7 @@ "description": "Type: `file`, default: `$id.$key.bigwig.bigwig`. bigWig coverage file relative to genes on the input file", "help_text": "Type: `file`, default: `$id.$key.bigwig.bigwig`. bigWig coverage file relative to genes on the input file" , - "default": "$id.$key.bigwig.bigwig" + "default":"$id.$key.bigwig.bigwig" } diff --git a/target/nextflow/umitools/umitools_dedup/.config.vsh.yaml b/target/nextflow/umitools/umitools_dedup/.config.vsh.yaml index 8bb1d72..4a9ca28 100644 --- a/target/nextflow/umitools/umitools_dedup/.config.vsh.yaml +++ b/target/nextflow/umitools/umitools_dedup/.config.vsh.yaml @@ -203,8 +203,8 @@ build_info: output: "target/nextflow/umitools/umitools_dedup" executable: "target/nextflow/umitools/umitools_dedup/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/umitools/umitools_dedup/main.nf b/target/nextflow/umitools/umitools_dedup/main.nf index 5621313..9ffcf54 100644 --- a/target/nextflow/umitools/umitools_dedup/main.nf +++ b/target/nextflow/umitools/umitools_dedup/main.nf @@ -3066,8 +3066,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/umitools/umitools_dedup", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/umitools/umitools_dedup/nextflow_schema.json b/target/nextflow/umitools/umitools_dedup/nextflow_schema.json index 9ddb086..199a96d 100644 --- a/target/nextflow/umitools/umitools_dedup/nextflow_schema.json +++ b/target/nextflow/umitools/umitools_dedup/nextflow_schema.json @@ -20,7 +20,7 @@ "description": "Type: `boolean`, default: `false`. Paired fastq files or not?", "help_text": "Type: `boolean`, default: `false`. Paired fastq files or not?" , - "default": "False" + "default":false } @@ -71,7 +71,7 @@ "description": "Type: `file`, default: `$id.$key.output_bam.bam`. Deduplicated BAM file", "help_text": "Type: `file`, default: `$id.$key.output_bam.bam`. Deduplicated BAM file" , - "default": "$id.$key.output_bam.bam" + "default":"$id.$key.output_bam.bam" } @@ -82,7 +82,7 @@ "description": "Type: `file`, default: `$id.$key.output_stats.stats`. Directory containing UMI based dedupllication statistics files", "help_text": "Type: `file`, default: `$id.$key.output_stats.stats`. Directory containing UMI based dedupllication statistics files" , - "default": "$id.$key.output_stats.stats" + "default":"$id.$key.output_stats.stats" } diff --git a/target/nextflow/umitools/umitools_extract/.config.vsh.yaml b/target/nextflow/umitools/umitools_extract/.config.vsh.yaml index 1fa7d95..55bb82a 100644 --- a/target/nextflow/umitools/umitools_extract/.config.vsh.yaml +++ b/target/nextflow/umitools/umitools_extract/.config.vsh.yaml @@ -261,8 +261,8 @@ build_info: output: "target/nextflow/umitools/umitools_extract" executable: "target/nextflow/umitools/umitools_extract/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/umitools/umitools_extract/main.nf b/target/nextflow/umitools/umitools_extract/main.nf index 017b934..1c0d1ab 100644 --- a/target/nextflow/umitools/umitools_extract/main.nf +++ b/target/nextflow/umitools/umitools_extract/main.nf @@ -3131,8 +3131,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/umitools/umitools_extract", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/umitools/umitools_extract/nextflow_schema.json b/target/nextflow/umitools/umitools_extract/nextflow_schema.json index abcf58d..5bc15e7 100644 --- a/target/nextflow/umitools/umitools_extract/nextflow_schema.json +++ b/target/nextflow/umitools/umitools_extract/nextflow_schema.json @@ -20,7 +20,7 @@ "description": "Type: `boolean`, default: `false`. Paired fastq files or not?", "help_text": "Type: `boolean`, default: `false`. Paired fastq files or not?" , - "default": "False" + "default":false } @@ -61,7 +61,7 @@ "description": "Type: `file`, required, default: `$id.$key.fastq_1.fastq`. Output file for read 1", "help_text": "Type: `file`, required, default: `$id.$key.fastq_1.fastq`. Output file for read 1." , - "default": "$id.$key.fastq_1.fastq" + "default":"$id.$key.fastq_1.fastq" } @@ -72,7 +72,7 @@ "description": "Type: `file`, default: `$id.$key.fastq_2.fastq`. Output file for read 2", "help_text": "Type: `file`, default: `$id.$key.fastq_2.fastq`. Output file for read 2." , - "default": "$id.$key.fastq_2.fastq" + "default":"$id.$key.fastq_2.fastq" } @@ -95,7 +95,7 @@ "enum": ["string", "regex"] , - "default": "string" + "default":"string" } @@ -106,7 +106,7 @@ "description": "Type: `string`, default: `_`. The character that separates the UMI in the read name", "help_text": "Type: `string`, default: `_`. The character that separates the UMI in the read name. Most likely a colon if you skipped the extraction with UMI-tools and used other software." , - "default": "_" + "default":"_" } @@ -119,7 +119,7 @@ "enum": ["unique", "percentile", "cluster", "adjacency", "directional"] , - "default": "directional" + "default":"directional" } @@ -132,7 +132,7 @@ "enum": [0, 1, 2] , - "default": "0" + "default":0 } diff --git a/target/nextflow/umitools_prepareforquant/.config.vsh.yaml b/target/nextflow/umitools_prepareforquant/.config.vsh.yaml index 6597bef..502ed5e 100644 --- a/target/nextflow/umitools_prepareforquant/.config.vsh.yaml +++ b/target/nextflow/umitools_prepareforquant/.config.vsh.yaml @@ -164,8 +164,8 @@ build_info: output: "target/nextflow/umitools_prepareforquant" executable: "target/nextflow/umitools_prepareforquant/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "add-labels" diff --git a/target/nextflow/umitools_prepareforquant/main.nf b/target/nextflow/umitools_prepareforquant/main.nf index c67e9a3..9671dea 100644 --- a/target/nextflow/umitools_prepareforquant/main.nf +++ b/target/nextflow/umitools_prepareforquant/main.nf @@ -3019,8 +3019,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/umitools_prepareforquant", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/umitools_prepareforquant/nextflow_schema.json b/target/nextflow/umitools_prepareforquant/nextflow_schema.json index e204915..5993e05 100644 --- a/target/nextflow/umitools_prepareforquant/nextflow_schema.json +++ b/target/nextflow/umitools_prepareforquant/nextflow_schema.json @@ -40,7 +40,7 @@ "description": "Type: `file`, default: `$id.$key.output.bam`. ", "help_text": "Type: `file`, default: `$id.$key.output.bam`. " , - "default": "$id.$key.output.bam" + "default":"$id.$key.output.bam" } @@ -51,7 +51,7 @@ "description": "Type: `file`, default: `$id.$key.log.log`. ", "help_text": "Type: `file`, default: `$id.$key.log.log`. " , - "default": "$id.$key.log.log" + "default":"$id.$key.log.log" } 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 0ec790a..ba91fc9 100644 --- a/target/nextflow/workflows/genome_alignment_and_quant/.config.vsh.yaml +++ b/target/nextflow/workflows/genome_alignment_and_quant/.config.vsh.yaml @@ -611,8 +611,8 @@ 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: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads" - "target/dependencies/vsh/vsh/biobox/main/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 cbc1f15..b1dfbc5 100644 --- a/target/nextflow/workflows/genome_alignment_and_quant/main.nf +++ b/target/nextflow/workflows/genome_alignment_and_quant/main.nf @@ -3543,8 +3543,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/genome_alignment_and_quant", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", @@ -3600,6 +3600,8 @@ include { rsem_calculate_expression } from "${meta.resources_dir}/../../../nextf // inner workflow // user-provided Nextflow code +// TODO: Improve logic of this wf, e.g. by splitting up in 2 subwfs +// TODO: See if this can be aligned with the pseudo-alignment branch of the logic workflow run_wf { take: input_ch diff --git a/target/nextflow/workflows/genome_alignment_and_quant/nextflow_schema.json b/target/nextflow/workflows/genome_alignment_and_quant/nextflow_schema.json index dfe1afe..0613c66 100644 --- a/target/nextflow/workflows/genome_alignment_and_quant/nextflow_schema.json +++ b/target/nextflow/workflows/genome_alignment_and_quant/nextflow_schema.json @@ -92,7 +92,7 @@ "description": "Type: `boolean`, default: `false`. When using pre-built STAR indices do not re-extract and use splice junctions from the GTF file", "help_text": "Type: `boolean`, default: `false`. When using pre-built STAR indices do not re-extract and use splice junctions from the GTF file" , - "default": "False" + "default":false } @@ -123,7 +123,7 @@ "description": "Type: `string`, default: ``. Extra arguments to pass to STAR alignment command in addition to defaults defined by the pipeline", "help_text": "Type: `string`, default: ``. Extra arguments to pass to STAR alignment command in addition to defaults defined by the pipeline." , - "default": "" + "default":"" } @@ -134,7 +134,7 @@ "description": "Type: `boolean`, default: `false`. Create a CSI index for BAM files instead of the traditional BAI index", "help_text": "Type: `boolean`, default: `false`. Create a CSI index for BAM files instead of the traditional BAI index. This will be required for genomes with larger chromosome sizes." , - "default": "False" + "default":false } @@ -145,7 +145,7 @@ "description": "Type: `boolean`, default: `false`. Generate output stats when running \"umi_tools dedup\"", "help_text": "Type: `boolean`, default: `false`. Generate output stats when running \"umi_tools dedup\"." , - "default": "False" + "default":false } @@ -156,7 +156,7 @@ "description": "Type: `boolean`, default: `false`. Enable UMI-based read deduplication", "help_text": "Type: `boolean`, default: `false`. Enable UMI-based read deduplication." , - "default": "False" + "default":false } @@ -177,7 +177,7 @@ "description": "Type: `string`, default: ``. Extra arguments to pass to salmon quant command in addition to defaults defined by the pipeline", "help_text": "Type: `string`, default: ``. Extra arguments to pass to salmon quant command in addition to defaults defined by the pipeline." , - "default": "" + "default":"" } @@ -188,7 +188,7 @@ "description": "Type: `string`, default: `gene_id`. Define the attribute type used to group features in the GTF file when running Salmon", "help_text": "Type: `string`, default: `gene_id`. Define the attribute type used to group features in the GTF file when running Salmon." , - "default": "gene_id" + "default":"gene_id" } @@ -199,7 +199,7 @@ "description": "Type: `string`, default: `gene_name`. By default, the pipeline uses the gene_name field to obtain additional gene identifiers from the input GTF file when running Salmon", "help_text": "Type: `string`, default: `gene_name`. By default, the pipeline uses the gene_name field to obtain additional gene identifiers from the input GTF file when running Salmon." , - "default": "gene_name" + "default":"gene_name" } @@ -222,7 +222,7 @@ "enum": ["star_salmon", "star_rsem", "hisat2"] , - "default": "star_salmon" + "default":"star_salmon" } @@ -263,7 +263,7 @@ "description": "Type: `file`, default: `$id.$key.star_multiqc.log`. ", "help_text": "Type: `file`, default: `$id.$key.star_multiqc.log`. " , - "default": "$id.$key.star_multiqc.log" + "default":"$id.$key.star_multiqc.log" } @@ -274,7 +274,7 @@ "description": "Type: `file`, default: `$id.$key.genome_bam_sorted.bam`. ", "help_text": "Type: `file`, default: `$id.$key.genome_bam_sorted.bam`. " , - "default": "$id.$key.genome_bam_sorted.bam" + "default":"$id.$key.genome_bam_sorted.bam" } @@ -285,7 +285,7 @@ "description": "Type: `file`, default: `$id.$key.genome_bam_index.bai`. ", "help_text": "Type: `file`, default: `$id.$key.genome_bam_index.bai`. " , - "default": "$id.$key.genome_bam_index.bai" + "default":"$id.$key.genome_bam_index.bai" } @@ -296,7 +296,7 @@ "description": "Type: `file`, default: `$id.$key.genome_bam_stats.stats`. ", "help_text": "Type: `file`, default: `$id.$key.genome_bam_stats.stats`. " , - "default": "$id.$key.genome_bam_stats.stats" + "default":"$id.$key.genome_bam_stats.stats" } @@ -307,7 +307,7 @@ "description": "Type: `file`, default: `$id.$key.genome_bam_flagstat.flagstat`. ", "help_text": "Type: `file`, default: `$id.$key.genome_bam_flagstat.flagstat`. " , - "default": "$id.$key.genome_bam_flagstat.flagstat" + "default":"$id.$key.genome_bam_flagstat.flagstat" } @@ -318,7 +318,7 @@ "description": "Type: `file`, default: `$id.$key.genome_bam_idxstats.idxstats`. ", "help_text": "Type: `file`, default: `$id.$key.genome_bam_idxstats.idxstats`. " , - "default": "$id.$key.genome_bam_idxstats.idxstats" + "default":"$id.$key.genome_bam_idxstats.idxstats" } @@ -329,7 +329,7 @@ "description": "Type: `file`, default: `$id.$key.transcriptome_bam.bam`. ", "help_text": "Type: `file`, default: `$id.$key.transcriptome_bam.bam`. " , - "default": "$id.$key.transcriptome_bam.bam" + "default":"$id.$key.transcriptome_bam.bam" } @@ -340,7 +340,7 @@ "description": "Type: `file`, default: `$id.$key.transcriptome_bam_index.bai`. ", "help_text": "Type: `file`, default: `$id.$key.transcriptome_bam_index.bai`. " , - "default": "$id.$key.transcriptome_bam_index.bai" + "default":"$id.$key.transcriptome_bam_index.bai" } @@ -351,7 +351,7 @@ "description": "Type: `file`, default: `$id.$key.transcriptome_bam_stats.stats`. ", "help_text": "Type: `file`, default: `$id.$key.transcriptome_bam_stats.stats`. " , - "default": "$id.$key.transcriptome_bam_stats.stats" + "default":"$id.$key.transcriptome_bam_stats.stats" } @@ -362,7 +362,7 @@ "description": "Type: `file`, default: `$id.$key.transcriptome_bam_flagstat.flagstat`. ", "help_text": "Type: `file`, default: `$id.$key.transcriptome_bam_flagstat.flagstat`. " , - "default": "$id.$key.transcriptome_bam_flagstat.flagstat" + "default":"$id.$key.transcriptome_bam_flagstat.flagstat" } @@ -373,7 +373,7 @@ "description": "Type: `file`, default: `$id.$key.transcriptome_bam_idxstats.idxstats`. ", "help_text": "Type: `file`, default: `$id.$key.transcriptome_bam_idxstats.idxstats`. " , - "default": "$id.$key.transcriptome_bam_idxstats.idxstats" + "default":"$id.$key.transcriptome_bam_idxstats.idxstats" } @@ -384,7 +384,7 @@ "description": "Type: `file`, default: `$id.$key.quant_out_dir.salmon_quant`. ", "help_text": "Type: `file`, default: `$id.$key.quant_out_dir.salmon_quant`. " , - "default": "$id.$key.quant_out_dir.salmon_quant" + "default":"$id.$key.quant_out_dir.salmon_quant" } @@ -395,7 +395,7 @@ "description": "Type: `file`, default: `$id.$key.quant_results_file.sf`. ", "help_text": "Type: `file`, default: `$id.$key.quant_results_file.sf`. " , - "default": "$id.$key.quant_results_file.sf" + "default":"$id.$key.quant_results_file.sf" } @@ -406,7 +406,7 @@ "description": "Type: `file`, default: `$id.$key.salmon_multiqc.salmon_multiqc`. ", "help_text": "Type: `file`, default: `$id.$key.salmon_multiqc.salmon_multiqc`. " , - "default": "$id.$key.salmon_multiqc.salmon_multiqc" + "default":"$id.$key.salmon_multiqc.salmon_multiqc" } @@ -417,7 +417,7 @@ "description": "Type: `file`, default: `$id.$key.rsem_counts_gene.results`. Expression counts on gene level", "help_text": "Type: `file`, default: `$id.$key.rsem_counts_gene.results`. Expression counts on gene level" , - "default": "$id.$key.rsem_counts_gene.results" + "default":"$id.$key.rsem_counts_gene.results" } @@ -428,7 +428,7 @@ "description": "Type: `file`, default: `$id.$key.counts_transcripts.results`. Expression counts on transcript level", "help_text": "Type: `file`, default: `$id.$key.counts_transcripts.results`. Expression counts on transcript level" , - "default": "$id.$key.counts_transcripts.results" + "default":"$id.$key.counts_transcripts.results" } @@ -439,7 +439,7 @@ "description": "Type: `file`, default: `$id.$key.rsem_multiqc.stat`. RSEM statistics", "help_text": "Type: `file`, default: `$id.$key.rsem_multiqc.stat`. RSEM statistics" , - "default": "$id.$key.rsem_multiqc.stat" + "default":"$id.$key.rsem_multiqc.stat" } @@ -450,7 +450,7 @@ "description": "Type: `file`, default: `$id.$key.bam_star_rsem.bam`. BAM file generated by STAR (optional)", "help_text": "Type: `file`, default: `$id.$key.bam_star_rsem.bam`. BAM file generated by STAR (optional)" , - "default": "$id.$key.bam_star_rsem.bam" + "default":"$id.$key.bam_star_rsem.bam" } @@ -461,7 +461,7 @@ "description": "Type: `file`, default: `$id.$key.bam_genome_rsem.bam`. Genome BAM file (optional)", "help_text": "Type: `file`, default: `$id.$key.bam_genome_rsem.bam`. Genome BAM file (optional)" , - "default": "$id.$key.bam_genome_rsem.bam" + "default":"$id.$key.bam_genome_rsem.bam" } @@ -472,7 +472,7 @@ "description": "Type: `file`, default: `$id.$key.bam_transcript_rsem.bam`. Transcript BAM file (optional)", "help_text": "Type: `file`, default: `$id.$key.bam_transcript_rsem.bam`. Transcript BAM file (optional)" , - "default": "$id.$key.bam_transcript_rsem.bam" + "default":"$id.$key.bam_transcript_rsem.bam" } diff --git a/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml b/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml index da7718a..a7ffe7c 100644 --- a/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml +++ b/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml @@ -286,8 +286,8 @@ 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: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@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 694663e..8c01ba9 100644 --- a/target/nextflow/workflows/merge_quant_results/main.nf +++ b/target/nextflow/workflows/merge_quant_results/main.nf @@ -3161,8 +3161,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/merge_quant_results", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/workflows/merge_quant_results/nextflow_schema.json b/target/nextflow/workflows/merge_quant_results/nextflow_schema.json index e8b9d19..46a1adb 100644 --- a/target/nextflow/workflows/merge_quant_results/nextflow_schema.json +++ b/target/nextflow/workflows/merge_quant_results/nextflow_schema.json @@ -50,7 +50,7 @@ "description": "Type: `string`, default: `gene_name`. ", "help_text": "Type: `string`, default: `gene_name`. " , - "default": "gene_name" + "default":"gene_name" } @@ -61,7 +61,7 @@ "description": "Type: `string`, default: `gene_id`. ", "help_text": "Type: `string`, default: `gene_id`. " , - "default": "gene_id" + "default":"gene_id" } @@ -74,7 +74,7 @@ "enum": ["salmon", "kallisto"] , - "default": "salmon" + "default":"salmon" } @@ -105,7 +105,7 @@ "description": "Type: `file`, default: `$id.$key.tpm_gene.tsv`, example: `gene_tpm.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.tpm_gene.tsv`, example: `gene_tpm.tsv`. " , - "default": "$id.$key.tpm_gene.tsv" + "default":"$id.$key.tpm_gene.tsv" } @@ -116,7 +116,7 @@ "description": "Type: `file`, default: `$id.$key.counts_gene.tsv`, example: `gene_counts.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.counts_gene.tsv`, example: `gene_counts.tsv`. " , - "default": "$id.$key.counts_gene.tsv" + "default":"$id.$key.counts_gene.tsv" } @@ -127,7 +127,7 @@ "description": "Type: `file`, default: `$id.$key.counts_gene_length_scaled.tsv`, example: `gene_counts_length_scaled.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.counts_gene_length_scaled.tsv`, example: `gene_counts_length_scaled.tsv`. " , - "default": "$id.$key.counts_gene_length_scaled.tsv" + "default":"$id.$key.counts_gene_length_scaled.tsv" } @@ -138,7 +138,7 @@ "description": "Type: `file`, default: `$id.$key.counts_gene_scaled.tsv`, example: `gene_counts_scaled.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.counts_gene_scaled.tsv`, example: `gene_counts_scaled.tsv`. " , - "default": "$id.$key.counts_gene_scaled.tsv" + "default":"$id.$key.counts_gene_scaled.tsv" } @@ -149,7 +149,7 @@ "description": "Type: `file`, default: `$id.$key.tpm_transcript.tsv`, example: `transcript_tpm.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.tpm_transcript.tsv`, example: `transcript_tpm.tsv`. " , - "default": "$id.$key.tpm_transcript.tsv" + "default":"$id.$key.tpm_transcript.tsv" } @@ -160,7 +160,7 @@ "description": "Type: `file`, default: `$id.$key.lengths_gene.tsv`, example: `gene_length.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.lengths_gene.tsv`, example: `gene_length.tsv`. " , - "default": "$id.$key.lengths_gene.tsv" + "default":"$id.$key.lengths_gene.tsv" } @@ -171,7 +171,7 @@ "description": "Type: `file`, default: `$id.$key.counts_transcript.tsv`, example: `transcript_counts.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.counts_transcript.tsv`, example: `transcript_counts.tsv`. " , - "default": "$id.$key.counts_transcript.tsv" + "default":"$id.$key.counts_transcript.tsv" } @@ -182,7 +182,7 @@ "description": "Type: `file`, default: `$id.$key.lengths_transcript.tsv`, example: `transcript_length.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.lengths_transcript.tsv`, example: `transcript_length.tsv`. " , - "default": "$id.$key.lengths_transcript.tsv" + "default":"$id.$key.lengths_transcript.tsv" } @@ -193,7 +193,7 @@ "description": "Type: `file`, default: `$id.$key.quant_merged_summarizedexperiment.quant_merged_summarizedexperiment`, example: `quant_merged_summarizedexperiment`. ", "help_text": "Type: `file`, default: `$id.$key.quant_merged_summarizedexperiment.quant_merged_summarizedexperiment`, example: `quant_merged_summarizedexperiment`. " , - "default": "$id.$key.quant_merged_summarizedexperiment.quant_merged_summarizedexperiment" + "default":"$id.