From 2589a59c53236edbf90cd85791d131784aedc974 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Thu, 27 Jun 2024 04:04:45 +0000 Subject: [PATCH 1/3] Updated .dockstore.yml and packed json to include /home/runner/work/cwl-ica/cwl-ica/workflows/dragen-transcriptome-pipeline/4.2.4/dragen-transcriptome-pipeline__4.2.4.cwl with tags dragen-transcriptome-pipeline/4.2.4, dragen-transcriptome-pipeline/4.2.4__20240627040250 --- .dockstore.yml | 13 + ...nscriptome-pipeline__4.2.4.packed.cwl.json | 2500 +++++++++++++++++ 2 files changed, 2513 insertions(+) create mode 100644 .dockstore/dragen-transcriptome-pipeline/4.2.4/dragen-transcriptome-pipeline__4.2.4.packed.cwl.json diff --git a/.dockstore.yml b/.dockstore.yml index d3550d81..564edfe4 100644 --- a/.dockstore.yml +++ b/.dockstore.yml @@ -57,3 +57,16 @@ workflows: tags: - dragen-alignment-pipeline/4.2.4 - dragen-alignment-pipeline/4.2.4__20240627030935 + - name: dragen-transcriptome-pipeline_4_2_4 + subclass: CWL + primaryDescriptorPath: + /.dockstore/dragen-transcriptome-pipeline/4.2.4/dragen-transcriptome-pipeline__4.2.4.packed.cwl.json + readMePath: + /.github/catalogue/docs/workflows/dragen-transcriptome-pipeline/4.2.4/dragen-transcriptome-pipeline__4.2.4.md + authors: + - name: Sehrish Kanwal + email: sehrish.kanwal@umccr.org + filters: + tags: + - dragen-transcriptome-pipeline/4.2.4 + - dragen-transcriptome-pipeline/4.2.4__20240627040250 diff --git a/.dockstore/dragen-transcriptome-pipeline/4.2.4/dragen-transcriptome-pipeline__4.2.4.packed.cwl.json b/.dockstore/dragen-transcriptome-pipeline/4.2.4/dragen-transcriptome-pipeline__4.2.4.packed.cwl.json new file mode 100644 index 00000000..fe904dd1 --- /dev/null +++ b/.dockstore/dragen-transcriptome-pipeline/4.2.4/dragen-transcriptome-pipeline__4.2.4.packed.cwl.json @@ -0,0 +1,2500 @@ +{ + "$graph": [ + { + "class": "CommandLineTool", + "id": "#arriba-drawing__2.4.0.cwl", + "label": "arriba-drawing v(2.4.0)", + "doc": "Documentation for arriba-drawing v2.4.0\n", + "hints": [ + { + "dockerPull": "public.ecr.aws/biocontainers/arriba:2.4.0--ha04fe3b_0", + "class": "DockerRequirement" + }, + { + "coresMin": 8, + "ramMin": 28000, + "class": "ResourceRequirement", + "https://platform.illumina.com/rdf/ica/resources:tier": "standard", + "https://platform.illumina.com/rdf/ica/resources:type": "standard", + "https://platform.illumina.com/rdf/ica/resources:size": "large" + } + ], + "requirements": [ + { + "class": "InlineJavascriptRequirement" + } + ], + "baseCommand": [ + "draw_fusions.R" + ], + "inputs": [ + { + "label": "annotation", + "doc": "Gene annotation in GTF format\n", + "type": "File", + "inputBinding": { + "prefix": "--annotation=", + "separate": false, + "position": 1 + }, + "id": "#arriba-drawing__2.4.0.cwl/arriba-drawing--2.4.0/annotation" + }, + { + "label": "alignment", + "doc": "BAM file containing normal alignments from STAR\n", + "type": "File", + "secondaryFiles": [ + { + "pattern": ".bai", + "required": null + } + ], + "inputBinding": { + "prefix": "--alignments=", + "separate": false, + "position": 4 + }, + "id": "#arriba-drawing__2.4.0.cwl/arriba-drawing--2.4.0/bam_file" + }, + { + "label": "color 1", + "doc": "color 1. Default #e5a5a5\n", + "type": [ + "null", + "string" + ], + "inputBinding": { + "prefix": "--color1=", + "separate": false, + "position": 12 + }, + "id": "#arriba-drawing__2.4.0.cwl/arriba-drawing--2.4.0/color_1" + }, + { + "label": "color 2", + "doc": "color 2. Default #a7c4e5\n", + "type": [ + "null", + "string" + ], + "inputBinding": { + "prefix": "--color2=", + "separate": false, + "position": 13 + }, + "id": "#arriba-drawing__2.4.0.cwl/arriba-drawing--2.4.0/color_2" + }, + { + "label": "coverage range", + "doc": "Coverage range. Default 0.\n", + "type": [ + "null", + "int" + ], + "inputBinding": { + "prefix": "--coverageRange=", + "separate": false, + "position": 20 + }, + "id": "#arriba-drawing__2.4.0.cwl/arriba-drawing--2.4.0/coverage_range" + }, + { + "label": "cytobands", + "doc": "Coordinates of the Giemsa staining bands. This information is used to draw ideograms\n", + "type": "File", + "inputBinding": { + "prefix": "--cytobands=", + "separate": false, + "position": 5 + }, + "id": "#arriba-drawing__2.4.0.cwl/arriba-drawing--2.4.0/cytobands" + }, + { + "label": "fixed scale", + "doc": "Fixed scale. Default 0.