$key.quant_merged_summarizedexperiment.quant_merged_summarizedexperiment" } diff --git a/target/nextflow/workflows/post_processing/.config.vsh.yaml b/target/nextflow/workflows/post_processing/.config.vsh.yaml index 4fd9eec..c9f56db 100644 --- a/target/nextflow/workflows/post_processing/.config.vsh.yaml +++ b/target/nextflow/workflows/post_processing/.config.vsh.yaml @@ -494,8 +494,8 @@ build_info: output: "target/nextflow/workflows/post_processing" executable: "target/nextflow/workflows/post_processing/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/picard_markduplicates" - "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort" diff --git a/target/nextflow/workflows/post_processing/main.nf b/target/nextflow/workflows/post_processing/main.nf index d4d2ae1..61595e5 100644 --- a/target/nextflow/workflows/post_processing/main.nf +++ b/target/nextflow/workflows/post_processing/main.nf @@ -3409,8 +3409,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/post_processing", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/workflows/post_processing/nextflow_schema.json b/target/nextflow/workflows/post_processing/nextflow_schema.json index ca7d7bf..1b74211 100644 --- a/target/nextflow/workflows/post_processing/nextflow_schema.json +++ b/target/nextflow/workflows/post_processing/nextflow_schema.json @@ -30,7 +30,7 @@ "description": "Type: `string`, default: `auto`. Sample strand-specificity", "help_text": "Type: `string`, default: `auto`. Sample strand-specificity. Must be one of unstranded, forward, reverse or auto" , - "default": "auto" + "default":"auto" } @@ -111,7 +111,7 @@ "description": "Type: `string`, default: ``. Extra arguments to pass to picard MarkDuplicates command in addition to defaults defined by the pipeline", "help_text": "Type: `string`, default: ``. Extra arguments to pass to picard MarkDuplicates command in addition to defaults defined by the pipeline." , - "default": "" + "default":"" } @@ -122,7 +122,7 @@ "description": "Type: `string`, default: ``. Extra arguments to pass to stringtie command in addition to defaults defined by the pipeline", "help_text": "Type: `string`, default: ``. Extra arguments to pass to stringtie command in addition to defaults defined by the pipeline." , - "default": "" + "default":"" } @@ -143,7 +143,7 @@ "description": "Type: `string`, default: ``. Extra arguments to pass to bedtools genomecov command in addition to defaults defined by the pipeline", "help_text": "Type: `string`, default: ``. Extra arguments to pass to bedtools genomecov command in addition to defaults defined by the pipeline." , - "default": "" + "default":"" } @@ -154,7 +154,7 @@ "description": "Type: `boolean`, default: `false`. Create a CSI index for BAM files instead of the traditional BAI index", "help_text": "Type: `boolean`, default: `false`. Create a CSI index for BAM files instead of the traditional BAI index. This will be required for genomes with larger chromosome sizes." , - "default": "False" + "default":false } @@ -175,7 +175,7 @@ "description": "Type: `boolean`, default: `false`. Enable UMI-based read deduplication", "help_text": "Type: `boolean`, default: `false`. Enable UMI-based read deduplication." , - "default": "False" + "default":false } @@ -236,7 +236,7 @@ "description": "Type: `file`, default: `$id.$key.processed_genome_bam.bam`. ", "help_text": "Type: `file`, default: `$id.$key.processed_genome_bam.bam`. " , - "default": "$id.$key.processed_genome_bam.bam" + "default":"$id.$key.processed_genome_bam.bam" } @@ -247,7 +247,7 @@ "description": "Type: `file`, default: `$id.$key.genome_bam_index.bai`. ", "help_text": "Type: `file`, default: `$id.$key.genome_bam_index.bai`. " , - "default": "$id.$key.genome_bam_index.bai" + "default":"$id.$key.genome_bam_index.bai" } @@ -258,7 +258,7 @@ "description": "Type: `file`, default: `$id.$key.genome_bam_stats.stats`. ", "help_text": "Type: `file`, default: `$id.$key.genome_bam_stats.stats`. " , - "default": "$id.$key.genome_bam_stats.stats" + "default":"$id.$key.genome_bam_stats.stats" } @@ -269,7 +269,7 @@ "description": "Type: `file`, default: `$id.$key.genome_bam_flagstat.flagstat`. ", "help_text": "Type: `file`, default: `$id.$key.genome_bam_flagstat.flagstat`. " , - "default": "$id.$key.genome_bam_flagstat.flagstat" + "default":"$id.$key.genome_bam_flagstat.flagstat" } @@ -280,7 +280,7 @@ "description": "Type: `file`, default: `$id.$key.genome_bam_idxstats.idxstats`. ", "help_text": "Type: `file`, default: `$id.$key.genome_bam_idxstats.idxstats`. " , - "default": "$id.$key.genome_bam_idxstats.idxstats" + "default":"$id.$key.genome_bam_idxstats.idxstats" } @@ -291,7 +291,7 @@ "description": "Type: `file`, default: `$id.$key.markduplicates_metrics.txt`. ", "help_text": "Type: `file`, default: `$id.$key.markduplicates_metrics.txt`. " , - "default": "$id.$key.markduplicates_metrics.txt" + "default":"$id.$key.markduplicates_metrics.txt" } @@ -302,7 +302,7 @@ "description": "Type: `file`, default: `$id.$key.stringtie_transcript_gtf.gtf`. ", "help_text": "Type: `file`, default: `$id.$key.stringtie_transcript_gtf.gtf`. " , - "default": "$id.$key.stringtie_transcript_gtf.gtf" + "default":"$id.$key.stringtie_transcript_gtf.gtf" } @@ -313,7 +313,7 @@ "description": "Type: `file`, default: `$id.$key.stringtie_coverage_gtf.gtf`. ", "help_text": "Type: `file`, default: `$id.$key.stringtie_coverage_gtf.gtf`. " , - "default": "$id.$key.stringtie_coverage_gtf.gtf" + "default":"$id.$key.stringtie_coverage_gtf.gtf" } @@ -324,7 +324,7 @@ "description": "Type: `file`, default: `$id.$key.stringtie_abundance.txt`. ", "help_text": "Type: `file`, default: `$id.$key.stringtie_abundance.txt`. " , - "default": "$id.$key.stringtie_abundance.txt" + "default":"$id.$key.stringtie_abundance.txt" } @@ -335,7 +335,7 @@ "description": "Type: `file`, default: `$id.$key.stringtie_ballgown.ballgown`. ", "help_text": "Type: `file`, default: `$id.$key.stringtie_ballgown.ballgown`. " , - "default": "$id.$key.stringtie_ballgown.ballgown" + "default":"$id.$key.stringtie_ballgown.ballgown" } @@ -346,7 +346,7 @@ "description": "Type: `file`, default: `$id.$key.bedgraph_forward.bedgraph`. ", "help_text": "Type: `file`, default: `$id.$key.bedgraph_forward.bedgraph`. " , - "default": "$id.$key.bedgraph_forward.bedgraph" + "default":"$id.$key.bedgraph_forward.bedgraph" } @@ -357,7 +357,7 @@ "description": "Type: `file`, default: `$id.$key.bedgraph_reverse.bedgraph`. ", "help_text": "Type: `file`, default: `$id.$key.bedgraph_reverse.bedgraph`. " , - "default": "$id.$key.bedgraph_reverse.bedgraph" + "default":"$id.$key.bedgraph_reverse.bedgraph" } @@ -368,7 +368,7 @@ "description": "Type: `file`, default: `$id.$key.bigwig_forward.bigwig`. ", "help_text": "Type: `file`, default: `$id.$key.bigwig_forward.bigwig`. " , - "default": "$id.$key.bigwig_forward.bigwig" + "default":"$id.$key.bigwig_forward.bigwig" } @@ -379,7 +379,7 @@ "description": "Type: `file`, default: `$id.$key.bigwig_reverse.bigwig`. ", "help_text": "Type: `file`, default: `$id.$key.bigwig_reverse.bigwig`. " , - "default": "$id.$key.bigwig_reverse.bigwig" + "default":"$id.$key.bigwig_reverse.bigwig" } diff --git a/target/nextflow/workflows/pre_processing/.config.vsh.yaml b/target/nextflow/workflows/pre_processing/.config.vsh.yaml index d920b38..e6b05d9 100644 --- a/target/nextflow/workflows/pre_processing/.config.vsh.yaml +++ b/target/nextflow/workflows/pre_processing/.config.vsh.yaml @@ -681,8 +681,8 @@ build_info: output: "target/nextflow/workflows/pre_processing" executable: "target/nextflow/workflows/pre_processing/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@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 bf9ec64..6eaa29e 100644 --- a/target/nextflow/workflows/pre_processing/main.nf +++ b/target/nextflow/workflows/pre_processing/main.nf @@ -3638,8 +3638,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/pre_processing", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/workflows/pre_processing/nextflow_schema.json b/target/nextflow/workflows/pre_processing/nextflow_schema.json index 1b49356..fa9429a 100644 --- a/target/nextflow/workflows/pre_processing/nextflow_schema.json +++ b/target/nextflow/workflows/pre_processing/nextflow_schema.json @@ -50,7 +50,7 @@ "description": "Type: `string`, default: `auto`. Sample strand-specificity", "help_text": "Type: `string`, default: `auto`. Sample strand-specificity. Must be one of unstranded, forward, reverse or auto" , - "default": "auto" + "default":"auto" } @@ -161,7 +161,7 @@ "description": "Type: `boolean`, default: `false`. Skip FatQC step", "help_text": "Type: `boolean`, default: `false`. Skip FatQC step." , - "default": "False" + "default":false } @@ -182,7 +182,7 @@ "description": "Type: `boolean`, default: `false`. Enable UMI-based read deduplication", "help_text": "Type: `boolean`, default: `false`. Enable UMI-based read deduplication." , - "default": "False" + "default":false } @@ -193,7 +193,7 @@ "description": "Type: `boolean`, default: `false`. Skip umi_tools extract step", "help_text": "Type: `boolean`, default: `false`. Skip umi_tools extract step." , - "default": "False" + "default":false } @@ -206,7 +206,7 @@ "enum": ["string", "regex"] , - "default": "string" + "default":"string" } @@ -217,7 +217,7 @@ "description": "Type: `string`, default: ``. The UMI barcode pattern to use e", "help_text": "Type: `string`, default: ``. The UMI barcode pattern to use e.g. \u0027NNNNNN\u0027 indicates that the first 6 nucleotides of the read are from the UMI." , - "default": "" + "default":"" } @@ -228,7 +228,7 @@ "description": "Type: `string`, default: ``. The UMI barcode pattern to use if the UMI is located in read 2", "help_text": "Type: `string`, default: ``. The UMI barcode pattern to use if the UMI is located in read 2." , - "default": "" + "default":"" } @@ -241,7 +241,7 @@ "enum": [0, 1, 2] , - "default": "0" + "default":0 } @@ -252,7 +252,7 @@ "description": "Type: `string`, default: `_`. The character that separates the UMI in the read name", "help_text": "Type: `string`, default: `_`. The character that separates the UMI in the read name. Most likely a colon if you skipped the extraction with UMI-tools and used other software." , - "default": "_" + "default":"_" } @@ -265,7 +265,7 @@ "enum": ["unique", "percentile", "cluster", "adjacency", "directional"] , - "default": "directional" + "default":"directional" } @@ -276,7 +276,7 @@ "description": "Type: `boolean`, default: `false`. If this option is specified, intermediate FastQ and BAM files produced by UMI-tools are also saved in the results directory", "help_text": "Type: `boolean`, default: `false`. If this option is specified, intermediate FastQ and BAM files produced by UMI-tools are also saved in the results directory." , - "default": "False" + "default":false } @@ -299,7 +299,7 @@ "enum": ["trimgalore", "fastp"] , - "default": "trimgalore" + "default":"trimgalore" } @@ -320,7 +320,7 @@ "description": "Type: `integer`, default: `10000`. Minimum number of trimmed reads below which samples are removed from further processing", "help_text": "Type: `integer`, default: `10000`. Minimum number of trimmed reads below which samples are removed from further processing. Some downstream steps in the pipeline will fail if this threshold is too low." , - "default": "10000" + "default":10000 } @@ -331,7 +331,7 @@ "description": "Type: `boolean`, default: `false`. Skip the adapter trimming step", "help_text": "Type: `boolean`, default: `false`. Skip the adapter trimming step." , - "default": "False" + "default":false } @@ -342,7 +342,7 @@ "description": "Type: `boolean`, default: `false`. Save the trimmed FastQ files in the results directory", "help_text": "Type: `boolean`, default: `false`. Save the trimmed FastQ files in the results directory." , - "default": "False" + "default":false } @@ -363,7 +363,7 @@ "description": "Type: `string`, default: ``. Extra arguments to pass to salmon quant command in addition to defaults defined by the pipeline", "help_text": "Type: `string`, default: ``. Extra arguments to pass to salmon quant command in addition to defaults defined by the pipeline." , - "default": "" + "default":"" } @@ -384,7 +384,7 @@ "description": "Type: `boolean_true`, default: `false`. Skip BBSplit for removal of non-reference genome reads", "help_text": "Type: `boolean_true`, default: `false`. Skip BBSplit for removal of non-reference genome reads." , - "default": "False" + "default":false } @@ -395,7 +395,7 @@ "description": "Type: `boolean_true`, default: `false`. Enable the removal of reads derived from ribosomal RNA using SortMeRNA", "help_text": "Type: `boolean_true`, default: `false`. Enable the removal of reads derived from ribosomal RNA using SortMeRNA." , - "default": "False" + "default":false } @@ -416,7 +416,7 @@ "description": "Type: `string`, default: `--record-count 1000000 --seed 1`. Extra arguments to pass to fq subsample command in addition to defaults defined by the pipeline", "help_text": "Type: `string`, default: `--record-count 1000000 --seed 1`. Extra arguments to pass to fq subsample command in addition to defaults defined by the pipeline." , - "default": "--record-count 1000000 --seed 1" + "default":"--record-count 1000000 --seed 1" } @@ -437,7 +437,7 @@ "description": "Type: `file`, default: `$id.$key.qc_output1.fastq`. Path to output directory", "help_text": "Type: `file`, default: `$id.$key.qc_output1.fastq`. Path to output directory" , - "default": "$id.$key.qc_output1.fastq" + "default":"$id.$key.qc_output1.fastq" } @@ -448,7 +448,7 @@ "description": "Type: `file`, default: `$id.$key.qc_output2.fastq`. Path to output directory", "help_text": "Type: `file`, default: `$id.$key.qc_output2.fastq`. Path to output directory" , - "default": "$id.$key.qc_output2.fastq" + "default":"$id.$key.qc_output2.fastq" } @@ -459,7 +459,7 @@ "description": "Type: `file`, default: `$id.$key.fastqc_html_1.html`. FastQC HTML report for read 1", "help_text": "Type: `file`, default: `$id.$key.fastqc_html_1.html`. FastQC HTML report for read 1." , - "default": "$id.$key.fastqc_html_1.html" + "default":"$id.$key.fastqc_html_1.html" } @@ -470,7 +470,7 @@ "description": "Type: `file`, default: `$id.$key.fastqc_html_2.html`. FastQC HTML report for read 2", "help_text": "Type: `file`, default: `$id.$key.fastqc_html_2.html`. FastQC HTML report for read 2." , - "default": "$id.$key.fastqc_html_2.html" + "default":"$id.$key.fastqc_html_2.html" } @@ -481,7 +481,7 @@ "description": "Type: `file`, default: `$id.$key.fastqc_zip_1.zip`. FastQC report archive for read 1", "help_text": "Type: `file`, default: `$id.$key.fastqc_zip_1.zip`. FastQC report archive for read 1." , - "default": "$id.$key.fastqc_zip_1.zip" + "default":"$id.$key.fastqc_zip_1.zip" } @@ -492,7 +492,7 @@ "description": "Type: `file`, default: `$id.$key.fastqc_zip_2.zip`. FastQC report archive for read 2", "help_text": "Type: `file`, default: `$id.$key.fastqc_zip_2.zip`. FastQC report archive for read 2." , - "default": "$id.$key.fastqc_zip_2.zip" + "default":"$id.$key.fastqc_zip_2.zip" } @@ -503,7 +503,7 @@ "description": "Type: `file`, default: `$id.$key.trim_log_1.txt`. ", "help_text": "Type: `file`, default: `$id.$key.trim_log_1.txt`. " , - "default": "$id.$key.trim_log_1.txt" + "default":"$id.$key.trim_log_1.txt" } @@ -514,7 +514,7 @@ "description": "Type: `file`, default: `$id.$key.trim_log_2.txt`. ", "help_text": "Type: `file`, default: `$id.$key.trim_log_2.txt`. " , - "default": "$id.$key.trim_log_2.txt" + "default":"$id.$key.trim_log_2.txt" } @@ -525,7 +525,7 @@ "description": "Type: `file`, default: `$id.$key.trim_html_1.html`. ", "help_text": "Type: `file`, default: `$id.$key.trim_html_1.html`. " , - "default": "$id.$key.trim_html_1.html" + "default":"$id.$key.trim_html_1.html" } @@ -536,7 +536,7 @@ "description": "Type: `file`, default: `$id.$key.trim_html_2.html`. ", "help_text": "Type: `file`, default: `$id.$key.trim_html_2.html`. " , - "default": "$id.$key.trim_html_2.html" + "default":"$id.$key.trim_html_2.html" } @@ -547,7 +547,7 @@ "description": "Type: `file`, default: `$id.$key.trim_zip_1.zip`. ", "help_text": "Type: `file`, default: `$id.$key.trim_zip_1.zip`. " , - "default": "$id.$key.trim_zip_1.zip" + "default":"$id.$key.trim_zip_1.zip" } @@ -558,7 +558,7 @@ "description": "Type: `file`, default: `$id.$key.trim_zip_2.zip`. ", "help_text": "Type: `file`, default: `$id.$key.trim_zip_2.zip`. " , - "default": "$id.$key.trim_zip_2.zip" + "default":"$id.$key.trim_zip_2.zip" } @@ -569,7 +569,7 @@ "description": "Type: `file`, default: `$id.$key.sortmerna_log.log`. Sortmerna log file", "help_text": "Type: `file`, default: `$id.$key.sortmerna_log.log`. Sortmerna log file." , - "default": "$id.$key.sortmerna_log.log" + "default":"$id.$key.sortmerna_log.log" } @@ -580,7 +580,7 @@ "description": "Type: `file`, default: `$id.$key.salmon_quant_output.salmon_quant_output`. Results from Salmon quant", "help_text": "Type: `file`, default: `$id.$key.salmon_quant_output.salmon_quant_output`. Results from Salmon quant" , - "default": "$id.$key.salmon_quant_output.salmon_quant_output" + "default":"$id.$key.salmon_quant_output.salmon_quant_output" } @@ -591,7 +591,7 @@ "description": "Type: `file`, default: `$id.$key.trim_json.json`. The fastp json format report file name", "help_text": "Type: `file`, default: `$id.$key.trim_json.json`. The fastp json format report file name" , - "default": "$id.$key.trim_json.json" + "default":"$id.$key.trim_json.json" } @@ -602,7 +602,7 @@ "description": "Type: `file`, default: `$id.$key.trim_html.html`. The fastp html format report file name", "help_text": "Type: `file`, default: `$id.$key.trim_html.html`. The fastp html format report file name" , - "default": "$id.$key.trim_html.html" + "default":"$id.$key.trim_html.html" } @@ -613,7 +613,7 @@ "description": "Type: `file`, default: `$id.$key.merged_out.merged_out`. File name to store merged fastp output", "help_text": "Type: `file`, default: `$id.$key.merged_out.merged_out`. File name to store merged fastp output." , - "default": "$id.$key.merged_out.merged_out" + "default":"$id.$key.merged_out.merged_out" } diff --git a/target/nextflow/workflows/prepare_genome/.config.vsh.yaml b/target/nextflow/workflows/prepare_genome/.config.vsh.yaml index d62c45e..2a88c06 100644 --- a/target/nextflow/workflows/prepare_genome/.config.vsh.yaml +++ b/target/nextflow/workflows/prepare_genome/.config.vsh.yaml @@ -509,8 +509,8 @@ build_info: output: "target/nextflow/workflows/prepare_genome" executable: "target/nextflow/workflows/prepare_genome/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/gunzip" - "target/dependencies/vsh/vsh/biobox/main/nextflow/gffread" diff --git a/target/nextflow/workflows/prepare_genome/main.nf b/target/nextflow/workflows/prepare_genome/main.nf index ef3ac7b..91bc9d0 100644 --- a/target/nextflow/workflows/prepare_genome/main.nf +++ b/target/nextflow/workflows/prepare_genome/main.nf @@ -3425,8 +3425,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/prepare_genome", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/workflows/prepare_genome/nextflow_schema.json b/target/nextflow/workflows/prepare_genome/nextflow_schema.json index e56ab59..dc9984f 100644 --- a/target/nextflow/workflows/prepare_genome/nextflow_schema.json +++ b/target/nextflow/workflows/prepare_genome/nextflow_schema.json @@ -170,7 +170,7 @@ "description": "Type: `integer`, default: `31`. Kmer length passed to indexing step of pseudoaligners", "help_text": "Type: `integer`, default: `31`. Kmer length passed to indexing step of pseudoaligners." , - "default": "31" + "default":31 } @@ -213,7 +213,7 @@ "enum": ["star_salmon", "star_rsem", "hisat2"] , - "default": "star_salmon" + "default":"star_salmon" } @@ -226,7 +226,7 @@ "enum": ["salmon", "kallisto"] , - "default": "salmon" + "default":"salmon" } @@ -237,7 +237,7 @@ "description": "Type: `boolean_true`, default: `false`. Skip all of the alignment-based processes within the pipeline", "help_text": "Type: `boolean_true`, default: `false`. Skip all of the alignment-based processes within the pipeline." , - "default": "False" + "default":false } @@ -258,7 +258,7 @@ "description": "Type: `file`, default: `$id.$key.fasta_uncompressed.fasta`. ", "help_text": "Type: `file`, default: `$id.$key.fasta_uncompressed.fasta`. " , - "default": "$id.$key.fasta_uncompressed.fasta" + "default":"$id.$key.fasta_uncompressed.fasta" } @@ -269,7 +269,7 @@ "description": "Type: `file`, default: `$id.$key.gtf_uncompressed.gtf`. ", "help_text": "Type: `file`, default: `$id.$key.gtf_uncompressed.gtf`. " , - "default": "$id.$key.gtf_uncompressed.gtf" + "default":"$id.$key.gtf_uncompressed.gtf" } @@ -280,7 +280,7 @@ "description": "Type: `file`, default: `$id.$key.transcript_fasta_uncompressed.fasta`. ", "help_text": "Type: `file`, default: `$id.$key.transcript_fasta_uncompressed.fasta`. " , - "default": "$id.$key.transcript_fasta_uncompressed.fasta" + "default":"$id.$key.transcript_fasta_uncompressed.fasta" } @@ -291,7 +291,7 @@ "description": "Type: `file`, default: `$id.$key.gene_bed_uncompressed.bed`. ", "help_text": "Type: `file`, default: `$id.$key.gene_bed_uncompressed.bed`. " , - "default": "$id.$key.gene_bed_uncompressed.bed" + "default":"$id.$key.gene_bed_uncompressed.bed" } @@ -302,7 +302,7 @@ "description": "Type: `file`, default: `$id.$key.star_index_uncompressed.star_index_uncompressed`. Path to STAR index", "help_text": "Type: `file`, default: `$id.$key.star_index_uncompressed.star_index_uncompressed`. Path to STAR index." , - "default": "$id.$key.star_index_uncompressed.star_index_uncompressed" + "default":"$id.$key.star_index_uncompressed.star_index_uncompressed" } @@ -313,7 +313,7 @@ "description": "Type: `file`, default: `$id.$key.rsem_index_uncompressed.rsem_index_uncompressed`. Path to directory or tar", "help_text": "Type: `file`, default: `$id.$key.rsem_index_uncompressed.rsem_index_uncompressed`. Path to directory or tar.gz archive for pre-built RSEM index." , - "default": "$id.$key.rsem_index_uncompressed.rsem_index_uncompressed" + "default":"$id.$key.rsem_index_uncompressed.rsem_index_uncompressed" } @@ -324,7 +324,7 @@ "description": "Type: `file`, default: `$id.$key.salmon_index_uncompressed.salmon_index_uncompressed`. Path to Salmon index", "help_text": "Type: `file`, default: `$id.$key.salmon_index_uncompressed.salmon_index_uncompressed`. Path to Salmon index." , - "default": "$id.