\n", + "type": [ + "null", + "int" + ], + "inputBinding": { + "prefix": "--fixedScale=", + "separate": false, + "position": 19 + }, + "id": "#arriba-drawing__2.4.0.cwl/arriba-drawing--2.4.0/fixed_scale" + }, + { + "label": "font family", + "doc": "Font family. Default Helvetica.\n", + "type": [ + "null", + "string" + ], + "inputBinding": { + "prefix": "--fontFamily=", + "separate": false, + "position": 17 + }, + "id": "#arriba-drawing__2.4.0.cwl/arriba-drawing--2.4.0/font_family" + }, + { + "label": "font size", + "doc": "Font size. Default 1.\n", + "type": [ + "null", + "int" + ], + "inputBinding": { + "prefix": "--fontSize=", + "separate": false, + "position": 16 + }, + "id": "#arriba-drawing__2.4.0.cwl/arriba-drawing--2.4.0/font_size" + }, + { + "label": "fusions", + "doc": "File containing fusion predictions from Arriba\n", + "type": "File", + "inputBinding": { + "prefix": "--fusions=", + "separate": false, + "position": 2 + }, + "id": "#arriba-drawing__2.4.0.cwl/arriba-drawing--2.4.0/fusions" + }, + { + "label": "merge domains overlapping", + "doc": "Merge domains overlapping. Default 0.9\n", + "type": [ + "null", + "int" + ], + "inputBinding": { + "prefix": "--mergeDomainsOverlappingBy=", + "separate": false, + "position": 14 + }, + "id": "#arriba-drawing__2.4.0.cwl/arriba-drawing--2.4.0/merge_domains_overlapping_by" + }, + { + "label": "optimize domain colors", + "doc": "Optimize domain colors. Default false.\n", + "type": [ + "null", + "boolean" + ], + "inputBinding": { + "prefix": "--optimizeDomainColors=", + "separate": false, + "position": 15 + }, + "id": "#arriba-drawing__2.4.0.cwl/arriba-drawing--2.4.0/optimize_domain_colors" + }, + { + "label": "output", + "doc": "Output file in PDF format containing the visualizations of the gene fusions\n", + "type": [ + "null", + "string" + ], + "default": "fusions.pdf", + "inputBinding": { + "prefix": "--output=", + "separate": false, + "position": 3 + }, + "id": "#arriba-drawing__2.4.0.cwl/arriba-drawing--2.4.0/output" + }, + { + "label": "pdf width", + "doc": "PDF width. Default 11.692\n", + "type": [ + "null", + "int" + ], + "inputBinding": { + "prefix": "--pdfWidth=", + "separate": false, + "position": 11 + }, + "id": "#arriba-drawing__2.4.0.cwl/arriba-drawing--2.4.0/pdf_width" + }, + { + "label": "print exon labels", + "doc": "Print exon labels. Default true\n", + "type": [ + "null", + "boolean" + ], + "inputBinding": { + "prefix": "--printExonLabels=", + "separate": false, + "position": 9 + }, + "id": "#arriba-drawing__2.4.0.cwl/arriba-drawing--2.4.0/print_exon_labels" + }, + { + "label": "protein domains", + "doc": "GFF3 file containing the genomic coordinates of protein domains\n", + "type": "File", + "inputBinding": { + "prefix": "--proteinDomains=", + "separate": false, + "position": 6 + }, + "id": "#arriba-drawing__2.4.0.cwl/arriba-drawing--2.4.0/protein_domains" + }, + { + "label": "render 3d effect", + "doc": "Render 3d effect. Default true\n", + "type": [ + "null", + "boolean" + ], + "inputBinding": { + "prefix": "--render3dEffect=", + "separate": false, + "position": 10 + }, + "id": "#arriba-drawing__2.4.0.cwl/arriba-drawing--2.4.0/render_3d_effect" + }, + { + "label": "sample name", + "doc": "Sample name\n", + "type": [ + "null", + "string" + ], + "inputBinding": { + "prefix": "--sampleName=", + "separate": false, + "position": 7 + }, + "id": "#arriba-drawing__2.4.0.cwl/arriba-drawing--2.4.0/sample_name" + }, + { + "label": "squish introns", + "doc": "Squish introns. Default true\n", + "type": [ + "null", + "boolean" + ], + "inputBinding": { + "prefix": "--squishIntrons=", + "separate": false, + "position": 8 + }, + "id": "#arriba-drawing__2.4.0.cwl/arriba-drawing--2.4.0/squish_introns" + }, + { + "label": "transcript selection", + "doc": "Transcript selection. Default coverage\n", + "type": [ + "null", + "string" + ], + "inputBinding": { + "prefix": "--transcriptSelection=", + "separate": false, + "position": 