$key.salmon_index_uncompressed.salmon_index_uncompressed" + "default":"$id.$key.salmon_index_uncompressed.salmon_index_uncompressed" } @@ -335,7 +335,7 @@ "description": "Type: `file`, default: `$id.$key.kallisto_index_uncompressed.kallisto_index_uncompressed`. Path to Kallisto index", "help_text": "Type: `file`, default: `$id.$key.kallisto_index_uncompressed.kallisto_index_uncompressed`. Path to Kallisto index." , - "default": "$id.$key.kallisto_index_uncompressed.kallisto_index_uncompressed" + "default":"$id.$key.kallisto_index_uncompressed.kallisto_index_uncompressed" } @@ -346,7 +346,7 @@ "description": "Type: `file`, default: `$id.$key.bbsplit_index_uncompressed.bbsplit_index_uncompressed`. Path to BBSplit index", "help_text": "Type: `file`, default: `$id.$key.bbsplit_index_uncompressed.bbsplit_index_uncompressed`. Path to BBSplit index." , - "default": "$id.$key.bbsplit_index_uncompressed.bbsplit_index_uncompressed" + "default":"$id.$key.bbsplit_index_uncompressed.bbsplit_index_uncompressed" } @@ -357,7 +357,7 @@ "description": "Type: `file`, default: `$id.$key.chrom_sizes.sizes`. File containing chromosome lengths", "help_text": "Type: `file`, default: `$id.$key.chrom_sizes.sizes`. File containing chromosome lengths" , - "default": "$id.$key.chrom_sizes.sizes" + "default":"$id.$key.chrom_sizes.sizes" } @@ -368,7 +368,7 @@ "description": "Type: `file`, default: `$id.$key.fai.fai`. FASTA index file", "help_text": "Type: `file`, default: `$id.$key.fai.fai`. FASTA index file" , - "default": "$id.$key.fai.fai" + "default":"$id.$key.fai.fai" } diff --git a/target/nextflow/workflows/pseudo_alignment_and_quant/.config.vsh.yaml b/target/nextflow/workflows/pseudo_alignment_and_quant/.config.vsh.yaml index d980c80..42b9501 100644 --- a/target/nextflow/workflows/pseudo_alignment_and_quant/.config.vsh.yaml +++ b/target/nextflow/workflows/pseudo_alignment_and_quant/.config.vsh.yaml @@ -291,8 +291,8 @@ build_info: output: "target/nextflow/workflows/pseudo_alignment_and_quant" executable: "target/nextflow/workflows/pseudo_alignment_and_quant/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant" - "target/nextflow/kallisto/kallisto_quant" diff --git a/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf b/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf index 73f6398..1dfb03a 100644 --- a/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf +++ b/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf @@ -3155,8 +3155,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/pseudo_alignment_and_quant", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", @@ -3204,6 +3204,7 @@ include { kallisto_quant } from "${meta.resources_dir}/../../../nextflow/kallist // inner workflow // user-provided Nextflow code +// TODO: See if the logic of this can be aligned with the STAR aligner logic workflow run_wf { take: input_ch diff --git a/target/nextflow/workflows/pseudo_alignment_and_quant/nextflow_schema.json b/target/nextflow/workflows/pseudo_alignment_and_quant/nextflow_schema.json index bbfd08f..d476fd9 100644 --- a/target/nextflow/workflows/pseudo_alignment_and_quant/nextflow_schema.json +++ b/target/nextflow/workflows/pseudo_alignment_and_quant/nextflow_schema.json @@ -84,7 +84,7 @@ "enum": ["salmon", "kallisto"] , - "default": "false" + "default":"false" } @@ -115,7 +115,7 @@ "description": "Type: `string`, default: ``. Override library type inferred based on strandedness defined in meta object", "help_text": "Type: `string`, default: ``. Override library type inferred based on strandedness defined in meta object" , - "default": "" + "default":"" } @@ -156,7 +156,7 @@ "description": "Type: `file`, default: `$id.$key.pseudo_multiqc.pseudo_multiqc`. ", "help_text": "Type: `file`, default: `$id.$key.pseudo_multiqc.pseudo_multiqc`. " , - "default": "$id.$key.pseudo_multiqc.pseudo_multiqc" + "default":"$id.$key.pseudo_multiqc.pseudo_multiqc" } @@ -167,7 +167,7 @@ "description": "Type: `file`, default: `$id.$key.quant_out_dir.quant`. ", "help_text": "Type: `file`, default: `$id.$key.quant_out_dir.quant`. " , - "default": "$id.$key.quant_out_dir.quant" + "default":"$id.$key.quant_out_dir.quant" } @@ -178,7 +178,7 @@ "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" + "default":"$id.$key.salmon_quant_results_file.sf" } @@ -189,7 +189,7 @@ "description": "Type: `file`, default: `$id.$key.kallisto_quant_results_file.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.kallisto_quant_results_file.tsv`. " , - "default": "$id.$key.kallisto_quant_results_file.tsv" + "default":"$id.$key.kallisto_quant_results_file.tsv" } diff --git a/target/nextflow/workflows/quality_control/.config.vsh.yaml b/target/nextflow/workflows/quality_control/.config.vsh.yaml index 3f55000..6870f06 100644 --- a/target/nextflow/workflows/quality_control/.config.vsh.yaml +++ b/target/nextflow/workflows/quality_control/.config.vsh.yaml @@ -1580,8 +1580,8 @@ build_info: output: "target/nextflow/workflows/quality_control" executable: "target/nextflow/workflows/quality_control/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@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 4d6dbed..5b29e71 100644 --- a/target/nextflow/workflows/quality_control/main.nf +++ b/target/nextflow/workflows/quality_control/main.nf @@ -4660,8 +4660,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/quality_control", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", @@ -4967,6 +4967,7 @@ workflow run_wf { def skip_qc = list.collect { id, state -> state.skip_qc }.unique()[0] def skip_align = list.collect { id, state -> state.skip_align }.unique()[0] def skip_pseudo_align = list.collect { id, state -> state.skip_pseudo_align }.unique()[0] + // TODO: Are these checks necessary? def quant_results = list.collect { id, state -> (state.quant_results_file instanceof java.nio.file.Path && state.quant_results_file.exists()) ? state.quant_results_file : @@ -5265,6 +5266,7 @@ workflow run_wf { ) | niceView() // Get list of samples that failed trimming, mapping, and strand check for MultiQC report + // TODO: Refactor this to a process/step | map { id, state -> def fail_trimming_header = ["Sample", "Reads after trimming"] def fail_trimming_multiqc = "" @@ -5393,6 +5395,7 @@ workflow run_wf { | map { list -> [list[0], list[1] + list[2]] } | map { id, state -> + // TODO: Check this, necessary for setState def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() } [ id, mod_state ] } diff --git a/target/nextflow/workflows/quality_control/nextflow_schema.json b/target/nextflow/workflows/quality_control/nextflow_schema.json index 92ad21f..3c7ab42 100644 --- a/target/nextflow/workflows/quality_control/nextflow_schema.json +++ b/target/nextflow/workflows/quality_control/nextflow_schema.json @@ -30,7 +30,7 @@ "description": "Type: `string`, default: `unstranded`. Sample strand-specificity", "help_text": "Type: `string`, default: `unstranded`. Sample strand-specificity. Must be one of unstranded, forward, reverse" , - "default": "unstranded" + "default":"unstranded" } @@ -91,7 +91,7 @@ "description": "Type: `string`, default: `gene_id`. Define the attribute type used to group features in the GTF file when running Salmon", "help_text": "Type: `string`, default: `gene_id`. Define the attribute type used to group features in the GTF file when running Salmon." , - "default": "gene_id" + "default":"gene_id" } @@ -102,7 +102,7 @@ "description": "Type: `string`, default: `gene_name`. By default, the pipeline uses the gene_name field to obtain additional gene identifiers from the input GTF file when running Salmon", "help_text": "Type: `string`, default: `gene_name`. By default, the pipeline uses the gene_name field to obtain additional gene identifiers from the input GTF file when running Salmon." , - "default": "gene_name" + "default":"gene_name" } @@ -203,7 +203,7 @@ "description": "Type: `boolean`, default: `false`. ", "help_text": "Type: `boolean`, default: `false`. " , - "default": "False" + "default":false } @@ -224,7 +224,7 @@ "description": "Type: `boolean`, default: `false`. ", "help_text": "Type: `boolean`, default: `false`. " , - "default": "False" + "default":false } @@ -245,7 +245,7 @@ "description": "Type: `boolean_true`, default: `false`. ", "help_text": "Type: `boolean_true`, default: `false`. " , - "default": "False" + "default":false } @@ -256,7 +256,7 @@ "description": "Type: `boolean_true`, default: `false`. ", "help_text": "Type: `boolean_true`, default: `false`. " , - "default": "False" + "default":false } @@ -267,7 +267,7 @@ "description": "Type: `boolean_true`, default: `false`. ", "help_text": "Type: `boolean_true`, default: `false`. " , - "default": "False" + "default":false } @@ -278,7 +278,7 @@ "description": "Type: `boolean_true`, default: `false`. ", "help_text": "Type: `boolean_true`, default: `false`. " , - "default": "False" + "default":false } @@ -289,7 +289,7 @@ "description": "Type: `boolean`, default: `false`. ", "help_text": "Type: `boolean`, default: `false`. " , - "default": "False" + "default":false } @@ -300,7 +300,7 @@ "description": "Type: `string`, default: `-verbose -bam -seed 1`. ", "help_text": "Type: `string`, default: `-verbose -bam -seed 1`. " , - "default": "-verbose -bam -seed 1" + "default":"-verbose -bam -seed 1" } @@ -311,7 +311,7 @@ "description": "Type: `string`, default: `gene_biotype`. The attribute type used to group feature types in the GTF file when generating the biotype plot with featureCounts", "help_text": "Type: `string`, default: `gene_biotype`. The attribute type used to group feature types in the GTF file when generating the biotype plot with featureCounts." , - "default": "gene_biotype" + "default":"gene_biotype" } @@ -322,7 +322,7 @@ "description": "Type: `string`, default: `exon`. By default, the pipeline assigns reads based on the \u0027exon\u0027 attribute within the GTF file", "help_text": "Type: `string`, default: `exon`. By default, the pipeline assigns reads based on the \u0027exon\u0027 attribute within the GTF file." , - "default": "exon" + "default":"exon" } @@ -343,7 +343,7 @@ "description": "Type: `file`, default: `src/assets/multiqc/biotypes_header.txt`. ", "help_text": "Type: `file`, default: `src/assets/multiqc/biotypes_header.txt`. " , - "default": "src/assets/multiqc/biotypes_header.txt" + "default":"src/assets/multiqc/biotypes_header.txt" } @@ -372,11 +372,9 @@ "type": "string", "description": "Type: List of `string`, default: `bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication`, multiple_sep: `\",\"`, choices: ``bam_stat`, `inner_distance`, `infer_experiment`, `junction_annotation`, `junction_saturation`, `read_distribution`, `read_duplication`, `tin``. Specify the RSeQC modules to run_wf", - "help_text": "Type: List of `string`, default: `bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication`, multiple_sep: `\",\"`, choices: ``bam_stat`, `inner_distance`, `infer_experiment`, `junction_annotation`, `junction_saturation`, `read_distribution`, `read_duplication`, `tin``. Specify the RSeQC modules to run_wf", - "enum": ["bam_stat", "inner_distance", "infer_experiment", "junction_annotation", "junction_saturation", "read_distribution", "read_duplication", "tin"] - + "help_text": "Type: List of `string`, default: `bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication`, multiple_sep: `\",\"`, choices: ``bam_stat`, `inner_distance`, `infer_experiment`, `junction_annotation`, `junction_saturation`, `read_distribution`, `read_duplication`, `tin``. Specify the RSeQC modules to run_wf" , - "default": "bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication" + "default":"bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication" } @@ -387,7 +385,7 @@ "description": "Type: `integer`, default: `200000`. Numer of reads sampled from SAM/BAM file to infer experiment and calculate inner distance, default = 200000", "help_text": "Type: `integer`, default: `200000`. Numer of reads sampled from SAM/BAM file to infer experiment and calculate inner distance, default = 200000." , - "default": "200000" + "default":200000 } @@ -398,7 +396,7 @@ "description": "Type: `integer`, default: `-250`. Lower bound of inner distance (bp)", "help_text": "Type: `integer`, default: `-250`. Lower bound of inner distance (bp). This option is used for ploting histograme, default = -250." , - "default": "-250" + "default":-250 } @@ -409,7 +407,7 @@ "description": "Type: `integer`, default: `250`. Upper bound of inner distance (bp)", "help_text": "Type: `integer`, default: `250`. Upper bound of inner distance (bp). This option is used for ploting histograme, default = 250." , - "default": "250" + "default":250 } @@ -420,7 +418,7 @@ "description": "Type: `integer`, default: `5`. Step size (bp) of histograme of inner distance", "help_text": "Type: `integer`, default: `5`. Step size (bp) of histograme of inner distance. This option is used for plotting histogram, default = 5." , - "default": "5" + "default":5 } @@ -431,7 +429,7 @@ "description": "Type: `integer`, default: `30`. Minimum mapping quality (phred scaled) to determine uniquely mapped reads, default = 30", "help_text": "Type: `integer`, default: `30`. Minimum mapping quality (phred scaled) to determine uniquely mapped reads, default = 30." , - "default": "30" + "default":30 } @@ -442,7 +440,7 @@ "description": "Type: `integer`, default: `50`. Minimum intron length (bp) to call a junction, default = 50", "help_text": "Type: `integer`, default: `50`. Minimum intron length (bp) to call a junction, default = 50." , - "default": "50" + "default":50 } @@ -453,7 +451,7 @@ "description": "Type: `integer`, default: `1`. Minimum number of supporting reads to call a junction, default = 1", "help_text": "Type: `integer`, default: `1`. Minimum number of supporting reads to call a junction, default = 1." , - "default": "1" + "default":1 } @@ -464,7 +462,7 @@ "description": "Type: `integer`, default: `5`. Read sampling for junction saturation starts from this percentile, must be an integer between 0 and 100, default = 5", "help_text": "Type: `integer`, default: `5`. Read sampling for junction saturation starts from this percentile, must be an integer between 0 and 100, default = 5." , - "default": "5" + "default":5 } @@ -475,7 +473,7 @@ "description": "Type: `integer`, default: `100`. Read sampling for junction saturation ends at this percentile, must be an integer between 0 and 100, default = 5", "help_text": "Type: `integer`, default: `100`. Read sampling for junction saturation ends at this percentile, must be an integer between 0 and 100, default = 5." , - "default": "100" + "default":100 } @@ -486,7 +484,7 @@ "description": "Type: `integer`, default: `5`. Read sampling for junction saturation frequency in %", "help_text": "Type: `integer`, default: `5`. Read sampling for junction saturation frequency in %. Smaller value means more sampling times. Must be an integer between 0 and 100, default = 5." , - "default": "5" + "default":5 } @@ -497,7 +495,7 @@ "description": "Type: `integer`, default: `500`. Upper limit of reads\u0027 occurence to determine read duplication", "help_text": "Type: `integer`, default: `500`. Upper limit of reads\u0027 occurence to determine read duplication. Only used for plotting, default = 500 (times)." , - "default": "500" + "default":500 } @@ -508,7 +506,7 @@ "description": "Type: `integer`, default: `10`. Minimum number of reads mapped to a transcript to determin tin, default = 10", "help_text": "Type: `integer`, default: `10`. Minimum number of reads mapped to a transcript to determin tin, default = 10." , - "default": "10" + "default":10 } @@ -519,7 +517,7 @@ "description": "Type: `integer`, default: `100`. Number of equal-spaced nucleotide positions picked from mRNA", "help_text": "Type: `integer`, default: `100`. Number of equal-spaced nucleotide positions picked from mRNA. Note, if this number is larger than the length of mRNA (L), it will be halved until it\u0027s smaller than L (default = 100)" , - "default": "100" + "default":100 } @@ -530,7 +528,7 @@ "description": "Type: `boolean_true`, default: `false`. Set flag to subtract background noise (estimated from intronic reads) to determine tin", "help_text": "Type: `boolean_true`, default: `false`. Set flag to subtract background noise (estimated from intronic reads) to determine tin. Only use this option if there are substantial intronic reads." , - "default": "False" + "default":false } @@ -543,7 +541,7 @@ "enum": ["html", "pdf"] , - "default": "html" + "default":"html" } @@ -554,7 +552,7 @@ "description": "Type: `integer`, default: `100`. Number of upstream/downstream nucleotide bases to compute 5\u0027-3\u0027 bias for qualimap (default = 100)", "help_text": "Type: `integer`, default: `100`. Number of upstream/downstream nucleotide bases to compute 5\u0027-3\u0027 bias for qualimap (default = 100)." , - "default": "100" + "default":100 } @@ -565,7 +563,7 @@ "description": "Type: `integer`, default: `1000`. Number of top highly expressed transcripts to compute 5\u0027-3\u0027 bias for qualimap (default = 1000)", "help_text": "Type: `integer`, default: `1000`. Number of top highly expressed transcripts to compute 5\u0027-3\u0027 bias for qualimap (default = 1000)." , - "default": "1000" + "default":1000 } @@ -576,7 +574,7 @@ "description": "Type: `string`, default: `uniquely-mapped-reads`. Counting algorithm for qualimap (uniquely-mapped-reads (default) or proportional)", "help_text": "Type: `string`, default: `uniquely-mapped-reads`. Counting algorithm for qualimap (uniquely-mapped-reads (default) or proportional)." , - "default": "uniquely-mapped-reads" + "default":"uniquely-mapped-reads" } @@ -589,7 +587,7 @@ "enum": ["non-strand-specific", "strand-specific-reverse", "strand-specific-forward"] , - "default": "non-strand-specific" + "default":"non-strand-specific" } @@ -600,7 +598,7 @@ "description": "Type: `boolean_true`, default: `false`. Setting this flag indicates that the input file is already sorted by name", "help_text": "Type: `boolean_true`, default: `false`. Setting this flag indicates that the input file is already sorted by name. If flag is not set, additional sorting by name will be performed for qualimap. Only requiredfor paired-end analysis." , - "default": "False" + "default":false } @@ -611,7 +609,7 @@ "description": "Type: `string`, default: `4G`. maximum Java heap memory size for qualimap, default = 4G", "help_text": "Type: `string`, default: `4G`. maximum Java heap memory size for qualimap, default = 4G." , - "default": "4G" + "default":"4G" } @@ -862,7 +860,7 @@ "description": "Type: `file`, default: `$id.$key.preseq_output.txt`. ", "help_text": "Type: `file`, default: `$id.$key.preseq_output.txt`. " , - "default": "$id.$key.preseq_output.txt" + "default":"$id.$key.preseq_output.txt" } @@ -873,7 +871,7 @@ "description": "Type: `file`, default: `$id.$key.bamstat_output.txt`. Path to output file (txt) of mapping quality statistics", "help_text": "Type: `file`, default: `$id.$key.bamstat_output.txt`. Path to output file (txt) of mapping quality statistics" , - "default": "$id.$key.bamstat_output.txt" + "default":"$id.$key.bamstat_output.txt" } @@ -884,7 +882,7 @@ "description": "Type: `file`, default: `$id.$key.strandedness_output.txt`. Path to output report (txt) of inferred strandedness", "help_text": "Type: `file`, default: `$id.$key.strandedness_output.txt`. Path to output report (txt) of inferred strandedness" , - "default": "$id.$key.strandedness_output.txt" + "default":"$id.$key.strandedness_output.txt" } @@ -895,7 +893,7 @@ "description": "Type: `file`, default: `$id.$key.inner_dist_output_stats.stats`. output file (txt) with summary statistics of inner distances of paired reads", "help_text": "Type: `file`, default: `$id.$key.inner_dist_output_stats.stats`. output file (txt) with summary statistics of inner distances of paired reads" , - "default": "$id.$key.inner_dist_output_stats.stats" + "default":"$id.$key.inner_dist_output_stats.stats" } @@ -906,7 +904,7 @@ "description": "Type: `file`, default: `$id.$key.inner_dist_output_dist.txt`. output file (txt) with inner distances of all paired reads", "help_text": "Type: `file`, default: `$id.$key.inner_dist_output_dist.txt`. output file (txt) with inner distances of all paired reads" , - "default": "$id.$key.inner_dist_output_dist.txt" + "default":"$id.$key.inner_dist_output_dist.txt" } @@ -917,7 +915,7 @@ "description": "Type: `file`, default: `$id.$key.inner_dist_output_freq.txt`. output file (txt) with frequencies of inner distances of all paired reads", "help_text": "Type: `file`, default: `$id.$key.inner_dist_output_freq.txt`. output file (txt) with frequencies of inner distances of all paired reads" , - "default": "$id.$key.inner_dist_output_freq.txt" + "default":"$id.$key.inner_dist_output_freq.txt" } @@ -928,7 +926,7 @@ "description": "Type: `file`, default: `$id.$key.inner_dist_output_plot.pdf`. output file (pdf) with histogram plot of of inner distances of all paired reads", "help_text": "Type: `file`, default: `$id.$key.inner_dist_output_plot.pdf`. output file (pdf) with histogram plot of of inner distances of all paired reads" , - "default": "$id.$key.inner_dist_output_plot.pdf" + "default":"$id.$key.inner_dist_output_plot.pdf" } @@ -939,7 +937,7 @@ "description": "Type: `file`, default: `$id.$key.inner_dist_output_plot_r.r`. output file (R) with script of histogram plot of of inner distances of all paired reads", "help_text": "Type: `file`, default: `$id.$key.inner_dist_output_plot_r.r`. output file (R) with script of histogram plot of of inner distances of all paired reads" , - "default": "$id.$key.inner_dist_output_plot_r.r" + "default":"$id.$key.inner_dist_output_plot_r.r" } @@ -950,7 +948,7 @@ "description": "Type: `file`, default: `$id.$key.junction_annotation_output_log.log`. output log of junction annotation script", "help_text": "Type: `file`, default: `$id.