18 + }, + "id": "#arriba-drawing__2.4.0.cwl/arriba-drawing--2.4.0/transcript_selection" + } + ], + "successCodes": [ + 0 + ], + "https://schema.org/author": { + "class": "https://schema.org/Person", + "https://schema.org/name": "Sehrish Kanwal", + "https://schema.org/email": "sehrish.kanwal@umccr.org" + }, + "outputs": [ + { + "label": "output PDF", + "doc": "Output pdf file with fusion drawing\n", + "type": "File", + "outputBinding": { + "glob": "$(inputs.output)" + }, + "id": "#arriba-drawing__2.4.0.cwl/arriba-drawing--2.4.0/output_pdf" + } + ] + }, + { + "class": "CommandLineTool", + "id": "#arriba-fusion-calling__2.4.0.cwl", + "label": "arriba-fusion-calling v(2.4.0)", + "doc": "Documentation for arriba-fusion-calling v2.4.0\n", + "hints": [ + { + "dockerPull": "public.ecr.aws/biocontainers/arriba:2.4.0--ha04fe3b_0", + "class": "DockerRequirement" + }, + { + "coresMin": 8, + "ramMin": 28000, + "class": "ResourceRequirement", + "https://platform.illumina.com/rdf/ica/resources:tier": "standard", + "https://platform.illumina.com/rdf/ica/resources:type": "standard", + "https://platform.illumina.com/rdf/ica/resources:size": "large" + } + ], + "requirements": [ + { + "class": "InlineJavascriptRequirement" + } + ], + "baseCommand": [ + "arriba" + ], + "inputs": [ + { + "label": "annotation", + "doc": "GTF file with gene annotation. The file may be gzip-compressed\n", + "type": "File", + "inputBinding": { + "prefix": "-g", + "position": 2 + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/annotation" + }, + { + "label": "bam file", + "doc": "File in SAM/BAM/CRAM format with main alignments as generated by STAR\n", + "type": "File", + "secondaryFiles": [ + { + "pattern": ".bai", + "required": null + } + ], + "inputBinding": { + "prefix": "-x", + "position": 1 + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/bam_file" + }, + { + "label": "bam without chimeric alignments", + "doc": "File in SAM/BAM/CRAM format with chimeric alignments as generated by STAR\n(Chimeric.out.sam). This parameter is only required, if STAR was run with the\nparameter '--chimOutType SeparateSAMold'. When STAR was run with the parameter\n'--chimOutType WithinBAM', it suffices to pass the parameter -x to Arriba and -c\ncan be omitted.\n", + "type": [ + "null", + "File" + ], + "inputBinding": { + "prefix": "-c", + "position": 8 + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/bam_without_chimeric_alignments" + }, + { + "label": "blacklist", + "doc": "File containing blacklisted ranges\n", + "type": "File", + "inputBinding": { + "prefix": "-b", + "position": 5 + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/blacklist" + }, + { + "label": "contigs", + "doc": "Comma-/space-separated list of interesting contigs. Fusions between genes on other contigs are ignored\n", + "type": [ + "null", + "string" + ], + "default": "1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y,AC_*,NC_*", + "inputBinding": { + "prefix": "-i", + "position": 4 + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/contigs" + }, + { + "label": "coordinates protein domains", + "doc": "File in GFF3 format containing coordinates of the protein domains of genes. The\nprotein domains retained in a fusion are listed in the column\n'retained_protein_domains'. The file may be gzip-compressed.\n", + "type": [ + "null", + "File" + ], + "inputBinding": { + "prefix": "-p", + "position": 12 + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/coordinates_protein_domains" + }, + { + "label": "coordinates structural variants", + "doc": "Tab-separated file with coordinates of structural variants found using\nwhole-genome sequencing data. These coordinates serve to increase sensitivity\ntowards weakly expressed fusions and to eliminate fusions with low evidence.\n", + "type": [ + "null", + "File" + ], + "inputBinding": { + "prefix": "-d", + "position": 13 + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/coordinates_structural_variants" + }, + { + "label": "covered fraction", + "doc": "Ignore virally associated events if the virus is not fully\nexpressed, i.e., less than the given fraction of the viral contig is\ntranscribed. Default: 0.050000\n", + "type": [ + "null", + "int" + ], + "inputBinding": { + "prefix": "-C", + "position": 33 + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/covered_fraction" + }, + { + "label": "discarded fusion", + "doc": "Output file with fusions that were discarded due to filtering\n", + "type": [ + "null", + "string" + ], + "default": "fusions-discarded.tsv", + "inputBinding": { + "prefix": "-O", + "position": 7 + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/discarded_fusions_filename" + }, + { + "label": "exonic fraction", + "doc": "The breakpoints of false-positive predictions of intragenic events\nare often both in exons. True predictions are more likely to have at\nleast one breakpoint in an intron, because introns are larger. If the\nfraction of exonic sequence between two breakpoints is smaller than\nthe given fraction, the 'intragenic_exonic' filter discards the\nevent. Default: 0.330000\n", + "type": [ + "null", + "int" + ], + "inputBinding": { + "prefix": "-e", + "position": 31 + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/exonic_fraction" + }, + { + "label": "filters", + "doc": "Comma-/space-separated list of filters to disable. By default all filters are\nenabled. Valid values: top_expressed_viral_contigs, viral_contigs,\nlow_coverage_viral_contigs, uninteresting_contigs,\nno_genomic_support, short_anchor, select_best, many_spliced, long_gap,\nmarginal_read_through, merge_adjacent, hairpin, small_insert_size,\nsame_gene, mismappers, spliced, genomic_support, read_through,\nno_coverage, mismatches, homopolymer, low_entropy, multimappers,\ninconsistently_clipped, duplicates, homologs, blacklist,\nrelative_support, min_support, end_to_end, known_fusions,\nnon_coding_neighbors, isoforms, intronic, in_vitro, intragenic_exonic,\ninternal_tandem_duplication\n", + "type": [ + "null", + "string" + ], + "inputBinding": { + "prefix": "-f", + "position": 17 + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/filters" + }, + { + "label": "fragment length", + "doc": "When paired-end data is given, the fragment length is estimated\nautomatically and this parameter has no effect. But when single-end\ndata is given, the mean fragment length should be specified to\neffectively filter fusions that arise from hairpin structures.\nDefault: 200\n", + "type": [ + "null", + "int" + ], + "inputBinding": { + "prefix": "-F", + "position": 28 + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/fragment_length" + }, + { + "label": "fusion", + "doc": "Output file with fusions that have passed all filters\n", + "type": [ + "null", + "string" + ], + "default": "fusions.tsv", + "inputBinding": { + "prefix": "-o", + "position": 6 + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/fusions_filename" + }, + { + "label": "genomic breakpoint", + "doc": "When a file with genomic breakpoints obtained via whole-genome sequencing is supplied via the -d\nparameter, this parameter determines how far a genomic breakpoint may be away from a\ntranscriptomic breakpoint to consider it as a related event. For events inside genes, the\ndistance is added to the end of the gene; for intergenic events, the distance threshold is\napplied as is. Default: 100000\n", + "type": [ + "null", + "int" + ], + "inputBinding": { + "prefix": "-D", + "position": 14 + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/genomic_breakpoint" + }, + { + "label": "GTF features", + "doc": "Comma-/space-separated list of names of GTF features.\nDefault: gene_name=gene_name|gene_id gene_id=gene_id\ntranscript_id=transcript_id feature_exon=exon feature_CDS=CDS\n", + "type": [ + "null", + "string" + ], + "inputBinding": { + "prefix": "-G", + "position": 9 + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/gtf_features" + }, + { + "label": "homopolymer length", + "doc": "The 'homopolymer' filter removes breakpoints adjacent to\nhomopolymers of the given length or more. Default: 6\n", + "type": [ + "null", + "int" + ], + "inputBinding": { + "prefix": "-H", + "position": 22 + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/homopolymer_length" + }, + { + "label": "known fusions", + "doc": "File containing known/recurrent fusions. Some cancer entities are often\ncharacterized by fusions between the same pair of genes. In order to boost\nsensitivity, a list of known fusions can be supplied using this parameter. The list\nmust contain two columns with the names of the fused genes, separated by tabs.