$key.junction_annotation_output_log.log`. output log of junction annotation script" , - "default": "$id.$key.junction_annotation_output_log.log" + "default":"$id.$key.junction_annotation_output_log.log" } @@ -961,7 +959,7 @@ "description": "Type: `file`, default: `$id.$key.junction_annotation_output_plot_r.r`. R script to generate splice_junction and splice_events plot", "help_text": "Type: `file`, default: `$id.$key.junction_annotation_output_plot_r.r`. R script to generate splice_junction and splice_events plot" , - "default": "$id.$key.junction_annotation_output_plot_r.r" + "default":"$id.$key.junction_annotation_output_plot_r.r" } @@ -972,7 +970,7 @@ "description": "Type: `file`, default: `$id.$key.junction_annotation_output_junction_bed.bed`. junction annotation file (bed format)", "help_text": "Type: `file`, default: `$id.$key.junction_annotation_output_junction_bed.bed`. junction annotation file (bed format)" , - "default": "$id.$key.junction_annotation_output_junction_bed.bed" + "default":"$id.$key.junction_annotation_output_junction_bed.bed" } @@ -983,7 +981,7 @@ "description": "Type: `file`, default: `$id.$key.junction_annotation_output_junction_interact.bed`. interact file (bed format) of junctions", "help_text": "Type: `file`, default: `$id.$key.junction_annotation_output_junction_interact.bed`. interact file (bed format) of junctions. Can be uploaded to UCSC genome browser or converted to bigInteract (using bedToBigBed program) for visualization." , - "default": "$id.$key.junction_annotation_output_junction_interact.bed" + "default":"$id.$key.junction_annotation_output_junction_interact.bed" } @@ -994,7 +992,7 @@ "description": "Type: `file`, default: `$id.$key.junction_annotation_output_junction_sheet.xls`. junction annotation file (xls format)", "help_text": "Type: `file`, default: `$id.$key.junction_annotation_output_junction_sheet.xls`. junction annotation file (xls format)" , - "default": "$id.$key.junction_annotation_output_junction_sheet.xls" + "default":"$id.$key.junction_annotation_output_junction_sheet.xls" } @@ -1005,7 +1003,7 @@ "description": "Type: `file`, default: `$id.$key.junction_annotation_output_splice_events_plot.pdf`. plot of splice events (pdf)", "help_text": "Type: `file`, default: `$id.$key.junction_annotation_output_splice_events_plot.pdf`. plot of splice events (pdf)" , - "default": "$id.$key.junction_annotation_output_splice_events_plot.pdf" + "default":"$id.$key.junction_annotation_output_splice_events_plot.pdf" } @@ -1016,7 +1014,7 @@ "description": "Type: `file`, default: `$id.$key.junction_annotation_output_splice_junctions_plot.pdf`. plot of junctions (pdf)", "help_text": "Type: `file`, default: `$id.$key.junction_annotation_output_splice_junctions_plot.pdf`. plot of junctions (pdf)" , - "default": "$id.$key.junction_annotation_output_splice_junctions_plot.pdf" + "default":"$id.$key.junction_annotation_output_splice_junctions_plot.pdf" } @@ -1027,7 +1025,7 @@ "description": "Type: `file`, default: `$id.$key.junction_saturation_output_plot_r.r`. r script to generate junction_saturation_plot plot", "help_text": "Type: `file`, default: `$id.$key.junction_saturation_output_plot_r.r`. r script to generate junction_saturation_plot plot" , - "default": "$id.$key.junction_saturation_output_plot_r.r" + "default":"$id.$key.junction_saturation_output_plot_r.r" } @@ -1038,7 +1036,7 @@ "description": "Type: `file`, default: `$id.$key.junction_saturation_output_plot.pdf`. plot of junction saturation (pdf", "help_text": "Type: `file`, default: `$id.$key.junction_saturation_output_plot.pdf`. plot of junction saturation (pdf" , - "default": "$id.$key.junction_saturation_output_plot.pdf" + "default":"$id.$key.junction_saturation_output_plot.pdf" } @@ -1049,7 +1047,7 @@ "description": "Type: `file`, default: `$id.$key.read_distribution_output.txt`. output file (txt) of read distribution analysis", "help_text": "Type: `file`, default: `$id.$key.read_distribution_output.txt`. output file (txt) of read distribution analysis." , - "default": "$id.$key.read_distribution_output.txt" + "default":"$id.$key.read_distribution_output.txt" } @@ -1060,7 +1058,7 @@ "description": "Type: `file`, default: `$id.$key.read_duplication_output_duplication_rate_plot_r.r`. R script for generating duplication rate plot", "help_text": "Type: `file`, default: `$id.$key.read_duplication_output_duplication_rate_plot_r.r`. R script for generating duplication rate plot" , - "default": "$id.$key.read_duplication_output_duplication_rate_plot_r.r" + "default":"$id.$key.read_duplication_output_duplication_rate_plot_r.r" } @@ -1071,7 +1069,7 @@ "description": "Type: `file`, default: `$id.$key.read_duplication_output_duplication_rate_plot.pdf`. duplication rate plot (pdf)", "help_text": "Type: `file`, default: `$id.$key.read_duplication_output_duplication_rate_plot.pdf`. duplication rate plot (pdf)" , - "default": "$id.$key.read_duplication_output_duplication_rate_plot.pdf" + "default":"$id.$key.read_duplication_output_duplication_rate_plot.pdf" } @@ -1082,7 +1080,7 @@ "description": "Type: `file`, default: `$id.$key.read_duplication_output_duplication_rate_mapping.xls`. Summary of mapping-based read duplication", "help_text": "Type: `file`, default: `$id.$key.read_duplication_output_duplication_rate_mapping.xls`. Summary of mapping-based read duplication" , - "default": "$id.$key.read_duplication_output_duplication_rate_mapping.xls" + "default":"$id.$key.read_duplication_output_duplication_rate_mapping.xls" } @@ -1093,7 +1091,7 @@ "description": "Type: `file`, default: `$id.$key.read_duplication_output_duplication_rate_sequence.xls`. Summary of sequencing-based read duplication", "help_text": "Type: `file`, default: `$id.$key.read_duplication_output_duplication_rate_sequence.xls`. Summary of sequencing-based read duplication" , - "default": "$id.$key.read_duplication_output_duplication_rate_sequence.xls" + "default":"$id.$key.read_duplication_output_duplication_rate_sequence.xls" } @@ -1104,7 +1102,7 @@ "description": "Type: `file`, default: `$id.$key.tin_output_summary.txt`. summary statistics (txt) of calculated TIN metrics", "help_text": "Type: `file`, default: `$id.$key.tin_output_summary.txt`. summary statistics (txt) of calculated TIN metrics" , - "default": "$id.$key.tin_output_summary.txt" + "default":"$id.$key.tin_output_summary.txt" } @@ -1115,7 +1113,7 @@ "description": "Type: `file`, default: `$id.$key.tin_output_metrics.xls`. file with TIN metrics (xls)", "help_text": "Type: `file`, default: `$id.$key.tin_output_metrics.xls`. file with TIN metrics (xls)" , - "default": "$id.$key.tin_output_metrics.xls" + "default":"$id.$key.tin_output_metrics.xls" } @@ -1126,7 +1124,7 @@ "description": "Type: `file`, default: `$id.$key.dupradar_output_dupmatrix.txt`. path to output file (txt) of duplicate tag counts", "help_text": "Type: `file`, default: `$id.$key.dupradar_output_dupmatrix.txt`. path to output file (txt) of duplicate tag counts" , - "default": "$id.$key.dupradar_output_dupmatrix.txt" + "default":"$id.$key.dupradar_output_dupmatrix.txt" } @@ -1137,7 +1135,7 @@ "description": "Type: `file`, default: `$id.$key.dupradar_output_dup_intercept_mqc.txt`. path to output file (txt) of multiqc intercept value DupRadar", "help_text": "Type: `file`, default: `$id.$key.dupradar_output_dup_intercept_mqc.txt`. path to output file (txt) of multiqc intercept value DupRadar" , - "default": "$id.$key.dupradar_output_dup_intercept_mqc.txt" + "default":"$id.$key.dupradar_output_dup_intercept_mqc.txt" } @@ -1148,7 +1146,7 @@ "description": "Type: `file`, default: `$id.$key.dupradar_output_duprate_exp_boxplot.pdf`. path to output file (pdf) of distribution of expression box plot", "help_text": "Type: `file`, default: `$id.$key.dupradar_output_duprate_exp_boxplot.pdf`. path to output file (pdf) of distribution of expression box plot" , - "default": "$id.$key.dupradar_output_duprate_exp_boxplot.pdf" + "default":"$id.$key.dupradar_output_duprate_exp_boxplot.pdf" } @@ -1159,7 +1157,7 @@ "description": "Type: `file`, default: `$id.$key.dupradar_output_duprate_exp_densplot.pdf`. path to output file (pdf) of 2D density scatter plot of duplicate tag counts", "help_text": "Type: `file`, default: `$id.$key.dupradar_output_duprate_exp_densplot.pdf`. path to output file (pdf) of 2D density scatter plot of duplicate tag counts" , - "default": "$id.$key.dupradar_output_duprate_exp_densplot.pdf" + "default":"$id.$key.dupradar_output_duprate_exp_densplot.pdf" } @@ -1170,7 +1168,7 @@ "description": "Type: `file`, default: `$id.$key.dupradar_output_duprate_exp_denscurve_mqc.pdf`. path to output file (pdf) of density curve of gene duplication multiqc", "help_text": "Type: `file`, default: `$id.$key.dupradar_output_duprate_exp_denscurve_mqc.pdf`. path to output file (pdf) of density curve of gene duplication multiqc" , - "default": "$id.$key.dupradar_output_duprate_exp_denscurve_mqc.pdf" + "default":"$id.$key.dupradar_output_duprate_exp_denscurve_mqc.pdf" } @@ -1181,7 +1179,7 @@ "description": "Type: `file`, default: `$id.$key.dupradar_output_expression_histogram.pdf`. path to output file (pdf) of distribution of RPK values per gene histogram", "help_text": "Type: `file`, default: `$id.$key.dupradar_output_expression_histogram.pdf`. path to output file (pdf) of distribution of RPK values per gene histogram" , - "default": "$id.$key.dupradar_output_expression_histogram.pdf" + "default":"$id.$key.dupradar_output_expression_histogram.pdf" } @@ -1192,7 +1190,7 @@ "description": "Type: `file`, default: `$id.$key.dupradar_output_intercept_slope.txt`. ", "help_text": "Type: `file`, default: `$id.$key.dupradar_output_intercept_slope.txt`. " , - "default": "$id.$key.dupradar_output_intercept_slope.txt" + "default":"$id.$key.dupradar_output_intercept_slope.txt" } @@ -1203,7 +1201,7 @@ "description": "Type: `file`, default: `$id.$key.qualimap_output_pdf.pdf`. ", "help_text": "Type: `file`, default: `$id.$key.qualimap_output_pdf.pdf`. " , - "default": "$id.$key.qualimap_output_pdf.pdf" + "default":"$id.$key.qualimap_output_pdf.pdf" } @@ -1214,7 +1212,7 @@ "description": "Type: `file`, default: `$id.$key.qualimap_output_dir.qualimap_output`. ", "help_text": "Type: `file`, default: `$id.$key.qualimap_output_dir.qualimap_output`. " , - "default": "$id.$key.qualimap_output_dir.qualimap_output" + "default":"$id.$key.qualimap_output_dir.qualimap_output" } @@ -1225,7 +1223,7 @@ "description": "Type: `file`, default: `$id.$key.deseq2_output.deseq2_output`. ", "help_text": "Type: `file`, default: `$id.$key.deseq2_output.deseq2_output`. " , - "default": "$id.$key.deseq2_output.deseq2_output" + "default":"$id.$key.deseq2_output.deseq2_output" } @@ -1236,7 +1234,7 @@ "description": "Type: `file`, default: `$id.$key.deseq2_output_pseudo.deseq2_output_pseudo`. ", "help_text": "Type: `file`, default: `$id.$key.deseq2_output_pseudo.deseq2_output_pseudo`. " , - "default": "$id.$key.deseq2_output_pseudo.deseq2_output_pseudo" + "default":"$id.$key.deseq2_output_pseudo.deseq2_output_pseudo" } @@ -1247,7 +1245,7 @@ "description": "Type: `file`, default: `$id.$key.multiqc_report.html`. ", "help_text": "Type: `file`, default: `$id.$key.multiqc_report.html`. " , - "default": "$id.$key.multiqc_report.html" + "default":"$id.$key.multiqc_report.html" } @@ -1258,7 +1256,7 @@ "description": "Type: `file`, default: `$id.$key.multiqc_data.multiqc_data`. ", "help_text": "Type: `file`, default: `$id.$key.multiqc_data.multiqc_data`. " , - "default": "$id.$key.multiqc_data.multiqc_data" + "default":"$id.$key.multiqc_data.multiqc_data" } @@ -1269,7 +1267,7 @@ "description": "Type: `file`, default: `$id.$key.multiqc_plots.multiqc_plots`. ", "help_text": "Type: `file`, default: `$id.$key.multiqc_plots.multiqc_plots`. " , - "default": "$id.$key.multiqc_plots.multiqc_plots" + "default":"$id.$key.multiqc_plots.multiqc_plots" } @@ -1280,7 +1278,7 @@ "description": "Type: `file`, default: `$id.$key.featurecounts.txt`. ", "help_text": "Type: `file`, default: `$id.$key.featurecounts.txt`. " , - "default": "$id.$key.featurecounts.txt" + "default":"$id.$key.featurecounts.txt" } @@ -1291,7 +1289,7 @@ "description": "Type: `file`, default: `$id.$key.featurecounts_summary.summary`. ", "help_text": "Type: `file`, default: `$id.$key.featurecounts_summary.summary`. " , - "default": "$id.$key.featurecounts_summary.summary" + "default":"$id.$key.featurecounts_summary.summary" } @@ -1302,7 +1300,7 @@ "description": "Type: `file`, default: `$id.$key.featurecounts_multiqc.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.featurecounts_multiqc.tsv`. " , - "default": "$id.$key.featurecounts_multiqc.tsv" + "default":"$id.$key.featurecounts_multiqc.tsv" } @@ -1313,7 +1311,7 @@ "description": "Type: `file`, default: `$id.$key.featurecounts_rrna_multiqc.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.featurecounts_rrna_multiqc.tsv`. " , - "default": "$id.$key.featurecounts_rrna_multiqc.tsv" + "default":"$id.$key.featurecounts_rrna_multiqc.tsv" } @@ -1324,7 +1322,7 @@ "description": "Type: `file`, default: `$id.$key.tpm_gene.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.tpm_gene.tsv`. " , - "default": "$id.$key.tpm_gene.tsv" + "default":"$id.$key.tpm_gene.tsv" } @@ -1335,7 +1333,7 @@ "description": "Type: `file`, default: `$id.$key.counts_gene.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.counts_gene.tsv`. " , - "default": "$id.$key.counts_gene.tsv" + "default":"$id.$key.counts_gene.tsv" } @@ -1346,7 +1344,7 @@ "description": "Type: `file`, default: `$id.$key.counts_gene_length_scaled.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.counts_gene_length_scaled.tsv`. " , - "default": "$id.$key.counts_gene_length_scaled.tsv" + "default":"$id.$key.counts_gene_length_scaled.tsv" } @@ -1357,7 +1355,7 @@ "description": "Type: `file`, default: `$id.$key.counts_gene_scaled.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.counts_gene_scaled.tsv`. " , - "default": "$id.$key.counts_gene_scaled.tsv" + "default":"$id.$key.counts_gene_scaled.tsv" } @@ -1368,7 +1366,7 @@ "description": "Type: `file`, default: `$id.$key.tpm_transcript.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.tpm_transcript.tsv`. " , - "default": "$id.$key.tpm_transcript.tsv" + "default":"$id.$key.tpm_transcript.tsv" } @@ -1379,7 +1377,7 @@ "description": "Type: `file`, default: `$id.$key.counts_transcript.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.counts_transcript.tsv`. " , - "default": "$id.$key.counts_transcript.tsv" + "default":"$id.$key.counts_transcript.tsv" } @@ -1390,7 +1388,7 @@ "description": "Type: `file`, default: `$id.$key.quant_merged_summarizedexperiment.quant_merged_summarizedexperiment`. ", "help_text": "Type: `file`, default: `$id.$key.quant_merged_summarizedexperiment.quant_merged_summarizedexperiment`. " , - "default": "$id.$key.quant_merged_summarizedexperiment.quant_merged_summarizedexperiment" + "default":"$id.$key.quant_merged_summarizedexperiment.quant_merged_summarizedexperiment" } @@ -1401,7 +1399,7 @@ "description": "Type: `file`, default: `$id.$key.pseudo_tpm_gene.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.pseudo_tpm_gene.tsv`. " , - "default": "$id.$key.pseudo_tpm_gene.tsv" + "default":"$id.$key.pseudo_tpm_gene.tsv" } @@ -1412,7 +1410,7 @@ "description": "Type: `file`, default: `$id.$key.pseudo_counts_gene.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.pseudo_counts_gene.tsv`. " , - "default": "$id.$key.pseudo_counts_gene.tsv" + "default":"$id.$key.pseudo_counts_gene.tsv" } @@ -1423,7 +1421,7 @@ "description": "Type: `file`, default: `$id.$key.pseudo_counts_gene_length_scaled.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.pseudo_counts_gene_length_scaled.tsv`. " , - "default": "$id.$key.pseudo_counts_gene_length_scaled.tsv" + "default":"$id.$key.pseudo_counts_gene_length_scaled.tsv" } @@ -1434,7 +1432,7 @@ "description": "Type: `file`, default: `$id.$key.pseudo_counts_gene_scaled.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.pseudo_counts_gene_scaled.tsv`. " , - "default": "$id.$key.pseudo_counts_gene_scaled.tsv" + "default":"$id.$key.pseudo_counts_gene_scaled.tsv" } @@ -1445,7 +1443,7 @@ "description": "Type: `file`, default: `$id.$key.pseudo_tpm_transcript.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.pseudo_tpm_transcript.tsv`. " , - "default": "$id.$key.pseudo_tpm_transcript.tsv" + "default":"$id.$key.pseudo_tpm_transcript.tsv" } @@ -1456,7 +1454,7 @@ "description": "Type: `file`, default: `$id.$key.pseudo_counts_transcript.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.pseudo_counts_transcript.tsv`. " , - "default": "$id.$key.pseudo_counts_transcript.tsv" + "default":"$id.$key.pseudo_counts_transcript.tsv" } @@ -1467,7 +1465,7 @@ "description": "Type: `file`, default: `$id.$key.pseudo_quant_merged_summarizedexperiment.pseudo_quant_merged_summarizedexperiment`. ", "help_text": "Type: `file`, default: `$id.$key.pseudo_quant_merged_summarizedexperiment.pseudo_quant_merged_summarizedexperiment`. " , - "default": "$id.$key.pseudo_quant_merged_summarizedexperiment.pseudo_quant_merged_summarizedexperiment" + "default":"$id.$key.pseudo_quant_merged_summarizedexperiment.pseudo_quant_merged_summarizedexperiment" } diff --git a/target/nextflow/workflows/rnaseq/.config.vsh.yaml b/target/nextflow/workflows/rnaseq/.config.vsh.yaml index 7c0320b..a1aa2a9 100644 --- a/target/nextflow/workflows/rnaseq/.config.vsh.yaml +++ b/target/nextflow/workflows/rnaseq/.config.vsh.yaml @@ -2090,8 +2090,8 @@ build_info: output: "target/nextflow/workflows/rnaseq" executable: "target/nextflow/workflows/rnaseq/main.nf" viash_version: "0.9.0" - git_commit: "89519f6e38f772746faa936930dbda45c0b09e83" - git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611" + git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@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 43fac7c..13b49cc 100644 --- a/target/nextflow/workflows/rnaseq/main.nf +++ b/target/nextflow/workflows/rnaseq/main.nf @@ -5254,8 +5254,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/rnaseq", "viash_version" : "0.9.0", - "git_commit" : "89519f6e38f772746faa936930dbda45c0b09e83", - "git_remote" : "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq" + "git_commit" : "c466555a20aa6b87f2d56e1b96126a1e87dd5611", + "git_remote" : "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", @@ -5315,222 +5315,473 @@ workflow run_wf { main: reference_ch = input_ch - | map { id, state -> - def biotype = state.gencode ? "gene_type" : state.featurecounts_group_type - def filter_gtf = - ( - ( !state.skip_alignment && state.aligner) // Condition 1: Alignment is required and aligner is set - || ( !state.skip_pseudo_alignment && state.pseudo_aligner ) // Condition 2: Pseudoalignment is required and pseudoaligner is set - || ( !state.transcript_fasta ) // Condition 3: Transcript FASTA file is not provided - ) - && - ( !state.skip_gtf_filter ) // Condition 4: --skip_gtf_filter is not provided - [ id, state + [ biotype: biotype, filter_gtf: filter_gtf ] ] - } - - | toSortedList - - | map { list -> - [ "ref", - [ fasta: list.collect { id, state -> state.fasta }.unique()[0], - gtf: list.collect { id, state -> state.gtf }.unique()[0], - gff: list.collect { id, state -> state.gff }.unique()[0], - additional_fasta: list.collect { id, state -> state.additional_fasta }.unique()[0], - transcript_fasta:list.collect { id, state -> state.transcript_fasta }.unique()[0], - gene_bed: list.collect { id, state -> state.gene_bed }.unique()[0], - bbsplit_fasta_list: list.collect { id, state -> state.bbsplit_fasta_list }.unique()[0], - aligner: list.collect { id, state -> state.aligner }.unique()[0], - pseudo_aligner: list.collect { id, state -> state.pseudo_aligner }.unique()[0], - star_index: list.collect { id, state -> state.star_index }.unique()[0], - rsem_index: list.collect { id, state -> state.rsem_index }.unique()[0], - salmon_index: list.collect { id, state -> state.salmon_index }.unique()[0], - kallisto_index: list.collect { id, state -> state.kallisto_index }.unique()[0], - // splicesites: list.collect { id, state -> state.splicesites }.unique()[0], - // hisat2_index: list.collect { id, state -> state.hisat2_index }.unique()[0], - bbsplit_index: list.collect { id, state -> state.bbsplit_index }.unique()[0], - skip_bbsplit: list.collect { id, state -> state.skip_bbsplit }.unique()[0], - gencode: list.collect { id, state -> state.gencode }.unique()[0], - biotype: list.collect { id, state -> state.biotype }.unique()[0], - filter_gtf: list.collect { id, state -> state.filter_gtf }.unique()[0], - pseudo_aligner_kmer_size: list.collect { id, state -> state.pseudo_aligner_kmer_size }.unique()[0] ] - ] - } + | map { id, state -> + def biotype = state.gencode ? "gene_type" : state.featurecounts_group_type + def filter_gtf = + ( + ( !state.skip_alignment && state.aligner) // Condition 1: Alignment is required and aligner is set + || ( !state.skip_pseudo_alignment && state.pseudo_aligner ) // Condition 2: Pseudoalignment is required and pseudoaligner is set + || ( !state.transcript_fasta ) // Condition 3: Transcript FASTA file is not provided + ) + && + ( !state.skip_gtf_filter ) // Condition 4: --skip_gtf_filter is not provided + [ id, state + [ biotype: biotype, filter_gtf: filter_gtf ] ] + } + + | toSortedList + + | map { list -> + [ "ref", + [ fasta: list.collect { id, state -> state.fasta }.unique()[0], + gtf: list.collect { id, state -> state.gtf }.unique()[0], + gff: list.collect { id, state -> state.gff }.unique()[0], + additional_fasta: list.collect { id, state -> state.additional_fasta }.unique()[0], + transcript_fasta:list.collect { id, state -> state.transcript_fasta }.unique()[0], + gene_bed: list.collect { id, state -> state.gene_bed }.unique()[0], + bbsplit_fasta_list: list.collect { id, state -> state.bbsplit_fasta_list }.unique()[0], + aligner: list.collect { id, state -> state.aligner }.unique()[0], + pseudo_aligner: list.collect { id, state -> state.pseudo_aligner }.unique()[0], + star_index: list.collect { id, state -> state.star_index }.unique()[0], + rsem_index: list.collect { id, state -> state.rsem_index }.unique()[0], + salmon_index: list.collect { id, state -> state.salmon_index }.unique()[0], + kallisto_index: list.collect { id, state -> state.kallisto_index }.unique()[0], + // splicesites: list.collect { id, state -> state.splicesites }.unique()[0], + // hisat2_index: list.collect { id, state -> state.hisat2_index }.unique()[0], + bbsplit_index: list.collect { id, state -> state.bbsplit_index }.unique()[0], + skip_bbsplit: list.collect { id, state -> state.skip_bbsplit }.unique()[0], + gencode: list.collect { id, state -> state.gencode }.unique()[0], + biotype: list.collect { id, state -> state.biotype }.unique()[0], + filter_gtf: list.collect { id, state -> state.filter_gtf }.unique()[0], + pseudo_aligner_kmer_size: list.collect { id, state -> state.pseudo_aligner_kmer_size }.unique()[0] ] + ] + } - // prepare all the necessary files for reference genome - | prepare_genome.run ( - fromState: [ - "fasta": "fasta", - "gtf": "gtf", - "gff": "gff", - "additional_fasta": "additional_fasta", - "transcript_fasta": "transcript_fasta", - "gene_bed": "gene_bed", - "bbsplit_fasta_list": "bbsplit_fasta_list", - "star_index": "star_index", - "rsem_index": "rsem_index", - "salmon_index": "salmon_index", - "kallisto_index": "kallisto_index", - "pseudo_aligner_kmer_size": "pseudo_aligner_kmer_size", - // "splicesites": "splicesites", - // "hisat2_index": "hisat2_index", - "bbsplit_index": "bbsplit_index", - "skip_bbsplit": "skip_bbsplit", - "gencode": "gencode", - "biotype": "biotype", - "filter_gtf": "filter_gtf", - "aligner": "aligner", - "pseudo_aligner": "pseudo_aligner", - "skip_alignment": "skip_alignment" - ], - toState: [ - "fasta": "uncompressed_fasta", - "gtf": "gtf_uncompressed", - "transcript_fasta": "transcript_fasta_uncompressed", - "fai": "fai", - "chrom_sizes": "chrom_sizes", - "bbsplit_index": "bbsplit_index_uncompressed", - "star_index": "star_index_uncompressed", - "salmon_index": "salmon_index_uncompressed", - "kallisto_index": "kallisto_index_uncompressed", - "gene_bed": "gene_bed_uncompressed" - ] - ) + // prepare all the necessary files for reference genome + | prepare_genome.run ( + fromState: [ + "fasta": "fasta", + "gtf": "gtf", + "gff": "gff", + "additional_fasta": "additional_fasta", + "transcript_fasta": "transcript_fasta", + "gene_bed": "gene_bed", + "bbsplit_fasta_list": "bbsplit_fasta_list", + "star_index": "star_index", + "rsem_index": "rsem_index", + "salmon_index": "salmon_index", + "kallisto_index": "kallisto_index", + "pseudo_aligner_kmer_size": "pseudo_aligner_kmer_size", + // "splicesites": "splicesites", + // "hisat2_index": "hisat2_index", + "bbsplit_index": "bbsplit_index", + "skip_bbsplit": "skip_bbsplit", + "gencode": "gencode", + "biotype": "biotype", + "filter_gtf": "filter_gtf", + "aligner": "aligner", + "pseudo_aligner": "pseudo_aligner", + "skip_alignment": "skip_alignment" + ], + toState: [ + "fasta": "uncompressed_fasta", + "gtf": "gtf_uncompressed", + "transcript_fasta": "transcript_fasta_uncompressed", + "fai": "fai", + "chrom_sizes": "chrom_sizes", + "bbsplit_index": "bbsplit_index_uncompressed", + "star_index": "star_index_uncompressed", + "salmon_index": "salmon_index_uncompressed", + "kallisto_index": "kallisto_index_uncompressed", + "gene_bed": "gene_bed_uncompressed" + ] + ) - // Check if contigs in genome fasta file > 512 Mbp - | map { id, state -> - (isBelowMaxContigSize(state.fai)) ? [id, state] : [id, state + [bam_csi_index: true]] - } + // Check if contigs in genome fasta file > 512 Mbp + // TODO: check where this is required and move if necessary + | map { id, state -> + (isBelowMaxContigSize(state.fai)) ? [id, state] : [id, state + [bam_csi_index: true]] + } - | map { list -> list[1]} + // Pick out the state + | map { list -> list[1]} analysis_ch = input_ch - | combine(reference_ch) + | combine(reference_ch) - | map { list -> [list[0], list[1] + list[2]] } + | map { list -> [list[0], list[1] + list[2]] } - // Concatenate FastQ files from same sample if required - | cat_fastq.run ( - fromState: [ - "read_1": "fastq_1", - "read_2": "fastq_2" - ], - toState: [ - "fastq_1": "fastq_1", - "fastq_2": "fastq_2" - ] - ) + // Concatenate FastQ files from same sample if required + | cat_fastq.run ( + fromState: [ + "read_1": "fastq_1", + "read_2": "fastq_2" + ], + toState: [ + "fastq_1": "fastq_1", + "fastq_2": "fastq_2" + ] + ) - // Pre-process fastq files - | pre_processing.run ( - fromState: [ - "id": "id", - "fastq_1": "fastq_1", - "fastq_2": "fastq_2", - "umitools_bc_pattern": "umitools_bc_pattern", - "umitools_bc_pattern2": "umitools_bc_pattern2", - "strandedness": "strandedness", - "transcript_fasta": "transcript_fasta", - "gtf": "gtf", - "with_umi": "with_umi", - "bbsplit_index": "bbsplit_index", - "bbsplit_fasta_list": "bbsplit_fasta_list", - "bc_pattern": "bc_pattern", - "ribo_database_manifest": "ribo_database_manifest", - "salmon_index": "salmon_index", - "skip_qc": "skip_qc", - "skip_fastqc": "skip_fastqc", - "skip_skip_umi_extract": "skip_umi_extract", - "umi_discard_read": "umi_discard_read", - "skip_trimming": "skip_trimming", - "trimmer": "trimmer", - "skip_bbsplit": "skip_bbsplit", - "remove_ribo_rna": "remove_ribo_rna" - ], - toState: [ + // Pre-process fastq files + | pre_processing.run ( + fromState: [ + "id": "id", + "fastq_1": "fastq_1", + "fastq_2": "fastq_2", + "umitools_bc_pattern": "umitools_bc_pattern", + "umitools_bc_pattern2": "umitools_bc_pattern2", + "strandedness": "strandedness", + "transcript_fasta": "transcript_fasta", + "gtf": "gtf", + "with_umi": "with_umi", + "bbsplit_index": "bbsplit_index", + "bbsplit_fasta_list": "bbsplit_fasta_list", + "bc_pattern": "bc_pattern", + "ribo_database_manifest": "ribo_database_manifest", + "salmon_index": "salmon_index", + "skip_qc": "skip_qc", + "skip_fastqc": "skip_fastqc", + "skip_skip_umi_extract": "skip_umi_extract", + "umi_discard_read": "umi_discard_read", + "skip_trimming": "skip_trimming", + "trimmer": "trimmer", + "skip_bbsplit": "skip_bbsplit", + "remove_ribo_rna": "remove_ribo_rna" + ], + toState: [ + "fastqc_html_1": "fastqc_html_1", + "fastqc_html_2": "fastqc_html_2", + "fastqc_zip_1": "fastqc_zip_1", + "fastqc_zip_2": "fastqc_zip_2", + "fastq_1": "qc_output1", + "fastq_2": "qc_output2", + "trim_log_1": "trim_log_1", + "trim_log_2": "trim_log_2", + "trim_zip_1": "trim_zip_1", + "trim_zip_2": "trim_zip_2", + "trim_html_1": "trim_html_1", + "trim_html_2": "trim_html_2", + "passed_trimmed_reads": "passed_trimmed_reads", + "num_trimmed_reads": "num_trimmed_reads", + "sortmerna_log": "sortmerna_log", + "salmon_quant_output": "salmon_quant_output", + "fastp_failed_trim": "failed_trim", + "fastp_failed_trim_unpaired1": "failed_trim_unpaired1", + "fastp_failed_trim_unpaired2": "failed_trim_unpaired2", + "fastp_trim_json": "trim_json", + "fastp_trim_html": "trim_html", + "fastp_trim_merged_out": "trim_merged_out" + ] + ) + + // Infer strandedness from Salmon pseudo-alignment results + // TODO: Turn this into a workflow step and include as a dependency + | map { id, state -> + (state.strandedness == 'auto') ? + [ id, state + [strandedness: getSalmonInferredStrandedness(state.salmon_quant_output)] ] : + [id, state] + } + + // Filter FastQ files based on minimum trimmed read count after adapter trimming + // TODO: Turn this into a workflow step and include as a dependency + | map { id, state -> + def input = state.fastq_2 ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ] + def num_reads = (state.skip_trimming) ? + state.min_trimmed_reads + 1 : + ( + (state.trimmer == "fastp") ? + getFastpReadsAfterFiltering(state.fastp_trim_json) : + ( + (!state.skip_trimming && input.size() == 2) ? + getTrimGaloreReadsAfterFiltering(state.trim_log_2) : + getTrimGaloreReadsAfterFiltering(state.trim_log_1) + ) + ) + def passed_trimmed_reads = + (state.skip_trimming || (num_reads >= state.min_trimmed_reads)) ? + true : + false + [ id, state + [num_trimmed_reads: num_reads, passed_trimmed_reads: passed_trimmed_reads] ] + } + + // Genome alignment and quantification + | genome_alignment_and_quant.run ( + runIf: { id, state -> !state.skip_alignment && state.passed_trimmed_reads }, + fromState: [ + "id": "id", + "fastq_1": "fastq_1", + "fastq_2": "fastq_2", + "strandedness": "strandedness", + "gtf": "gtf", + "transcript_fasta": "transcript_fasta", + "bam_csi_index": "bam_csi_index", + "aligner": "aligner", + "rsem_index": "rsem_index", + "star_index": "star_index", + "extra_star_align_args": "extra_star_align_args", + "star_ignore_sjdbgtf": "star_ignore_sjdbgtf", + "seq_platform": "seq_platform", + "seq_center": "seq_center", + "with_umi": "with_umi", + "umi_dedup_stats": "umi_dedup_stats", + "gtf_group_features": "gtf_group_features", + "gtf_extra_attributes": "gtf_extra_attributes", + "salmon_quant_libtype": "salmon_quant_libtype", + "salmon_index": "salmon_index", + "extra_rsem_calculate_expression_args": "extra_rsem_calculate_expression_args" + ], + toState: [ + "star_multiqc": "star_multiqc", + "rsem_multiqc": "rsem_multiqc", + "salmon_multiqc": "salmon_multiqc", + "genome_bam_sorted": "genome_bam_sorted", + "genome_bam_index": "genome_bam_index", + "genome_bam_stats": "genome_bam_stats", + "genome_bam_flagstat": "genome_bam_flagstat", + "genome_bam_idxstats": "genome_bam_idxstats", + "transcriptome_bam": "transcriptome_bam", + "transcriptome_bam_index": "transcriptome_bam_index", + "transcriptome_bam_stats": "transcriptome_bam_stats", + "transcriptome_bam_flagstat": "transcriptome_bam_flagstat", + "transcriptome_bam_idxstats": "transcriptome_bam_idxstats", + "quant_out_dir": "quant_out_dir", + "quant_results_file": "quant_results_file", + "rsem_counts_gene": "rsem_counts_gene", + "rsem_counts_transcripts": "rsem_counts_transcripts", + "bam_genome_rsem": "bam_genome_rsem", + "bam_transcript_rsem": "bam_transcript_rsem" + ] + ) + + // Filter channels to get samples that passed STAR minimum mapping percentage + // TODO: Move to reporting or later step + | map { id, state -> + def percent_mapped = (!state.skip_alignment) ? getStarPercentMapped(state.star_multiqc) : 0.0 + def passed_mapping = (percent_mapped >= state.min_mapped_reads) ? true : false + [ id, state + [percent_mapped: percent_mapped, passed_mapping: passed_mapping] ] + } + + // Pseudo-alignment and quantification + | pseudo_alignment_and_quant.run ( + runIf: { id, state -> !state.skip_pseudo_alignment && state.passed_trimmed_reads }, + fromState: [ + "id": "id", + "fastq_1": "fastq_1", + "fastq_2": "fastq_2", + "strandedness": "strandedness", + "gtf": "gtf", + "transcript_fasta": "transcript_fasta", + "pseudo_aligner": "pseudo_aligner", + "salmon_index": "salmon_index", + "kallisto_index": "kallisto_index", + "extra_star_align_args": "extra_star_align_args", + "star_ignore_sjdbgtf": "star_ignore_sjdbgtf", + "seq_platform": "seq_platform", + "seq_center": "seq_center", + "with_umi": "with_umi", + "umi_dedup_stats": "umi_dedup_stats", + "gtf_group_features": "gtf_group_features", + "gtf_extra_attributes": "gtf_extra_attributes", + "lib_type": "salmon_quant_libtype", + "kallisto_quant_fragment_length": "kallisto_quant_fragment_length", + "kallisto_quant_fragment_length_sd": "kallisto_quant_fragment_length_sd" + ], + toState: [ + "pseudo_quant_out_dir": "quant_out_dir", + "pseudo_salmon_quant_results_file": "salmon_quant_results_file", + "pseudo_kallisto_quant_results_file": "kallisto_quant_results_file", + "pseudo_multiqc": "pseudo_multiqc" + ] + ) + + | map { id, state -> + def input = state.fastq_2 ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ] + def paired = input.size() == 2 + [ id, state + [ paired: paired ] ] + } + + // Post-processing + | post_processing.run ( + runIf: { id, state -> !state.skip_alignment && state.passed_trimmed_reads && state.passed_mapping }, + fromState: [ + "id": "id", + "paired": "paired", + "strandedness": "strandedness", + "fasta": "fasta", + "fai": "fai", + "gtf": "gtf", + "genome_bam": "genome_bam_sorted", + "chrom_sizes": "chrom_sizes", + "star_multiqc": "star_multiqc", + "extra_picard_args": "extra_picard_args", + "extra_stringtie_args": "extra_stringtie_args", + "stringtie_ignore_gtf": "stringtie_ignore_gtf", + "extra_bedtools_args": "extra_bedtools_args", + "bam_csi_index": "bam_csi_index", + "min_mapped_reads": "min_mapped_reads", + "with_umi": "with_umi", + "skip_qc": "skip_qc", + "skip_markduplicates": "skip_markduplicates", + "skip_stringtie": "skip_stringtie", + "skip_bigwig":"gencode" + ], + toState: [ + "genome_bam_sorted": "processed_genome_bam", + "genome_bam_index": "genome_bam_index", + "genome_bam_stats": "genome_bam_stats", + "genome_bam_flagstat": "genome_bam_flagstat", + "genome_bam_idxstats": "genome_bam_idxstats", + "markduplicates_metrics": "markduplicates_metrics", + "stringtie_transcript_gtf": "stringtie_transcript_gtf", + "stringtie_coverage_gtf": "stringtie_coverage_gtf", + "stringtie_abundance": "stringtie_abundance", + "stringtie_ballgown": "stringtie_ballgown", + "bedgraph_forward": "bedgraph_forward", + "bedgraph_reverse": "bedgraph_reverse", + "bigwig_forward": "bigwig_forward", + "bigwig_reverse": "bigwig_reverse" + ] + ) + + // Final QC + | quality_control.run ( + fromState: [ + "id": "id", + "paired": "paired", + "strandedness": "strandedness", + "skip_align": "skip_alignment", + "skip_pseudo_align": "skip_pseudo_alignment", + "skip_dupradar": "skip_dupradar", + "skip_qualimap": "skip_qualimap", + "skip_rseqc": "skip_rseqc", + "skip_multiqc": "skip_multiqc", + "skip_preseq": "skip_preseq", + "gtf": "gtf", + "num_trimmed_reads": "num_trimmed_reads", + "passed_trimmed_reads": "passed_trimmed_reads", + "passed_mapping": "passed_mapping", + "percent_mapped": "percent_mapped", + "genome_bam": "genome_bam_sorted", + "genome_bam_index": "genome_bam_index", + "salmon_multiqc": "salmon_multiqc", + "quant_results_file": "quant_results_file", + "rsem_multiqc": "rsem_multiqc", + "rsem_counts_gene": "rsem_counts_gene", + "rsem_counts_transcripts": "rsem_counts_transcripts", + "pseudo_multiqc": "pseudo_multiqc", + "pseudo_quant_out_dir": "pseudo_quant_out_dir", + "pseudo_salmon_quant_results_file": "pseudo_salmon_quant_results_file", + "pseudo_kallisto_quant_results_file": "pseudo_kallisto_quant_results_file", + "aligner": "aligner", + "pseudo_aligner": "pseudo_aligner", + "gene_bed": "gene_bed", + "extra_preseq_args": "extra_preseq_args", + "biotype": "biotype", + "skip_biotype_qc": "skip_biotype_qc", + "featurecounts_group_type": "featurecounts_group_type", + "featurecounts_feature_type": "featurecounts_feature_type", + "gencode": "gencode", + "skip_deseq2_qc": "skip_deseq2_qc", + "deseq2_vst": "deseq2_vst", + "multiqc_custom_config": "multiqc_custom_config", + "multiqc_title": "multiqc_title", + "multiqc_methods_description": "multiqc_methods_description", + "fastqc_zip_1": "fastqc_zip_1", + "fastqc_zip_2": "fastqc_zip_2", + "trim_log_1": "trim_log_1", + "trim_log_2": "trim_log_2", + "trim_zip_1": "trim_zip_1", + "trim_zip_2": "trim_zip_2", + "sortmerna_multiqc": "sortmerna_log", + "star_multiqc": "star_multiqc", + "genome_bam_stats": "genome_bam_stats", + "genome_bam_flagstat": "genome_bam_flagstat", + "genome_bam_idxstats": "genome_bam_idxstats", + "markduplicates_multiqc": "markduplicates_metrics", + "rseqc_modules": "rseqc_modules" + ], + toState: [ + "preseq_output": "preseq_output", + "bamstat_output": "bamstat_output", + "strandedness_output": "strandedness_output", + "inner_dist_output_stats": "inner_dist_output_stats", + "inner_dist_output_dist": "inner_dist_output_dist", + "inner_dist_output_freq": "inner_dist_output_freq", + "inner_dist_output_plot": "inner_dist_output_plot", + "inner_dist_output_plot_r": "inner_dist_output_plot_r", + "junction_annotation_output_log": "junction_annotation_output_log", + "junction_annotation_output_plot_r": "junction_annotation_output_plot_r", + "junction_annotation_output_junction_bed": "junction_annotation_output_junction_bed", + "junction_annotation_output_junction_interact": "junction_annotation_output_junction_interact", + "junction_annotation_output_junction_sheet": "junction_annotation_output_junction_sheet", + "junction_annotation_output_splice_events_plot": "junction_annotation_output_splice_events_plot", + "junction_annotation_output_splice_junctions_plot": "junction_annotation_output_splice_junctions_plot", + "junction_saturation_output_plot_r": "junction_saturation_output_plot_r", + "junction_saturation_output_plot": "junction_saturation_output_plot", + "read_distribution_output": "read_distribution_output", + "read_duplication_output_duplication_rate_plot_r": "read_duplication_output_duplication_rate_plot_r", + "read_duplication_output_duplication_rate_plot": "read_duplication_output_duplication_rate_plot", + "read_duplication_output_duplication_rate_mapping": "read_duplication_output_duplication_rate_mapping", + "read_duplication_output_duplication_rate_sequence": "read_duplication_output_duplication_rate_sequence", + "tin_output_summary": "tin_output_summary", + "tin_output_metrics": "tin_output_metrics", + "dupradar_output_dupmatrix": "dupradar_output_dupmatrix", + "dupradar_output_dup_intercept_mqc": "dupradar_output_dup_intercept_mqc", + "dupradar_output_duprate_exp_boxplot": "dupradar_output_duprate_exp_boxplot", + "dupradar_output_duprate_exp_densplot": "dupradar_output_duprate_exp_densplot", + "dupradar_output_duprate_exp_denscurve_mqc": "dupradar_output_duprate_exp_denscurve_mqc", + "dupradar_output_expression_histogram": "dupradar_output_expression_histogram", + "dupradar_output_intercept_slope": "dupradar_output_intercept_slope", + "qualimap_output_dir": "qualimap_output_dir", + "qualimap_output_pdf": "qualimap_output_pdf", + "featurecounts": "featurecounts", + "featurecounts_summary": "featurecounts_summary", + "featurecounts_multiqc": "featurecounts_multiqc", + "featurecounts_rrna_multiqc": "featurecounts_rrna_multiqc", + "tpm_gene": "tpm_gene", + "counts_gene": "counts_gene", + "counts_gene_length_scaled": "counts_gene_length_scaled", + "counts_gene_scaled": "counts_gene_scaled", + "tpm_transcript": "tpm_transcript", + "counts_transcript": "counts_transcript", + "qunat_merged_summarizedexperiment": "quant_merged_summarizedexperiment", + "deseq2_output": "deseq2_output", + "multiqc_report": "multiqc_report", + "multiqc_data": "multiqc_data", + "multiqc_plots": "multiqc_plots" + ] + ) + + | map { id, state -> + def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() } + [ id, mod_state ] + } + + | setState ( + [ + "output_fasta": "fasta", + "output_gtf": "gtf", + "output_transcript_fasta": "transcript_fasta", + "output_gene_bed": "gene_bed", + "output_bbsplit_index": "bbsplit_index", + "output_star_index": "star_index", + "output_salmon_index": "salmon_index", + "output_kallisto_index": "kallisto_index", "fastqc_html_1": "fastqc_html_1", "fastqc_html_2": "fastqc_html_2", "fastqc_zip_1": "fastqc_zip_1", "fastqc_zip_2": "fastqc_zip_2", - "fastq_1": "qc_output1", - "fastq_2": "qc_output2", + "output_fastq_1": "fastq_1", + "output_fastq_2": "fastq_2", "trim_log_1": "trim_log_1", "trim_log_2": "trim_log_2", "trim_zip_1": "trim_zip_1", "trim_zip_2": "trim_zip_2", "trim_html_1": "trim_html_1", "trim_html_2": "trim_html_2", - "passed_trimmed_reads": "passed_trimmed_reads", - "num_trimmed_reads": "num_trimmed_reads", "sortmerna_log": "sortmerna_log", - "salmon_quant_output": "salmon_quant_output", - "fastp_failed_trim": "failed_trim", - "fastp_failed_trim_unpaired1": "failed_trim_unpaired1", - "fastp_failed_trim_unpaired2": "failed_trim_unpaired2", - "fastp_trim_json": "trim_json", - "fastp_trim_html": "trim_html", - "fastp_trim_merged_out": "trim_merged_out" - ] - ) - - // Infer strandedness from Salmon pseudo-alignment results - | map { id, state -> - (state.strandedness == 'auto') ? - [ id, state + [strandedness: getSalmonInferredStrandedness(state.salmon_quant_output)] ] : - [id, state] - } - - // Filter FastQ files based on minimum trimmed read count after adapter trimming - | map { id, state -> - def input = state.fastq_2 ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ] - def num_reads = (state.skip_trimming) ? - state.min_trimmed_reads + 1 : - ( - (state.trimmer == "fastp") ? - getFastpReadsAfterFiltering(state.fastp_trim_json) : - ( - (!state.skip_trimming && input.size() == 2) ? - getTrimGaloreReadsAfterFiltering(state.trim_log_2) : - getTrimGaloreReadsAfterFiltering(state.trim_log_1) - ) - ) - def passed_trimmed_reads = - (state.skip_trimming || (num_reads >= state.min_trimmed_reads)) ? - true : - false - [ id, state + [num_trimmed_reads: num_reads, passed_trimmed_reads: passed_trimmed_reads] ] - } - - // Genome alignment and quantification - | genome_alignment_and_quant.run ( - runIf: { id, state -> !state.skip_alignment && state.passed_trimmed_reads }, - fromState: [ - "id": "id", - "fastq_1": "fastq_1", - "fastq_2": "fastq_2", - "strandedness": "strandedness", - "gtf": "gtf", - "transcript_fasta": "transcript_fasta", - "bam_csi_index": "bam_csi_index", - "aligner": "aligner", - "rsem_index": "rsem_index", - "star_index": "star_index", - "extra_star_align_args": "extra_star_align_args", - "star_ignore_sjdbgtf": "star_ignore_sjdbgtf", - "seq_platform": "seq_platform", - "seq_center": "seq_center", - "with_umi": "with_umi", - "umi_dedup_stats": "umi_dedup_stats", - "gtf_group_features": "gtf_group_features", - "gtf_extra_attributes": "gtf_extra_attributes", - "salmon_quant_libtype": "salmon_quant_libtype", - "salmon_index": "salmon_index", - "extra_rsem_calculate_expression_args": "extra_rsem_calculate_expression_args" - ], - toState: [ - "star_multiqc": "star_multiqc", - "rsem_multiqc": "rsem_multiqc", - "salmon_multiqc": "salmon_multiqc", + "star_log": "star_multiqc", "genome_bam_sorted": "genome_bam_sorted", "genome_bam_index": "genome_bam_index", "genome_bam_stats": "genome_bam_stats", @@ -5541,162 +5792,21 @@ workflow run_wf { "transcriptome_bam_stats": "transcriptome_bam_stats", "transcriptome_bam_flagstat": "transcriptome_bam_flagstat", "transcriptome_bam_idxstats": "transcriptome_bam_idxstats", - "quant_out_dir": "quant_out_dir", - "quant_results_file": "quant_results_file", - "rsem_counts_gene": "rsem_counts_gene", - "rsem_counts_transcripts": "rsem_counts_transcripts", - "bam_genome_rsem": "bam_genome_rsem", - "bam_transcript_rsem": "bam_transcript_rsem" - ] - ) - - // Filter channels to get samples that passed STAR minimum mapping percentage - | map { id, state -> - def percent_mapped = (!state.skip_alignment) ? getStarPercentMapped(state.star_multiqc) : 0.0 - def passed_mapping = (percent_mapped >= state.min_mapped_reads) ? true : false - [ id, state + [percent_mapped: percent_mapped, passed_mapping: passed_mapping] ] - } - - // Pseudo-alignment and quantification - | pseudo_alignment_and_quant.run ( - runIf: { id, state -> !state.skip_pseudo_alignment && state.passed_trimmed_reads }, - fromState: [ - "id": "id", - "fastq_1": "fastq_1", - "fastq_2": "fastq_2", - "strandedness": "strandedness", - "gtf": "gtf", - "transcript_fasta": "transcript_fasta", - "pseudo_aligner": "pseudo_aligner", - "salmon_index": "salmon_index", - "kallisto_index": "kallisto_index", - "extra_star_align_args": "extra_star_align_args", - "star_ignore_sjdbgtf": "star_ignore_sjdbgtf", - "seq_platform": "seq_platform", - "seq_center": "seq_center", - "with_umi": "with_umi", - "umi_dedup_stats": "umi_dedup_stats", - "gtf_group_features": "gtf_group_features", - "gtf_extra_attributes": "gtf_extra_attributes", - "lib_type": "salmon_quant_libtype", - "kallisto_quant_fragment_length": "kallisto_quant_fragment_length", - "kallisto_quant_fragment_length_sd": "kallisto_quant_fragment_length_sd" - ], - toState: [ - "pseudo_quant_out_dir": "quant_out_dir", - "pseudo_salmon_quant_results_file": "salmon_quant_results_file", - "pseudo_kallisto_quant_results_file": "kallisto_quant_results_file", - "pseudo_multiqc": "pseudo_multiqc" - ] - ) - - | map { id, state -> - def input = state.fastq_2 ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ] - def paired = input.size() == 2 - [ id, state + [ paired: paired ] ] - } - - // Post-processing - | post_processing.run ( - runIf: { id, state -> !state.skip_alignment && state.passed_trimmed_reads && state.passed_mapping }, - fromState: [ - "id": "id", - "paired": "paired", - "strandedness": "strandedness", - "fasta": "fasta", - "fai": "fai", - "gtf": "gtf", - "genome_bam": "genome_bam_sorted", - "chrom_sizes": "chrom_sizes", - "star_multiqc": "star_multiqc", - "extra_picard_args": "extra_picard_args", - "extra_stringtie_args": "extra_stringtie_args", - "stringtie_ignore_gtf": "stringtie_ignore_gtf", - "extra_bedtools_args": "extra_bedtools_args", - "bam_csi_index": "bam_csi_index", - "min_mapped_reads": "min_mapped_reads", - "with_umi": "with_umi", - "skip_qc": "skip_qc", - "skip_markduplicates": "skip_markduplicates", - "skip_stringtie": "skip_stringtie", - "skip_bigwig":"gencode" - ], - toState: [ - "genome_bam_sorted": "processed_genome_bam", - "genome_bam_index": "genome_bam_index", - "genome_bam_stats": "genome_bam_stats", - "genome_bam_flagstat": "genome_bam_flagstat", - "genome_bam_idxstats": "genome_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", "stringtie_ballgown": "stringtie_ballgown", + "featurecounts": "featurecounts", + "featurecounts_summary": "featurecounts_summary", + "featurecounts_multiqc": "featurecounts_multiqc", + "featurecounts_rrna_multiqc": "featurecounts_rrna_multiqc", "bedgraph_forward": "bedgraph_forward", "bedgraph_reverse": "bedgraph_reverse", "bigwig_forward": "bigwig_forward", - "bigwig_reverse": "bigwig_reverse" - ] - ) - - // Final QC - | quality_control.run ( - fromState: [ - "id": "id", - "paired": "paired", - "strandedness": "strandedness", - "skip_align": "skip_alignment", - "skip_pseudo_align": "skip_pseudo_alignment", - "skip_dupradar": "skip_dupradar", - "skip_qualimap": "skip_qualimap", - "skip_rseqc": "skip_rseqc", - "skip_multiqc": "skip_multiqc", - "skip_preseq": "skip_preseq", - "gtf": "gtf", - "num_trimmed_reads": "num_trimmed_reads", - "passed_trimmed_reads": "passed_trimmed_reads", - "passed_mapping": "passed_mapping", - "percent_mapped": "percent_mapped", - "genome_bam": "genome_bam_sorted", - "genome_bam_index": "genome_bam_index", - "salmon_multiqc": "salmon_multiqc", - "quant_results_file": "quant_results_file", - "rsem_multiqc": "rsem_multiqc", - "rsem_counts_gene": "rsem_counts_gene", - "rsem_counts_transcripts": "rsem_counts_transcripts", - "pseudo_multiqc": "pseudo_multiqc", - "pseudo_quant_out_dir": "pseudo_quant_out_dir", - "pseudo_salmon_quant_results_file": "pseudo_salmon_quant_results_file", - "pseudo_kallisto_quant_results_file": "pseudo_kallisto_quant_results_file", - "aligner": "aligner", - "pseudo_aligner": "pseudo_aligner", - "gene_bed": "gene_bed", - "extra_preseq_args": "extra_preseq_args", - "biotype": "biotype", - "skip_biotype_qc": "skip_biotype_qc", - "featurecounts_group_type": "featurecounts_group_type", - "featurecounts_feature_type": "featurecounts_feature_type", - "gencode": "gencode", - "skip_deseq2_qc": "skip_deseq2_qc", - "deseq2_vst": "deseq2_vst", - "multiqc_custom_config": "multiqc_custom_config", - "multiqc_title": "multiqc_title", - "multiqc_methods_description": "multiqc_methods_description", - "fastqc_zip_1": "fastqc_zip_1", - "fastqc_zip_2": "fastqc_zip_2", - "trim_log_1": "trim_log_1", - "trim_log_2": "trim_log_2", - "trim_zip_1": "trim_zip_1", - "trim_zip_2": "trim_zip_2", - "sortmerna_multiqc": "sortmerna_log", - "star_multiqc": "star_multiqc", - "genome_bam_stats": "genome_bam_stats", - "genome_bam_flagstat": "genome_bam_flagstat", - "genome_bam_idxstats": "genome_bam_idxstats", - "markduplicates_multiqc": "markduplicates_metrics", - "rseqc_modules": "rseqc_modules" - ], - toState: [ + "bigwig_reverse": "bigwig_reverse", "preseq_output": "preseq_output", "bamstat_output": "bamstat_output", "strandedness_output": "strandedness_output", @@ -5729,140 +5839,33 @@ workflow run_wf { "dupradar_output_expression_histogram": "dupradar_output_expression_histogram", "dupradar_output_intercept_slope": "dupradar_output_intercept_slope", "qualimap_output_dir": "qualimap_output_dir", - "qualimap_output_pdf": "qualimap_output_pdf", - "featurecounts": "featurecounts", - "featurecounts_summary": "featurecounts_summary", - "featurecounts_multiqc": "featurecounts_multiqc", - "featurecounts_rrna_multiqc": "featurecounts_rrna_multiqc", + "qualimap_output_pdf": "qualimap_output_pdf", "tpm_gene": "tpm_gene", "counts_gene": "counts_gene", "counts_gene_length_scaled": "counts_gene_length_scaled", "counts_gene_scaled": "counts_gene_scaled", "tpm_transcript": "tpm_transcript", "counts_transcript": "counts_transcript", - "qunat_merged_summarizedexperiment": "quant_merged_summarizedexperiment", + "quant_merged_summarizedexperiment": "quant_merged_summarizedexperiment", "deseq2_output": "deseq2_output", + "pseudo_tpm_gene": "pseudo_tpm_gene", + "pseudo_counts_gene": "pseudo_counts_gene", + "pseudo_counts_gene_length_scaled": "pseudo_counts_gene_length_scaled", + "pseudo_counts_gene_scaled": "pseudo_counts_gene_scaled", + "pseudo_tpm_transcript": "pseudo_tpm_transcript", + "pseudo_counts_transcript": "pseudo_counts_transcript", + "pseudo_lengths_gene": "pseudo_lengths_gene", + "pseudo_lengths_transcript": "pseudo_lengths_transcript", + "pseudo_quant_merged_summarizedexperiment": "pseudo_quant_merged_summarizedexperiment", + "deseq2_output_pseudo": "deseq2_output_pseudo", "multiqc_report": "multiqc_report", "multiqc_data": "multiqc_data", "multiqc_plots": "multiqc_plots" - ] - ) - - | map { id, state -> - def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() } - [ id, mod_state ] - } - - | setState ( - [ - "output_fasta": "fasta", - "output_gtf": "gtf", - "output_transcript_fasta": "transcript_fasta", - "output_gene_bed": "gene_bed", - "output_bbsplit_index": "bbsplit_index", - "output_star_index": "star_index", - "output_salmon_index": "salmon_index", - "output_kallisto_index": "kallisto_index", - "fastqc_html_1": "fastqc_html_1", - "fastqc_html_2": "fastqc_html_2", - "fastqc_zip_1": "fastqc_zip_1", - "fastqc_zip_2": "fastqc_zip_2", - "output_fastq_1": "fastq_1", - "output_fastq_2": "fastq_2", - "trim_log_1": "trim_log_1", - "trim_log_2": "trim_log_2", - "trim_zip_1": "trim_zip_1", - "trim_zip_2": "trim_zip_2", - "trim_html_1": "trim_html_1", - "trim_html_2": "trim_html_2", - "sortmerna_log": "sortmerna_log", - "star_log": "star_multiqc", - "genome_bam_sorted": "genome_bam_sorted", - "genome_bam_index": "genome_bam_index", - "genome_bam_stats": "genome_bam_stats", - "genome_bam_flagstat": "genome_bam_flagstat", - "genome_bam_idxstats": "genome_bam_idxstats", - "transcriptome_bam": "transcriptome_bam", - "transcriptome_bam_index": "transcriptome_bam_index", - "transcriptome_bam_stats": "transcriptome_bam_stats", - "transcriptome_bam_flagstat": "transcriptome_bam_flagstat", - "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", - "stringtie_ballgown": "stringtie_ballgown", - "featurecounts": "featurecounts", - "featurecounts_summary": "featurecounts_summary", - "featurecounts_multiqc": "featurecounts_multiqc", - "featurecounts_rrna_multiqc": "featurecounts_rrna_multiqc", - "bedgraph_forward": "bedgraph_forward", - "bedgraph_reverse": "bedgraph_reverse", - "bigwig_forward": "bigwig_forward", - "bigwig_reverse": "bigwig_reverse", - "preseq_output": "preseq_output", - "bamstat_output": "bamstat_output", - "strandedness_output": "strandedness_output", - "inner_dist_output_stats": "inner_dist_output_stats", - "inner_dist_output_dist": "inner_dist_output_dist", - "inner_dist_output_freq": "inner_dist_output_freq", - "inner_dist_output_plot": "inner_dist_output_plot", - "inner_dist_output_plot_r": "inner_dist_output_plot_r", - "junction_annotation_output_log": "junction_annotation_output_log", - "junction_annotation_output_plot_r": "junction_annotation_output_plot_r", - "junction_annotation_output_junction_bed": "junction_annotation_output_junction_bed", - "junction_annotation_output_junction_interact": "junction_annotation_output_junction_interact", - "junction_annotation_output_junction_sheet": "junction_annotation_output_junction_sheet", - "junction_annotation_output_splice_events_plot": "junction_annotation_output_splice_events_plot", - "junction_annotation_output_splice_junctions_plot": "junction_annotation_output_splice_junctions_plot", - "junction_saturation_output_plot_r": "junction_saturation_output_plot_r", - "junction_saturation_output_plot": "junction_saturation_output_plot", - "read_distribution_output": "read_distribution_output", - "read_duplication_output_duplication_rate_plot_r": "read_duplication_output_duplication_rate_plot_r", - "read_duplication_output_duplication_rate_plot": "read_duplication_output_duplication_rate_plot", - "read_duplication_output_duplication_rate_mapping": "read_duplication_output_duplication_rate_mapping", - "read_duplication_output_duplication_rate_sequence": "read_duplication_output_duplication_rate_sequence", - "tin_output_summary": "tin_output_summary", - "tin_output_metrics": "tin_output_metrics", - "dupradar_output_dupmatrix": "dupradar_output_dupmatrix", - "dupradar_output_dup_intercept_mqc": "dupradar_output_dup_intercept_mqc", - "dupradar_output_duprate_exp_boxplot": "dupradar_output_duprate_exp_boxplot", - "dupradar_output_duprate_exp_densplot": "dupradar_output_duprate_exp_densplot", - "dupradar_output_duprate_exp_denscurve_mqc": "dupradar_output_duprate_exp_denscurve_mqc", - "dupradar_output_expression_histogram": "dupradar_output_expression_histogram", - "dupradar_output_intercept_slope": "dupradar_output_intercept_slope", - "qualimap_output_dir": "qualimap_output_dir", - "qualimap_output_pdf": "qualimap_output_pdf", - "tpm_gene": "tpm_gene", - "counts_gene": "counts_gene", - "counts_gene_length_scaled": "counts_gene_length_scaled", - "counts_gene_scaled": "counts_gene_scaled", - "tpm_transcript": "tpm_transcript", - "counts_transcript": "counts_transcript", - "quant_merged_summarizedexperiment": "quant_merged_summarizedexperiment", - "deseq2_output": "deseq2_output", - "pseudo_tpm_gene": "pseudo_tpm_gene", - "pseudo_counts_gene": "pseudo_counts_gene", - "pseudo_counts_gene_length_scaled": "pseudo_counts_gene_length_scaled", - "pseudo_counts_gene_scaled": "pseudo_counts_gene_scaled", - "pseudo_tpm_transcript": "pseudo_tpm_transcript", - "pseudo_counts_transcript": "pseudo_counts_transcript", - "pseudo_lengths_gene": "pseudo_lengths_gene", - "pseudo_lengths_transcript": "pseudo_lengths_transcript", - "pseudo_quant_merged_summarizedexperiment": "pseudo_quant_merged_summarizedexperiment", - "deseq2_output_pseudo": "deseq2_output_pseudo", - "multiqc_report": "multiqc_report", - "multiqc_data": "multiqc_data", - "multiqc_plots": "multiqc_plots" - ] - ) - - output_ch = analysis_ch + ] + ) emit: - output_ch + analysis_ch } import nextflow.Nextflow diff --git a/target/nextflow/workflows/rnaseq/nextflow_schema.json b/target/nextflow/workflows/rnaseq/nextflow_schema.json index ae7190a..bc0c6ba 100644 --- a/target/nextflow/workflows/rnaseq/nextflow_schema.json +++ b/target/nextflow/workflows/rnaseq/nextflow_schema.json @@ -52,7 +52,7 @@ "enum": ["unstranded", "forward", "reverse", "auto"] , - "default": "auto" + "default":"auto" } @@ -183,7 +183,7 @@ "description": "Type: `boolean_true`, default: `false`. Specify if the GTF annotation is in GENCODE format", "help_text": "Type: `boolean_true`, default: `false`. Specify if the GTF annotation is in GENCODE format." , - "default": "False" + "default":false } @@ -194,7 +194,7 @@ "description": "Type: `string`, default: `gene_name`. Additional gene identifiers from the input GTF file when running Salmon", "help_text": "Type: `string`, default: `gene_name`. Additional gene identifiers from the input GTF file when running Salmon. More than one value can be specified separated by comma." , - "default": "gene_name" + "default":"gene_name" } @@ -205,7 +205,7 @@ "description": "Type: `string`, default: `gene_id`. Define the attribute type used to group features in the GTF file when running Salmon", "help_text": "Type: `string`, default: `gene_id`. Define the attribute type used to group features in the GTF file when running Salmon." , - "default": "gene_id" + "default":"gene_id" } @@ -216,7 +216,7 @@ "description": "Type: `string`, default: `gene_biotype`. The attribute type used to group feature types in the GTF file when generating the biotype plot with featureCounts", "help_text": "Type: `string`, default: `gene_biotype`. The attribute type used to group feature types in the GTF file when generating the biotype plot with featureCounts." , - "default": "gene_biotype" + "default":"gene_biotype" } @@ -227,7 +227,7 @@ "description": "Type: `string`, default: `exon`. By default, the pipeline assigns reads based on the \u0027exon\u0027 attribute within the GTF file", "help_text": "Type: `string`, default: `exon`. By default, the pipeline assigns reads based on the \u0027exon\u0027 attribute within the GTF file." , - "default": "exon" + "default":"exon" } @@ -250,7 +250,7 @@ "enum": ["trimgalore", "fastp"] , - "default": "trimgalore" + "default":"trimgalore" } @@ -281,7 +281,7 @@ "description": "Type: `integer`, default: `10000`. Minimum number of trimmed reads below which samples are removed from further processing", "help_text": "Type: `integer`, default: `10000`. Minimum number of trimmed reads below which samples are removed from further processing. Some downstream steps in the pipeline will fail if this threshold is too low." , - "default": "10000" + "default":10000 } @@ -322,7 +322,7 @@ "description": "Type: `boolean_true`, default: `false`. Enable the removal of reads derived from ribosomal RNA using SortMeRNA", "help_text": "Type: `boolean_true`, default: `false`. Enable the removal of reads derived from ribosomal RNA using SortMeRNA." , - "default": "False" + "default":false } @@ -333,7 +333,7 @@ "description": "Type: `file`, default: `src/assets/rrna-db-defaults.txt`. Text file containing paths to fasta files (one per line) that will be used to create the database for SortMeRNA", "help_text": "Type: `file`, default: `src/assets/rrna-db-defaults.txt`. Text file containing paths to fasta files (one per line) that will be used to create the database for SortMeRNA." , - "default": "src/assets/rrna-db-defaults.txt" + "default":"src/assets/rrna-db-defaults.txt" } @@ -354,7 +354,7 @@ "description": "Type: `boolean_true`, default: `false`. Enable UMI-based read deduplication", "help_text": "Type: `boolean_true`, default: `false`. Enable UMI-based read deduplication." , - "default": "False" + "default":false } @@ -367,7 +367,7 @@ "enum": ["string", "regex"] , - "default": "string" + "default":"string" } @@ -400,7 +400,7 @@ "enum": [0, 1, 2] , - "default": "0" + "default":0 } @@ -411,7 +411,7 @@ "description": "Type: `string`, default: `_`. The character that separates the UMI in the read name", "help_text": "Type: `string`, default: `_`. The character that separates the UMI in the read name. Most likely a colon if you skipped the extraction with UMI-tools and used other software." , - "default": "_" + "default":"_" } @@ -424,7 +424,7 @@ "enum": ["unique", "percentile", "cluster", "adjacency", "directional"] , - "default": "directional" + "default":"directional" } @@ -435,7 +435,7 @@ "description": "Type: `boolean_true`, default: `false`. Generate output stats when running \"umi_tools dedup\"", "help_text": "Type: `boolean_true`, default: `false`. Generate output stats when running \"umi_tools dedup\"." , - "default": "False" + "default":false } @@ -458,7 +458,7 @@ "enum": ["star_salmon", "star_rsem", "hisat2"] , - "default": "star_salmon" + "default":"star_salmon" } @@ -471,7 +471,7 @@ "enum": ["salmon", "kallisto"] , - "default": "salmon" + "default":"salmon" } @@ -482,7 +482,7 @@ "description": "Type: `integer`, default: `31`. Kmer length passed to indexing step of pseudoaligners", "help_text": "Type: `integer`, default: `31`. Kmer length passed to indexing step of pseudoaligners." , - "default": "31" + "default":31 } @@ -513,7 +513,7 @@ "description": "Type: `boolean_true`, default: `false`. Create a CSI index for BAM files instead of the traditional BAI index", "help_text": "Type: `boolean_true`, default: `false`. Create a CSI index for BAM files instead of the traditional BAI index. This will be required for genomes with larger chromosome sizes." , - "default": "False" + "default":false } @@ -534,7 +534,7 @@ "description": "Type: `string`, default: `-v`. Extra arguments to pass to salmon quant command in addition to defaults defined by the pipeline", "help_text": "Type: `string`, default: `-v`. Extra arguments to pass to salmon quant command in addition to defaults defined by the pipeline." , - "default": "-v" + "default":"-v" } @@ -545,7 +545,7 @@ "description": "Type: `integer`, default: `5`. Minimum percentage of uniquely mapped reads below which samples are removed from further processing", "help_text": "Type: `integer`, default: `5`. Minimum percentage of uniquely mapped reads below which samples are removed from further processing." , - "default": "5" + "default":5 } @@ -556,7 +556,7 @@ "description": "Type: `boolean_true`, default: `false`. Perform reference-guided de novo assembly of transcripts using StringTie, i", "help_text": "Type: `boolean_true`, default: `false`. Perform reference-guided de novo assembly of transcripts using StringTie, i.e. don\u0027t restrict to those in GTF file." , - "default": "False" + "default":false } @@ -567,7 +567,7 @@ "description": "Type: `string`, default: `-v`. Extra arguments to pass to stringtie command in addition to defaults defined by the pipeline", "help_text": "Type: `string`, default: `-v`. Extra arguments to pass to stringtie command in addition to defaults defined by the pipeline." , - "default": "-v" + "default":"-v" } @@ -578,7 +578,7 @@ "description": "Type: `boolean_true`, default: `false`. Where possible, save unaligned reads from either STAR, HISAT2 or Salmon to the results directory", "help_text": "Type: `boolean_true`, default: `false`. Where possible, save unaligned reads from either STAR, HISAT2 or Salmon to the results directory." , - "default": "False" + "default":false } @@ -589,7 +589,7 @@ "description": "Type: `boolean_true`, default: `false`. Save the intermediate BAM files from the alignment step", "help_text": "Type: `boolean_true`, default: `false`. Save the intermediate BAM files from the alignment step." , - "default": "False" + "default":false } @@ -600,7 +600,7 @@ "description": "Type: `boolean_true`, default: `false`. Skip all of the alignment-based processes within the pipeline", "help_text": "Type: `boolean_true`, default: `false`. Skip all of the alignment-based processes within the pipeline." , - "default": "False" + "default":false } @@ -611,7 +611,7 @@ "description": "Type: `boolean_true`, default: `false`. Skip all of the pseudo-alignment-based processes within the pipeline", "help_text": "Type: `boolean_true`, default: `false`. Skip all of the pseudo-alignment-based processes within the pipeline." , - "default": "False" + "default":false } @@ -622,7 +622,7 @@ "description": "Type: `string`, default: `--star --star-output-genome-bam --star-gzipped-read-file --estimate-rspd --seed 1`. Extra arguments to pass