\n", + "type": [ + "null", + "File" + ], + "inputBinding": { + "prefix": "-k", + "position": 10 + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/known_fusions" + }, + { + "label": "many spliced events", + "doc": "The 'many_spliced' filter recovers fusions between genes that\nhave at least this many spliced breakpoints. Default: 4\n", + "type": [ + "null", + "int" + ], + "inputBinding": { + "prefix": "-M", + "position": 25 + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/many_spliced_events" + }, + { + "label": "max e value", + "doc": "Arriba estimates the number of fusions with a given number of supporting\nreads which one would expect to see by random chance. If the expected number\nof fusions (e-value) is higher than this threshold, the fusion is\ndiscarded by the 'relative_support' filter. Note: Increasing this\nthreshold can dramatically increase the number of false positives and may\nincrease the runtime of resource-intensive steps. Fractional values are\npossible. Default: 0.300000\n", + "type": [ + "null", + "int" + ], + "inputBinding": { + "prefix": "-E", + "position": 18 + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/max_e_value" + }, + { + "label": "max homolog identity", + "doc": "Genes with more than the given fraction of sequence identity are\nconsidered homologs and removed by the 'homologs' filter.\nDefault: 0.300000\n", + "type": [ + "null", + "int" + ], + "inputBinding": { + "prefix": "-L", + "position": 21 + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/max_homolog_identity" + }, + { + "label": "max itd length", + "doc": "Maximum length of internal tandem duplications. Note: Increasing\nthis value beyond the default can impair performance and lead to many\nfalse positives. Default: 100\n", + "type": [ + "null", + "int" + ], + "inputBinding": { + "prefix": "-l", + "position": 34 + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/max_itd_length" + }, + { + "label": "max kmer content", + "doc": "The 'low_entropy' filter removes reads with repetitive 3-mers. If\nthe 3-mers make up more than the given fraction of the sequence, then\nthe read is discarded. Default: 0.600000\n", + "type": [ + "null", + "int" + ], + "inputBinding": { + "prefix": "-K", + "position": 26 + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/max_kmer_content" + }, + { + "label": "max mismappers", + "doc": "When more than this fraction of supporting reads turns out to be\nmismappers, the 'mismappers' filter discards the fusion. Default:\n0.800000\n", + "type": [ + "null", + "int" + ], + "inputBinding": { + "prefix": "-m", + "position": 20 + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/max_mismappers" + }, + { + "label": "max mismatch pvalue", + "doc": "The 'mismatches' filter uses a binomial model to calculate a\np-value for observing a given number of mismatches in a read. If\nthe number of mismatches is too high, the read is discarded.\nDefault: 0.010000\n", + "type": [ + "null", + "int" + ], + "inputBinding": { + "prefix": "-V", + "position": 27 + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/max_mismatch_pvalue" + }, + { + "label": "max reads", + "doc": "Subsample fusions with more than the given number of supporting reads. This\nimproves performance without compromising sensitivity, as long as the\nthreshold is high. Counting of supporting reads beyond the threshold is\ninaccurate, obviously. Default: 300\n", + "type": [ + "null", + "int" + ], + "inputBinding": { + "prefix": "-U", + "position": 29 + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/max_reads" + }, + { + "label": "min anchor length", + "doc": "Alignment artifacts are often characterized by split reads coming\nfrom only one gene and no discordant mates. Moreover, the split\nreads only align to a short stretch in one of the genes. The\n'short_anchor' filter removes these fusions. This parameter sets\nthe threshold in bp for what the filter considers short. Default: 23\n", + "type": [ + "null", + "int" + ], + "inputBinding": { + "prefix": "-A", + "position": 24 + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/min_anchor_length" + }, + { + "label": "min itd allele fraction", + "doc": "Required fraction of supporting reads to report an internal\ntandem duplication. Default: 0.070000\n", + "type": [ + "null", + "int" + ], + "inputBinding": { + "prefix": "-z", + "position": 35 + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/min_itd_allele_fraction" + }, + { + "label": "min itd supporting reads", + "doc": "Required absolute number of supporting reads to report an\ninternal tandem duplication. Default: 10\n", + "type": [ + "null", + "int" + ], + "inputBinding": { + "prefix": "-Z", + "position": 36 + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/min_itd_supporting_reads" + }, + { + "label": "min supporting reads", + "doc": "The 'min_support' filter discards all fusions with fewer than\nthis many supporting reads (split reads and discordant mates\ncombined). Default: 2\n", + "type": [ + "null", + "int" + ], + "inputBinding": { + "prefix": "-S", + "position": 19 + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/min_supporting_reads" + }, + { + "label": "quantile", + "doc": "Highly expressed genes are prone to produce artifacts during library\npreparation. Genes with an expression above the given quantile are eligible\nfor filtering by the 'in_vitro' filter. Default: 0.998000\n", + "type": [ + "null", + "int" + ], + "inputBinding": { + "prefix": "-Q", + "position": 30 + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/quantile" + }, + { + "label": "read through distance", + "doc": "The 'read_through' filter removes read-through fusions\nwhere the breakpoints are less than the given distance away\nfrom each other. Default: 10000\n", + "type": [ + "null", + "int" + ], + "inputBinding": { + "prefix": "-R", + "position": 23 + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/read_through_distance" + }, + { + "label": "reference", + "doc": "FastA file with genome sequence (assembly). The file may be gzip-compressed\n", + "type": "File", + "inputBinding": { + "prefix": "-a", + "position": 3 + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/reference" + }, + { + "label": "strandedness", + "doc": "Whether a strand-specific protocol was used for library preparation,\nand if so, the type of strandedness (auto/yes/no/reverse). When\nunstranded data is processed, the strand can sometimes be inferred from\nsplice-patterns. But in unclear situations, stranded data helps\nresolve ambiguities. Default: auto\n", + "type": [ + "null", + "string" + ], + "inputBinding": { + "prefix": "-s", + "position": 15 + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/strandedness" + }, + { + "label": "tags", + "doc": "Tab-separated file containing fusions to annotate with tags in the 'tags' column.\nThe first two columns specify the genes; the third column specifies the tag. The\nfile may be gzip-compressed.\n", + "type": [ + "null", + "File" + ], + "inputBinding": { + "prefix": "-t", + "position": 11 + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/tags" + }, + { + "label": "top N", + "doc": "Only report viral integration sites of the top N most highly expressed viral\ncontigs. Default: 5\n", + "type": [ + "null", + "int" + ], + "inputBinding": { + "prefix": "-T", + "position": 32 + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/top_n" + }, + { + "label": "viral contigs", + "doc": "Comma-/space-separated list of viral contigs. Asterisks (*) are treated as\nwild-cards.