to rsem-calculate-expression command in addition to defaults defined by the pipeline", "help_text": "Type: `string`, default: `--star --star-output-genome-bam --star-gzipped-read-file --estimate-rspd --seed 1`. Extra arguments to pass to rsem-calculate-expression command in addition to defaults defined by the pipeline." , - "default": "--star --star-output-genome-bam --star-gzipped-read-file --estimate-rspd --seed 1" + "default":"--star --star-output-genome-bam --star-gzipped-read-file --estimate-rspd --seed 1" } @@ -643,7 +643,7 @@ "description": "Type: `boolean`, default: `false`. Skip FatQC step", "help_text": "Type: `boolean`, default: `false`. Skip FatQC step." , - "default": "False" + "default":false } @@ -654,7 +654,7 @@ "description": "Type: `boolean`, default: `false`. Skip the adapter trimming step", "help_text": "Type: `boolean`, default: `false`. Skip the adapter trimming step." , - "default": "False" + "default":false } @@ -665,7 +665,7 @@ "description": "Type: `boolean_true`, default: `false`. Skip BBSplit for removal of non-reference genome reads", "help_text": "Type: `boolean_true`, default: `false`. Skip BBSplit for removal of non-reference genome reads." , - "default": "False" + "default":false } @@ -676,7 +676,7 @@ "description": "Type: `boolean`, default: `false`. Skip umi_tools extract step", "help_text": "Type: `boolean`, default: `false`. Skip umi_tools extract step." , - "default": "False" + "default":false } @@ -687,7 +687,7 @@ "description": "Type: `boolean_true`, default: `false`. Skip all QC steps except for MultiQC", "help_text": "Type: `boolean_true`, default: `false`. Skip all QC steps except for MultiQC." , - "default": "False" + "default":false } @@ -698,7 +698,7 @@ "description": "Type: `boolean_true`, default: `false`. Skip picard MarkDuplicates step", "help_text": "Type: `boolean_true`, default: `false`. Skip picard MarkDuplicates step." , - "default": "False" + "default":false } @@ -709,7 +709,7 @@ "description": "Type: `boolean_true`, default: `false`. Skip StringTie", "help_text": "Type: `boolean_true`, default: `false`. Skip StringTie." , - "default": "False" + "default":false } @@ -720,7 +720,7 @@ "description": "Type: `boolean_true`, default: `false`. Skip additional featureCounts process for biotype QC", "help_text": "Type: `boolean_true`, default: `false`. Skip additional featureCounts process for biotype QC." , - "default": "False" + "default":false } @@ -731,7 +731,7 @@ "description": "Type: `boolean_true`, default: `false`. Skip bigWig file creation", "help_text": "Type: `boolean_true`, default: `false`. Skip bigWig file creation." , - "default": "False" + "default":false } @@ -742,7 +742,7 @@ "description": "Type: `boolean_true`, default: `false`. Skip Preseq", "help_text": "Type: `boolean_true`, default: `false`. Skip Preseq." , - "default": "False" + "default":false } @@ -753,7 +753,7 @@ "description": "Type: `boolean_true`, default: `false`. Skip DESeq2 PCA and heatmap plotting", "help_text": "Type: `boolean_true`, default: `false`. Skip DESeq2 PCA and heatmap plotting." , - "default": "False" + "default":false } @@ -764,7 +764,7 @@ "description": "Type: `boolean_true`, default: `false`. Skip dupRadar", "help_text": "Type: `boolean_true`, default: `false`. Skip dupRadar." , - "default": "False" + "default":false } @@ -775,7 +775,7 @@ "description": "Type: `boolean_true`, default: `false`. Skip Qualimap", "help_text": "Type: `boolean_true`, default: `false`. Skip Qualimap." , - "default": "False" + "default":false } @@ -786,7 +786,7 @@ "description": "Type: `boolean_true`, default: `false`. Skip RSeQC", "help_text": "Type: `boolean_true`, default: `false`. Skip RSeQC." , - "default": "False" + "default":false } @@ -797,7 +797,7 @@ "description": "Type: `boolean_true`, default: `false`. Skip MultiQC", "help_text": "Type: `boolean_true`, default: `false`. Skip MultiQC." , - "default": "False" + "default":false } @@ -818,7 +818,7 @@ "description": "Type: `string`, default: ` --record-count 1000000 --seed 1`. Extra arguments to pass to fq subsample command in addition to defaults defined by the pipeline", "help_text": "Type: `string`, default: ` --record-count 1000000 --seed 1`. Extra arguments to pass to fq subsample command in addition to defaults defined by the pipeline." , - "default": " --record-count 1000000 --seed 1" + "default":" --record-count 1000000 --seed 1" } @@ -829,7 +829,7 @@ "description": "Type: `string`, default: ` --ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp`. Extra arguments to pass to picard MarkDuplicates command in addition to defaults defined by the pipeline", "help_text": "Type: `string`, default: ` --ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp`. Extra arguments to pass to picard MarkDuplicates command in addition to defaults defined by the pipeline." , - "default": " --ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp" + "default":" --ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp" } @@ -840,7 +840,7 @@ "description": "Type: `string`, default: ` -split -du`. Extra arguments to pass to bedtools genomecov command in addition to defaults defined by the pipeline", "help_text": "Type: `string`, default: ` -split -du`. Extra arguments to pass to bedtools genomecov command in addition to defaults defined by the pipeline." , - "default": " -split -du" + "default":" -split -du" } @@ -851,7 +851,7 @@ "description": "Type: `string`, default: `-verbose -seed 1 -seg_len 100000000`. Extra arguments to pass to preseq lc_extrap command in addition to defaults defined by the pipeline", "help_text": "Type: `string`, default: `-verbose -seed 1 -seg_len 100000000`. Extra arguments to pass to preseq lc_extrap command in addition to defaults defined by the pipeline" , - "default": "-verbose -seed 1 -seg_len 100000000" + "default":"-verbose -seed 1 -seg_len 100000000" } @@ -862,7 +862,7 @@ "description": "Type: `boolean`, default: `true`. Use vst transformation instead of rlog with DESeq2", "help_text": "Type: `boolean`, default: `true`. Use vst transformation instead of rlog with DESeq2" , - "default": "True" + "default":true } @@ -871,11 +871,9 @@ "type": "string", "description": "Type: List of `string`, default: `bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication`, multiple_sep: `\",\"`, choices: ``bam_stat`, `inner_distance`, `infer_experiment`, `junction_annotation`, `junction_saturation`, `read_distribution`, `read_duplication`, `tin``. Specify the RSeQC modules to run_wf", - "help_text": "Type: List of `string`, default: `bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication`, multiple_sep: `\",\"`, choices: ``bam_stat`, `inner_distance`, `infer_experiment`, `junction_annotation`, `junction_saturation`, `read_distribution`, `read_duplication`, `tin``. Specify the RSeQC modules to run_wf", - "enum": ["bam_stat", "inner_distance", "infer_experiment", "junction_annotation", "junction_saturation", "read_distribution", "read_duplication", "tin"] - + "help_text": "Type: List of `string`, default: `bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication`, multiple_sep: `\",\"`, choices: ``bam_stat`, `inner_distance`, `infer_experiment`, `junction_annotation`, `junction_saturation`, `read_distribution`, `read_duplication`, `tin``. Specify the RSeQC modules to run_wf" , - "default": "bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication" + "default":"bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication" } @@ -896,7 +894,7 @@ "description": "Type: `file`, default: `src/assets/multiqc_config.yml`. ", "help_text": "Type: `file`, default: `src/assets/multiqc_config.yml`. " , - "default": "src/assets/multiqc_config.yml" + "default":"src/assets/multiqc_config.yml" } @@ -917,7 +915,7 @@ "description": "Type: `file`, default: `src/assets/methods_description_template.yml`. ", "help_text": "Type: `file`, default: `src/assets/methods_description_template.yml`. " , - "default": "src/assets/methods_description_template.yml" + "default":"src/assets/methods_description_template.yml" } @@ -938,7 +936,7 @@ "description": "Type: `file`, default: `$id.$key.output_fasta.fasta`. ", "help_text": "Type: `file`, default: `$id.$key.output_fasta.fasta`. " , - "default": "$id.$key.output_fasta.fasta" + "default":"$id.$key.output_fasta.fasta" } @@ -949,7 +947,7 @@ "description": "Type: `file`, default: `$id.$key.output_gtf.gtf`. ", "help_text": "Type: `file`, default: `$id.$key.output_gtf.gtf`. " , - "default": "$id.$key.output_gtf.gtf" + "default":"$id.$key.output_gtf.gtf" } @@ -960,7 +958,7 @@ "description": "Type: `file`, default: `$id.$key.output_transcript_fasta.fasta`. ", "help_text": "Type: `file`, default: `$id.$key.output_transcript_fasta.fasta`. " , - "default": "$id.$key.output_transcript_fasta.fasta" + "default":"$id.$key.output_transcript_fasta.fasta" } @@ -971,7 +969,7 @@ "description": "Type: `file`, default: `$id.$key.output_gene_bed.bed`. ", "help_text": "Type: `file`, default: `$id.$key.output_gene_bed.bed`. " , - "default": "$id.$key.output_gene_bed.bed" + "default":"$id.$key.output_gene_bed.bed" } @@ -982,7 +980,7 @@ "description": "Type: `file`, default: `$id.$key.output_star_index.output_star_index`. Path to STAR index", "help_text": "Type: `file`, default: `$id.$key.output_star_index.output_star_index`. Path to STAR index." , - "default": "$id.$key.output_star_index.output_star_index" + "default":"$id.$key.output_star_index.output_star_index" } @@ -993,7 +991,7 @@ "description": "Type: `file`, default: `$id.$key.output_salmon_index.output_salmon_index`. Path to Salmon index", "help_text": "Type: `file`, default: `$id.$key.output_salmon_index.output_salmon_index`. Path to Salmon index." , - "default": "$id.$key.output_salmon_index.output_salmon_index" + "default":"$id.$key.output_salmon_index.output_salmon_index" } @@ -1004,7 +1002,7 @@ "description": "Type: `file`, default: `$id.$key.output_bbsplit_index.output_bbsplit_index`. Path to BBSplit index", "help_text": "Type: `file`, default: `$id.$key.output_bbsplit_index.output_bbsplit_index`. Path to BBSplit index." , - "default": "$id.$key.output_bbsplit_index.output_bbsplit_index" + "default":"$id.$key.output_bbsplit_index.output_bbsplit_index" } @@ -1015,7 +1013,7 @@ "description": "Type: `file`, default: `$id.$key.output_kallisto_index.output_kallisto_index`. Path to Kallisto index", "help_text": "Type: `file`, default: `$id.$key.output_kallisto_index.output_kallisto_index`. Path to Kallisto index." , - "default": "$id.$key.output_kallisto_index.output_kallisto_index" + "default":"$id.$key.output_kallisto_index.output_kallisto_index" } @@ -1026,7 +1024,7 @@ "description": "Type: `file`, default: `$id.$key.output_fastq_1.fastq`. Path to output directory", "help_text": "Type: `file`, default: `$id.$key.output_fastq_1.fastq`. Path to output directory" , - "default": "$id.$key.output_fastq_1.fastq" + "default":"$id.$key.output_fastq_1.fastq" } @@ -1037,7 +1035,7 @@ "description": "Type: `file`, default: `$id.$key.output_fastq_2.fastq`. Path to output directory", "help_text": "Type: `file`, default: `$id.$key.output_fastq_2.fastq`. Path to output directory" , - "default": "$id.$key.output_fastq_2.fastq" + "default":"$id.$key.output_fastq_2.fastq" } @@ -1048,7 +1046,7 @@ "description": "Type: `file`, default: `$id.$key.fastqc_html_1.html`. FastQC HTML report for read 1", "help_text": "Type: `file`, default: `$id.$key.fastqc_html_1.html`. FastQC HTML report for read 1." , - "default": "$id.$key.fastqc_html_1.html" + "default":"$id.$key.fastqc_html_1.html" } @@ -1059,7 +1057,7 @@ "description": "Type: `file`, default: `$id.$key.fastqc_html_2.html`. FastQC HTML report for read 2", "help_text": "Type: `file`, default: `$id.$key.fastqc_html_2.html`. FastQC HTML report for read 2." , - "default": "$id.$key.fastqc_html_2.html" + "default":"$id.$key.fastqc_html_2.html" } @@ -1070,7 +1068,7 @@ "description": "Type: `file`, default: `$id.$key.fastqc_zip_1.zip`. FastQC report archive for read 1", "help_text": "Type: `file`, default: `$id.$key.fastqc_zip_1.zip`. FastQC report archive for read 1." , - "default": "$id.$key.fastqc_zip_1.zip" + "default":"$id.$key.fastqc_zip_1.zip" } @@ -1081,7 +1079,7 @@ "description": "Type: `file`, default: `$id.$key.fastqc_zip_2.zip`. FastQC report archive for read 2", "help_text": "Type: `file`, default: `$id.$key.fastqc_zip_2.zip`. FastQC report archive for read 2." , - "default": "$id.$key.fastqc_zip_2.zip" + "default":"$id.$key.fastqc_zip_2.zip" } @@ -1092,7 +1090,7 @@ "description": "Type: `file`, default: `$id.$key.trim_html_1.html`. ", "help_text": "Type: `file`, default: `$id.$key.trim_html_1.html`. " , - "default": "$id.$key.trim_html_1.html" + "default":"$id.$key.trim_html_1.html" } @@ -1103,7 +1101,7 @@ "description": "Type: `file`, default: `$id.$key.trim_html_2.html`. ", "help_text": "Type: `file`, default: `$id.$key.trim_html_2.html`. " , - "default": "$id.$key.trim_html_2.html" + "default":"$id.$key.trim_html_2.html" } @@ -1114,7 +1112,7 @@ "description": "Type: `file`, default: `$id.$key.trim_zip_1.zip`. ", "help_text": "Type: `file`, default: `$id.$key.trim_zip_1.zip`. " , - "default": "$id.$key.trim_zip_1.zip" + "default":"$id.$key.trim_zip_1.zip" } @@ -1125,7 +1123,7 @@ "description": "Type: `file`, default: `$id.$key.trim_zip_2.zip`. ", "help_text": "Type: `file`, default: `$id.$key.trim_zip_2.zip`. " , - "default": "$id.$key.trim_zip_2.zip" + "default":"$id.$key.trim_zip_2.zip" } @@ -1136,7 +1134,7 @@ "description": "Type: `file`, default: `$id.$key.trim_log_1.txt`. ", "help_text": "Type: `file`, default: `$id.$key.trim_log_1.txt`. " , - "default": "$id.$key.trim_log_1.txt" + "default":"$id.$key.trim_log_1.txt" } @@ -1147,7 +1145,7 @@ "description": "Type: `file`, default: `$id.$key.trim_log_2.txt`. ", "help_text": "Type: `file`, default: `$id.$key.trim_log_2.txt`. " , - "default": "$id.$key.trim_log_2.txt" + "default":"$id.$key.trim_log_2.txt" } @@ -1158,7 +1156,7 @@ "description": "Type: `file`, default: `$id.$key.fastp_trim_json.json`. The fastp json format report file name", "help_text": "Type: `file`, default: `$id.$key.fastp_trim_json.json`. The fastp json format report file name" , - "default": "$id.$key.fastp_trim_json.json" + "default":"$id.$key.fastp_trim_json.json" } @@ -1169,7 +1167,7 @@ "description": "Type: `file`, default: `$id.$key.fastp_trim_html.html`. The fastp html format report file name", "help_text": "Type: `file`, default: `$id.$key.fastp_trim_html.html`. The fastp html format report file name" , - "default": "$id.$key.fastp_trim_html.html" + "default":"$id.$key.fastp_trim_html.html" } @@ -1180,7 +1178,7 @@ "description": "Type: `file`, default: `$id.$key.sortmerna_log.log`. Sortmerna log file", "help_text": "Type: `file`, default: `$id.$key.sortmerna_log.log`. Sortmerna log file." , - "default": "$id.$key.sortmerna_log.log" + "default":"$id.$key.sortmerna_log.log" } @@ -1191,7 +1189,7 @@ "description": "Type: `file`, default: `$id.$key.star_alignment.star_alignment`. ", "help_text": "Type: `file`, default: `$id.$key.star_alignment.star_alignment`. " , - "default": "$id.$key.star_alignment.star_alignment" + "default":"$id.$key.star_alignment.star_alignment" } @@ -1202,7 +1200,7 @@ "description": "Type: `file`, default: `$id.$key.genome_bam_sorted.bam`. ", "help_text": "Type: `file`, default: `$id.$key.genome_bam_sorted.bam`. " , - "default": "$id.$key.genome_bam_sorted.bam" + "default":"$id.$key.genome_bam_sorted.bam" } @@ -1213,7 +1211,7 @@ "description": "Type: `file`, default: `$id.$key.genome_bam_index.bai`. ", "help_text": "Type: `file`, default: `$id.$key.genome_bam_index.bai`. " , - "default": "$id.$key.genome_bam_index.bai" + "default":"$id.$key.genome_bam_index.bai" } @@ -1224,7 +1222,7 @@ "description": "Type: `file`, default: `$id.$key.transcriptome_bam.bam`. ", "help_text": "Type: `file`, default: `$id.$key.transcriptome_bam.bam`. " , - "default": "$id.$key.transcriptome_bam.bam" + "default":"$id.$key.transcriptome_bam.bam" } @@ -1235,7 +1233,7 @@ "description": "Type: `file`, default: `$id.$key.transcriptome_bam_index.bai`. ", "help_text": "Type: `file`, default: `$id.$key.transcriptome_bam_index.bai`. " , - "default": "$id.$key.transcriptome_bam_index.bai" + "default":"$id.$key.transcriptome_bam_index.bai" } @@ -1246,7 +1244,7 @@ "description": "Type: `file`, default: `$id.$key.star_log.log`. ", "help_text": "Type: `file`, default: `$id.$key.star_log.log`. " , - "default": "$id.$key.star_log.log" + "default":"$id.$key.star_log.log" } @@ -1257,7 +1255,7 @@ "description": "Type: `file`, default: `$id.$key.genome_bam_stats.stats`. ", "help_text": "Type: `file`, default: `$id.$key.genome_bam_stats.stats`. " , - "default": "$id.$key.genome_bam_stats.stats" + "default":"$id.$key.genome_bam_stats.stats" } @@ -1268,7 +1266,7 @@ "description": "Type: `file`, default: `$id.$key.genome_bam_flagstat.flagstat`. ", "help_text": "Type: `file`, default: `$id.$key.genome_bam_flagstat.flagstat`. " , - "default": "$id.$key.genome_bam_flagstat.flagstat" + "default":"$id.$key.genome_bam_flagstat.flagstat" } @@ -1279,7 +1277,7 @@ "description": "Type: `file`, default: `$id.$key.genome_bam_idxstats.idxstats`. ", "help_text": "Type: `file`, default: `$id.$key.genome_bam_idxstats.idxstats`. " , - "default": "$id.$key.genome_bam_idxstats.idxstats" + "default":"$id.$key.genome_bam_idxstats.idxstats" } @@ -1290,7 +1288,7 @@ "description": "Type: `file`, default: `$id.$key.transcriptome_bam_stats.stats`. ", "help_text": "Type: `file`, default: `$id.$key.transcriptome_bam_stats.stats`. " , - "default": "$id.$key.transcriptome_bam_stats.stats" + "default":"$id.$key.transcriptome_bam_stats.stats" } @@ -1301,7 +1299,7 @@ "description": "Type: `file`, default: `$id.$key.transcriptome_bam_flagstat.flagstat`. ", "help_text": "Type: `file`, default: `$id.$key.transcriptome_bam_flagstat.flagstat`. " , - "default": "$id.$key.transcriptome_bam_flagstat.flagstat" + "default":"$id.$key.transcriptome_bam_flagstat.flagstat" } @@ -1312,7 +1310,7 @@ "description": "Type: `file`, default: `$id.$key.transcriptome_bam_idxstats.idxstats`. ", "help_text": "Type: `file`, default: `$id.$key.transcriptome_bam_idxstats.idxstats`. " , - "default": "$id.$key.transcriptome_bam_idxstats.idxstats" + "default":"$id.$key.transcriptome_bam_idxstats.idxstats" } @@ -1323,7 +1321,7 @@ "description": "Type: `file`, default: `$id.$key.salmon_quant_results.salmon_quant_results`. ", "help_text": "Type: `file`, default: `$id.$key.salmon_quant_results.salmon_quant_results`. " , - "default": "$id.$key.salmon_quant_results.salmon_quant_results" + "default":"$id.$key.salmon_quant_results.salmon_quant_results" } @@ -1334,7 +1332,7 @@ "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" + "default":"$id.$key.salmon_quant_results_file.sf" } @@ -1345,7 +1343,7 @@ "description": "Type: `file`, default: `$id.$key.pseudo_quant_results.pseudo_quant_results`. ", "help_text": "Type: `file`, default: `$id.$key.pseudo_quant_results.pseudo_quant_results`. " , - "default": "$id.$key.pseudo_quant_results.pseudo_quant_results" + "default":"$id.$key.pseudo_quant_results.pseudo_quant_results" } @@ -1356,7 +1354,7 @@ "description": "Type: `file`, default: `$id.$key.rsem_counts_gene.results`. Expression counts on gene level", "help_text": "Type: `file`, default: `$id.$key.rsem_counts_gene.results`. Expression counts on gene level" , - "default": "$id.$key.rsem_counts_gene.results" + "default":"$id.$key.rsem_counts_gene.results" } @@ -1367,7 +1365,7 @@ "description": "Type: `file`, default: `$id.$key.rsem_counts_transcripts.results`. Expression counts on transcript level", "help_text": "Type: `file`, default: `$id.$key.rsem_counts_transcripts.results`. Expression counts on transcript level" , - "default": "$id.$key.rsem_counts_transcripts.results" + "default":"$id.$key.rsem_counts_transcripts.results" } @@ -1378,7 +1376,7 @@ "description": "Type: `file`, default: `$id.$key.bam_star_rsem.bam`. BAM file generated by STAR (from RSEM)", "help_text": "Type: `file`, default: `$id.$key.bam_star_rsem.bam`. BAM file generated by STAR (from RSEM)" , - "default": "$id.$key.bam_star_rsem.bam" + "default":"$id.$key.bam_star_rsem.bam" } @@ -1389,7 +1387,7 @@ "description": "Type: `file`, default: `$id.$key.bam_genome_rsem.bam`. Genome BAM file (from RSEM)", "help_text": "Type: `file`, default: `$id.$key.bam_genome_rsem.bam`. Genome BAM file (from RSEM)" , - "default": "$id.$key.bam_genome_rsem.bam" + "default":"$id.$key.bam_genome_rsem.bam" } @@ -1400,7 +1398,7 @@ "description": "Type: `file`, default: `$id.$key.bam_transcript_rsem.bam`. Transcript BAM file (from RSEM)", "help_text": "Type: `file`, default: `$id.$key.bam_transcript_rsem.bam`. Transcript BAM file (from RSEM)" , - "default": "$id.$key.bam_transcript_rsem.bam" + "default":"$id.$key.bam_transcript_rsem.bam" } @@ -1411,7 +1409,7 @@ "description": "Type: `file`, default: `$id.$key.tpm_gene.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.tpm_gene.tsv`. " , - "default": "$id.$key.tpm_gene.tsv" + "default":"$id.$key.tpm_gene.tsv" } @@ -1422,7 +1420,7 @@ "description": "Type: `file`, default: `$id.$key.counts_gene.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.counts_gene.tsv`. " , - "default": "$id.$key.counts_gene.tsv" + "default":"$id.$key.counts_gene.tsv" } @@ -1433,7 +1431,7 @@ "description": "Type: `file`, default: `$id.$key.counts_gene_length_scaled.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.counts_gene_length_scaled.tsv`. " , - "default": "$id.$key.counts_gene_length_scaled.tsv" + "default":"$id.$key.counts_gene_length_scaled.tsv" } @@ -1444,7 +1442,7 @@ "description": "Type: `file`, default: `$id.$key.counts_gene_scaled.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.counts_gene_scaled.tsv`. " , - "default": "$id.$key.counts_gene_scaled.tsv" + "default":"$id.$key.counts_gene_scaled.tsv" } @@ -1455,7 +1453,7 @@ "description": "Type: `file`, default: `$id.$key.tpm_transcript.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.tpm_transcript.tsv`. " , - "default": "$id.$key.tpm_transcript.tsv" + "default":"$id.$key.tpm_transcript.tsv" } @@ -1466,7 +1464,7 @@ "description": "Type: `file`, default: `$id.$key.counts_transcript.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.counts_transcript.tsv`. " , - "default": "$id.$key.counts_transcript.tsv" + "default":"$id.$key.counts_transcript.tsv" } @@ -1477,7 +1475,7 @@ "description": "Type: `file`, default: `$id.$key.quant_merged_summarizedexperiment.quant_merged_summarizedexperiment`. ", "help_text": "Type: `file`, default: `$id.$key.quant_merged_summarizedexperiment.quant_merged_summarizedexperiment`. " , - "default": "$id.$key.quant_merged_summarizedexperiment.quant_merged_summarizedexperiment" + "default":"$id.$key.quant_merged_summarizedexperiment.quant_merged_summarizedexperiment" } @@ -1488,7 +1486,7 @@ "description": "Type: `file`, default: `$id.$key.markduplicates_metrics.txt`. ", "help_text": "Type: `file`, default: `$id.$key.markduplicates_metrics.txt`. " , - "default": "$id.$key.markduplicates_metrics.txt" + "default":"$id.$key.markduplicates_metrics.txt" } @@ -1499,7 +1497,7 @@ "description": "Type: `file`, default: `$id.$key.stringtie_transcript_gtf.gtf`. ", "help_text": "Type: `file`, default: `$id.$key.stringtie_transcript_gtf.gtf`. " , - "default": "$id.$key.stringtie_transcript_gtf.gtf" + "default":"$id.$key.stringtie_transcript_gtf.gtf" } @@ -1510,7 +1508,7 @@ "description": "Type: `file`, default: `$id.$key.stringtie_coverage_gtf.gtf`. ", "help_text": "Type: `file`, default: `$id.$key.stringtie_coverage_gtf.gtf`. " , - "default": "$id.$key.stringtie_coverage_gtf.gtf" + "default":"$id.$key.stringtie_coverage_gtf.gtf" } @@ -1521,7 +1519,7 @@ "description": "Type: `file`, default: `$id.$key.stringtie_abundance.txt`. ", "help_text": "Type: `file`, default: `$id.$key.stringtie_abundance.txt`. " , - "default": "$id.$key.stringtie_abundance.txt" + "default":"$id.$key.stringtie_abundance.txt" } @@ -1532,7 +1530,7 @@ "description": "Type: `file`, default: `$id.$key.stringtie_ballgown.ballgown`. ", "help_text": "Type: `file`, default: `$id.$key.stringtie_ballgown.ballgown`. " , - "default": "$id.$key.stringtie_ballgown.ballgown" + "default":"$id.$key.stringtie_ballgown.ballgown" } @@ -1543,7 +1541,7 @@ "description": "Type: `file`, default: `$id.$key.featurecounts.txt`. ", "help_text": "Type: `file`, default: `$id.$key.featurecounts.txt`. " , - "default": "$id.$key.featurecounts.txt" + "default":"$id.$key.featurecounts.txt" } @@ -1554,7 +1552,7 @@ "description": "Type: `file`, default: `$id.$key.featurecounts_summary.summary`. ", "help_text": "Type: `file`, default: `$id.$key.featurecounts_summary.summary`. " , - "default": "$id.$key.featurecounts_summary.summary" + "default":"$id.$key.featurecounts_summary.summary" } @@ -1565,7 +1563,7 @@ "description": "Type: `file`, default: `$id.$key.featurecounts_multiqc.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.featurecounts_multiqc.tsv`. " , - "default": "$id.$key.featurecounts_multiqc.tsv" + "default":"$id.$key.featurecounts_multiqc.tsv" } @@ -1576,7 +1574,7 @@ "description": "Type: `file`, default: `$id.$key.featurecounts_rrna_multiqc.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.featurecounts_rrna_multiqc.tsv`. " , - "default": "$id.$key.featurecounts_rrna_multiqc.tsv" + "default":"$id.$key.featurecounts_rrna_multiqc.tsv" } @@ -1587,7 +1585,7 @@ "description": "Type: `file`, default: `$id.$key.bedgraph_forward.bedgraph`. ", "help_text": "Type: `file`, default: `$id.$key.bedgraph_forward.bedgraph`. " , - "default": "$id.$key.bedgraph_forward.bedgraph" + "default":"$id.$key.bedgraph_forward.bedgraph" } @@ -1598,7 +1596,7 @@ "description": "Type: `file`, default: `$id.$key.bedgraph_reverse.bedgraph`. ", "help_text": "Type: `file`, default: `$id.$key.bedgraph_reverse.bedgraph`. " , - "default": "$id.$key.bedgraph_reverse.bedgraph" + "default":"$id.$key.bedgraph_reverse.bedgraph" } @@ -1609,7 +1607,7 @@ "description": "Type: `file`, default: `$id.$key.bigwig_forward.bigwig`. ", "help_text": "Type: `file`, default: `$id.$key.bigwig_forward.bigwig`. " , - "default": "$id.$key.bigwig_forward.bigwig" + "default":"$id.$key.bigwig_forward.bigwig" } @@ -1620,7 +1618,7 @@ "description": "Type: `file`, default: `$id.$key.bigwig_reverse.bigwig`. ", "help_text": "Type: `file`, default: `$id.$key.bigwig_reverse.bigwig`. " , - "default": "$id.$key.bigwig_reverse.bigwig" + "default":"$id.$key.bigwig_reverse.bigwig" } @@ -1631,7 +1629,7 @@ "description": "Type: `file`, default: `$id.$key.preseq_output.txt`. ", "help_text": "Type: `file`, default: `$id.$key.preseq_output.txt`. " , - "default": "$id.$key.preseq_output.txt" + "default":"$id.$key.preseq_output.txt" } @@ -1642,7 +1640,7 @@ "description": "Type: `file`, default: `$id.$key.bamstat_output.txt`. Path to output file (txt) of mapping quality statistics", "help_text": "Type: `file`, default: `$id.$key.bamstat_output.txt`. Path to output file (txt) of mapping quality statistics" , - "default": "$id.$key.bamstat_output.txt" + "default":"$id.$key.bamstat_output.txt" } @@ -1653,7 +1651,7 @@ "description": "Type: `file`, default: `$id.$key.strandedness_output.txt`. Path to output report (txt) of inferred strandedness", "help_text": "Type: `file`, default: `$id.$key.strandedness_output.txt`. Path to output report (txt) of inferred strandedness" , - "default": "$id.$key.strandedness_output.txt" + "default":"$id.$key.strandedness_output.txt" } @@ -1664,7 +1662,7 @@ "description": "Type: `file`, default: `$id.$key.inner_dist_output_stats.stats`. output file (txt) with summary statistics of inner distances of paired reads", "help_text": "Type: `file`, default: `$id.$key.inner_dist_output_stats.stats`. output file (txt) with summary statistics of inner distances of paired reads" , - "default": "$id.$key.inner_dist_output_stats.stats" + "default":"$id.$key.inner_dist_output_stats.stats" } @@ -1675,7 +1673,7 @@ "description": "Type: `file`, default: `$id.$key.inner_dist_output_dist.txt`. output file (txt) with inner distances of all paired reads", "help_text": "Type: `file`, default: `$id.$key.inner_dist_output_dist.txt`. output file (txt) with inner distances of all paired reads" , - "default": "$id.$key.inner_dist_output_dist.txt" + "default":"$id.$key.inner_dist_output_dist.txt" } @@ -1686,7 +1684,7 @@ "description": "Type: `file`, default: `$id.$key.inner_dist_output_freq.txt`. output file (txt) with frequencies of inner distances of all paired reads", "help_text": "Type: `file`, default: `$id.$key.inner_dist_output_freq.txt`. output file (txt) with frequencies of inner distances of all paired reads" , - "default": "$id.$key.inner_dist_output_freq.txt" + "default":"$id.$key.inner_dist_output_freq.txt" } @@ -1697,7 +1695,7 @@ "description": "Type: `file`, default: `$id.$key.inner_dist_output_plot.pdf`. output file (pdf) with histogram plot of of inner distances of all paired reads", "help_text": "Type: `file`, default: `$id.$key.inner_dist_output_plot.pdf`. output file (pdf) with histogram plot of of inner distances of all paired reads" , - "default": "$id.$key.inner_dist_output_plot.pdf" + "default":"$id.$key.inner_dist_output_plot.pdf" } @@ -1708,7 +1706,7 @@ "description": "Type: `file`, default: `$id.$key.inner_dist_output_plot_r.r`. output file (R) with script of histogram plot of of inner distances of all paired reads", "help_text": "Type: `file`, default: `$id.$key.inner_dist_output_plot_r.r`. output file (R) with script of histogram plot of of inner distances of all paired reads" , - "default": "$id.$key.inner_dist_output_plot_r.r" + "default":"$id.$key.inner_dist_output_plot_r.r" } @@ -1719,7 +1717,7 @@ "description": "Type: `file`, default: `$id.$key.junction_annotation_output_log.log`. output log of junction annotation script", "help_text": "Type: `file`, default: `$id.$key.junction_annotation_output_log.log`. output log of junction annotation script" , - "default": "$id.$key.junction_annotation_output_log.log" + "default":"$id.$key.junction_annotation_output_log.log" } @@ -1730,7 +1728,7 @@ "description": "Type: `file`, default: `$id.$key.junction_annotation_output_plot_r.r`. R script to generate splice_junction and splice_events plot", "help_text": "Type: `file`, default: `$id.$key.junction_annotation_output_plot_r.r`. R script to generate splice_junction and splice_events plot" , - "default": "$id.$key.junction_annotation_output_plot_r.r" + "default":"$id.$key.junction_annotation_output_plot_r.r" } @@ -1741,7 +1739,7 @@ "description": "Type: `file`, default: `$id.$key.junction_annotation_output_junction_bed.bed`. junction annotation file (bed format)", "help_text": "Type: `file`, default: `$id.$key.junction_annotation_output_junction_bed.bed`. junction annotation file (bed format)" , - "default": "$id.$key.junction_annotation_output_junction_bed.bed" + "default":"$id.$key.junction_annotation_output_junction_bed.bed" } @@ -1752,7 +1750,7 @@ "description": "Type: `file`, default: `$id.$key.junction_annotation_output_junction_interact.bed`. interact file (bed format) of junctions", "help_text": "Type: `file`, default: `$id.$key.junction_annotation_output_junction_interact.bed`. interact file (bed format) of junctions. Can be uploaded to UCSC genome browser or converted to bigInteract (using bedToBigBed program) for visualization." , - "default": "$id.$key.junction_annotation_output_junction_interact.bed" + "default":"$id.$key.junction_annotation_output_junction_interact.bed" } @@ -1763,7 +1761,7 @@ "description": "Type: `file`, default: `$id.$key.junction_annotation_output_junction_sheet.xls`. junction annotation file (xls format)", "help_text": "Type: `file`, default: `$id.$key.junction_annotation_output_junction_sheet.xls`. junction annotation file (xls format)" , - "default": "$id.$key.junction_annotation_output_junction_sheet.xls" + "default":"$id.$key.junction_annotation_output_junction_sheet.xls" } @@ -1774,7 +1772,7 @@ "description": "Type: `file`, default: `$id.$key.junction_annotation_output_splice_events_plot.pdf`. plot of splice events (pdf)", "help_text": "Type: `file`, default: `$id.$key.junction_annotation_output_splice_events_plot.pdf`. plot of splice events (pdf)" , - "default": "$id.$key.junction_annotation_output_splice_events_plot.pdf" + "default":"$id.$key.junction_annotation_output_splice_events_plot.pdf" } @@ -1785,7 +1783,7 @@ "description": "Type: `file`, default: `$id.$key.junction_annotation_output_splice_junctions_plot.pdf`. plot of junctions (pdf)", "help_text": "Type: `file`, default: `$id.$key.junction_annotation_output_splice_junctions_plot.pdf`. plot of junctions (pdf)" , - "default": "$id.$key.junction_annotation_output_splice_junctions_plot.pdf" + "default":"$id.$key.junction_annotation_output_splice_junctions_plot.pdf" } @@ -1796,7 +1794,7 @@ "description": "Type: `file`, default: `$id.$key.junction_saturation_output_plot_r.r`. r script to generate junction_saturation_plot plot", "help_text": "Type: `file`, default: `$id.$key.junction_saturation_output_plot_r.r`. r script to generate junction_saturation_plot plot" , - "default": "$id.$key.junction_saturation_output_plot_r.r" + "default":"$id.$key.junction_saturation_output_plot_r.r" } @@ -1807,7 +1805,7 @@ "description": "Type: `file`, default: `$id.$key.junction_saturation_output_plot.pdf`. plot of junction saturation (pdf", "help_text": "Type: `file`, default: `$id.$key.junction_saturation_output_plot.pdf`. plot of junction saturation (pdf" , - "default": "$id.$key.junction_saturation_output_plot.pdf" + "default":"$id.$key.junction_saturation_output_plot.pdf" } @@ -1818,7 +1816,7 @@ "description": "Type: `file`, default: `$id.$key.read_distribution_output.txt`. output file (txt) of read distribution analysis", "help_text": "Type: `file`, default: `$id.$key.read_distribution_output.txt`. output file (txt) of read distribution analysis." , - "default": "$id.$key.read_distribution_output.txt" + "default":"$id.$key.read_distribution_output.txt" } @@ -1829,7 +1827,7 @@ "description": "Type: `file`, default: `$id.$key.read_duplication_output_duplication_rate_plot_r.r`. R script for generating duplication rate plot", "help_text": "Type: `file`, default: `$id.$key.read_duplication_output_duplication_rate_plot_r.r`. R script for generating duplication rate plot" , - "default": "$id.$key.read_duplication_output_duplication_rate_plot_r.r" + "default":"$id.$key.read_duplication_output_duplication_rate_plot_r.r" } @@ -1840,7 +1838,7 @@ "description": "Type: `file`, default: `$id.$key.read_duplication_output_duplication_rate_plot.pdf`. duplication rate plot (pdf)", "help_text": "Type: `file`, default: `$id.$key.read_duplication_output_duplication_rate_plot.pdf`. duplication rate plot (pdf)" , - "default": "$id.$key.read_duplication_output_duplication_rate_plot.pdf" + "default":"$id.$key.read_duplication_output_duplication_rate_plot.pdf" } @@ -1851,7 +1849,7 @@ "description": "Type: `file`, default: `$id.$key.read_duplication_output_duplication_rate_mapping.xls`. Summary of mapping-based read duplication", "help_text": "Type: `file`, default: `$id.$key.read_duplication_output_duplication_rate_mapping.xls`. Summary of mapping-based read duplication" , - "default": "$id.$key.read_duplication_output_duplication_rate_mapping.xls" + "default":"$id.$key.read_duplication_output_duplication_rate_mapping.xls" } @@ -1862,7 +1860,7 @@ "description": "Type: `file`, default: `$id.$key.read_duplication_output_duplication_rate_sequence.xls`. Summary of sequencing-based read duplication", "help_text": "Type: `file`, default: `$id.$key.read_duplication_output_duplication_rate_sequence.xls`. Summary of sequencing-based read duplication" , - "default": "$id.$key.read_duplication_output_duplication_rate_sequence.xls" + "default":"$id.$key.read_duplication_output_duplication_rate_sequence.xls" } @@ -1873,7 +1871,7 @@ "description": "Type: `file`, default: `$id.$key.tin_output_summary.txt`. summary statistics (txt) of calculated TIN metrics", "help_text": "Type: `file`, default: `$id.$key.tin_output_summary.txt`. summary statistics (txt) of calculated TIN metrics" , - "default": "$id.$key.tin_output_summary.txt" + "default":"$id.$key.tin_output_summary.txt" } @@ -1884,7 +1882,7 @@ "description": "Type: `file`, default: `$id.$key.tin_output_metrics.xls`. file with TIN metrics (xls)", "help_text": "Type: `file`, default: `$id.$key.tin_output_metrics.xls`. file with TIN metrics (xls)" , - "default": "$id.$key.tin_output_metrics.xls" + "default":"$id.$key.tin_output_metrics.xls" } @@ -1895,7 +1893,7 @@ "description": "Type: `file`, default: `$id.$key.dupradar_output_dupmatrix.txt`. path to output file (txt) of duplicate tag counts", "help_text": "Type: `file`, default: `$id.$key.dupradar_output_dupmatrix.txt`. path to output file (txt) of duplicate tag counts" , - "default": "$id.$key.dupradar_output_dupmatrix.txt" + "default":"$id.$key.dupradar_output_dupmatrix.txt" } @@ -1906,7 +1904,7 @@ "description": "Type: `file`, default: `$id.$key.dupradar_output_dup_intercept_mqc.txt`. path to output file (txt) of multiqc intercept value DupRadar", "help_text": "Type: `file`, default: `$id.$key.dupradar_output_dup_intercept_mqc.txt`. path to output file (txt) of multiqc intercept value DupRadar" , - "default": "$id.$key.dupradar_output_dup_intercept_mqc.txt" + "default":"$id.$key.dupradar_output_dup_intercept_mqc.txt" } @@ -1917,7 +1915,7 @@ "description": "Type: `file`, default: `$id.$key.dupradar_output_duprate_exp_boxplot.pdf`. path to output file (pdf) of distribution of expression box plot", "help_text": "Type: `file`, default: `$id.$key.dupradar_output_duprate_exp_boxplot.pdf`. path to output file (pdf) of distribution of expression box plot" , - "default": "$id.$key.dupradar_output_duprate_exp_boxplot.pdf" + "default":"$id.$key.dupradar_output_duprate_exp_boxplot.pdf" } @@ -1928,7 +1926,7 @@ "description": "Type: `file`, default: `$id.$key.dupradar_output_duprate_exp_densplot.pdf`. path to output file (pdf) of 2D density scatter plot of duplicate tag counts", "help_text": "Type: `file`, default: `$id.$key.dupradar_output_duprate_exp_densplot.pdf`. path to output file (pdf) of 2D density scatter plot of duplicate tag counts" , - "default": "$id.$key.dupradar_output_duprate_exp_densplot.pdf" + "default":"$id.$key.dupradar_output_duprate_exp_densplot.pdf" } @@ -1939,7 +1937,7 @@ "description": "Type: `file`, default: `$id.$key.dupradar_output_duprate_exp_denscurve_mqc.pdf`. path to output file (pdf) of density curve of gene duplication multiqc", "help_text": "Type: `file`, default: `$id.$key.dupradar_output_duprate_exp_denscurve_mqc.pdf`. path to output file (pdf) of density curve of gene duplication multiqc" , - "default": "$id.$key.dupradar_output_duprate_exp_denscurve_mqc.pdf" + "default":"$id.$key.dupradar_output_duprate_exp_denscurve_mqc.pdf" } @@ -1950,7 +1948,7 @@ "description": "Type: `file`, default: `$id.$key.dupradar_output_expression_histogram.pdf`. path to output file (pdf) of distribution of RPK values per gene histogram", "help_text": "Type: `file`, default: `$id.$key.dupradar_output_expression_histogram.pdf`. path to output file (pdf) of distribution of RPK values per gene histogram" , - "default": "$id.$key.dupradar_output_expression_histogram.pdf" + "default":"$id.$key.dupradar_output_expression_histogram.pdf" } @@ -1961,7 +1959,7 @@ "description": "Type: `file`, default: `$id.$key.dupradar_output_intercept_slope.txt`. ", "help_text": "Type: `file`, default: `$id.$key.dupradar_output_intercept_slope.txt`. " , - "default": "$id.$key.dupradar_output_intercept_slope.txt" + "default":"$id.$key.dupradar_output_intercept_slope.txt" } @@ -1972,7 +1970,7 @@ "description": "Type: `file`, default: `$id.$key.qualimap_output_pdf.pdf`. ", "help_text": "Type: `file`, default: `$id.$key.qualimap_output_pdf.pdf`. " , - "default": "$id.$key.qualimap_output_pdf.pdf" + "default":"$id.$key.qualimap_output_pdf.pdf" } @@ -1983,7 +1981,7 @@ "description": "Type: `file`, default: `$id.$key.qualimap_output_dir.qualimap_output_dir`. ", "help_text": "Type: `file`, default: `$id.$key.qualimap_output_dir.qualimap_output_dir`. " , - "default": "$id.$key.qualimap_output_dir.qualimap_output_dir" + "default":"$id.$key.qualimap_output_dir.qualimap_output_dir" } @@ -1994,7 +1992,7 @@ "description": "Type: `file`, default: `$id.$key.deseq2_output.deseq2_output`. ", "help_text": "Type: `file`, default: `$id.$key.deseq2_output.deseq2_output`. " , - "default": "$id.$key.deseq2_output.deseq2_output" + "default":"$id.$key.deseq2_output.deseq2_output" } @@ -2005,7 +2003,7 @@ "description": "Type: `file`, default: `$id.$key.multiqc_report.html`. ", "help_text": "Type: `file`, default: `$id.$key.multiqc_report.html`. " , - "default": "$id.$key.multiqc_report.html" + "default":"$id.$key.multiqc_report.html" } @@ -2016,7 +2014,7 @@ "description": "Type: `file`, default: `$id.$key.multiqc_data.multiqc_data`. ", "help_text": "Type: `file`, default: `$id.$key.multiqc_data.multiqc_data`. " , - "default": "$id.$key.multiqc_data.multiqc_data" + "default":"$id.$key.multiqc_data.multiqc_data" } @@ -2027,7 +2025,7 @@ "description": "Type: `file`, default: `$id.$key.multiqc_plots.multiqc_plots`. ", "help_text": "Type: `file`, default: `$id.$key.multiqc_plots.multiqc_plots`. " , - "default": "$id.$key.multiqc_plots.multiqc_plots" + "default":"$id.$key.multiqc_plots.multiqc_plots" } @@ -2038,7 +2036,7 @@ "description": "Type: `file`, default: `$id.$key.multiqc_versions.multiqc_versions`. ", "help_text": "Type: `file`, default: `$id.$key.multiqc_versions.multiqc_versions`. " , - "default": "$id.$key.multiqc_versions.multiqc_versions" + "default":"$id.$key.multiqc_versions.multiqc_versions" } @@ -2049,7 +2047,7 @@ "description": "Type: `file`, default: `$id.$key.pseudo_counts_gene.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.pseudo_counts_gene.tsv`. " , - "default": "$id.$key.pseudo_counts_gene.tsv" + "default":"$id.$key.pseudo_counts_gene.tsv" } @@ -2060,7 +2058,7 @@ "description": "Type: `file`, default: `$id.$key.pseudo_counts_gene_length_scaled.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.pseudo_counts_gene_length_scaled.tsv`. " , - "default": "$id.$key.pseudo_counts_gene_length_scaled.tsv" + "default":"$id.$key.pseudo_counts_gene_length_scaled.tsv" } @@ -2071,7 +2069,7 @@ "description": "Type: `file`, default: `$id.$key.pseudo_counts_gene_scaled.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.pseudo_counts_gene_scaled.tsv`. " , - "default": "$id.$key.pseudo_counts_gene_scaled.tsv" + "default":"$id.$key.pseudo_counts_gene_scaled.tsv" } @@ -2082,7 +2080,7 @@ "description": "Type: `file`, default: `$id.$key.pseudo_tpm_transcript.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.pseudo_tpm_transcript.tsv`. " , - "default": "$id.$key.pseudo_tpm_transcript.tsv" + "default":"$id.$key.pseudo_tpm_transcript.tsv" } @@ -2093,7 +2091,7 @@ "description": "Type: `file`, default: `$id.$key.pseudo_counts_transcript.tsv`. ", "help_text": "Type: `file`, default: `$id.$key.pseudo_counts_transcript.tsv`. " , - "default": "$id.$key.pseudo_counts_transcript.tsv" + "default":"$id.$key.pseudo_counts_transcript.tsv" } @@ -2104,7 +2102,7 @@ "description": "Type: `file`, default: `$id.$key.pseudo_quant_merged_summarizedexperiment.pseudo_quant_merged_summarizedexperiment`. ", "help_text": "Type: `file`, default: `$id.$key.pseudo_quant_merged_summarizedexperiment.pseudo_quant_merged_summarizedexperiment`. " , - "default": "$id.$key.pseudo_quant_merged_summarizedexperiment.pseudo_quant_merged_summarizedexperiment" + "default":"$id.$key.pseudo_quant_merged_summarizedexperiment.pseudo_quant_merged_summarizedexperiment" }