\nDefault: AC_* NC_*\n", + "type": [ + "null", + "string" + ], + "inputBinding": { + "prefix": "-v", + "position": 16 + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/viral_contigs" + } + ], + "outputs": [ + { + "label": "discarded fusions", + "doc": "file with discarded fusions\n", + "type": "File", + "outputBinding": { + "glob": "$(inputs.discarded_fusions_filename)" + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/discarded_fusions" + }, + { + "label": "fusions", + "doc": "file with output fusions\n", + "type": "File", + "outputBinding": { + "glob": "$(inputs.fusions_filename)" + }, + "id": "#arriba-fusion-calling__2.4.0.cwl/arriba-fusion-calling--2.4.0/fusions" + } + ], + "successCodes": [ + 0 + ], + "https://schema.org/author": { + "class": "https://schema.org/Person", + "https://schema.org/name": "Sehrish Kanwal", + "https://schema.org/email": "sehrish.kanwal@umccr.org" + } + }, + { + "class": "CommandLineTool", + "id": "#custom-create-directory__1.0.0.cwl", + "label": "custom-create-directory v(1.0.0)", + "doc": "Documentation for custom-create-directory v1.0.0\nCreate a directory based on a list of inputs generated as input files or input directories\n", + "hints": [ + { + "dockerPull": "ghcr.io/umccr/alpine-rsync:3.2.3", + "class": "DockerRequirement" + }, + { + "coresMin": 15, + "ramMin": 28, + "class": "ResourceRequirement", + "https://platform.illumina.com/rdf/ica/resources:tier": "standard", + "https://platform.illumina.com/rdf/ica/resources:type": "standardHiCpu", + "https://platform.illumina.com/rdf/ica/resources:size": "small" + } + ], + "requirements": [ + { + "class": "InlineJavascriptRequirement" + } + ], + "baseCommand": [ + "rsync" + ], + "arguments": [ + { + "position": -1, + "valueFrom": "--archive" + } + ], + "inputs": [ + { + "label": "input directories", + "doc": "List of input directories to go into the output directory\n", + "type": [ + "null", + { + "type": "array", + "items": "Directory" + } + ], + "inputBinding": { + "position": 2, + "valueFrom": "${\n return self.map(function(a) {return a.path.replace(/\\/$/, \"\")});\n}\n" + }, + "id": "#custom-create-directory__1.0.0.cwl/custom-create-directory--1.0.0/input_directories" + }, + { + "label": "input files", + "doc": "List of input files to go into the output directory\n", + "type": [ + "null", + { + "type": "array", + "items": "File" + } + ], + "inputBinding": { + "position": 1 + }, + "id": "#custom-create-directory__1.0.0.cwl/custom-create-directory--1.0.0/input_files" + }, + { + "label": "output directory name", + "doc": "The name of the output directory\n", + "type": "string", + "inputBinding": { + "position": 3, + "valueFrom": "${\n return self.replace(/\\/$/, \"\") + \"/\";\n}\n" + }, + "id": "#custom-create-directory__1.0.0.cwl/custom-create-directory--1.0.0/output_directory_name" + } + ], + "outputs": [ + { + "label": "output directory", + "doc": "The output directory with all of the outputs collected\n", + "type": "Directory", + "outputBinding": { + "glob": "$(inputs.output_directory_name)" + }, + "id": "#custom-create-directory__1.0.0.cwl/custom-create-directory--1.0.0/output_directory" + } + ], + "successCodes": [ + 0 + ], + "https://schema.org/author": { + "class": "https://schema.org/Person", + "https://schema.org/name": "Alexis Lucattini", + "https://schema.org/email": "Alexis.Lucattini@umccr.org", + "https://schema.org/identifier": "https://orcid.org/0000-0001-9754-647X" + } + }, + { + "class": "CommandLineTool", + "id": "#custom-touch-file__1.0.0.cwl", + "label": "custom-create-dummy-file v(1.0.0)", + "doc": "Documentation for custom-create-dummy-file v1.0.0\n", + "hints": [ + { + "dockerPull": "public.ecr.aws/docker/library/alpine:latest", + "class": "DockerRequirement" + }, + { + "coresMin": 1, + "ramMin": 1000, + "class": "ResourceRequirement", + "https://platform.illumina.com/rdf/ica/resources:tier": "standard", + "https://platform.illumina.com/rdf/ica/resources:type": "standard", + "https://platform.illumina.com/rdf/ica/resources:size": "small" + } + ], + "requirements": [ + { + "class": "InlineJavascriptRequirement" + } + ], + "baseCommand": [ + "touch" + ], + "inputs": [ + { + "label": "file name", + "doc": "Name of the file to create\n", + "type": "string", + "default": "dummy_file.txt", + "inputBinding": { + "position": 1 + }, + "id": "#custom-touch-file__1.0.0.cwl/custom-create-dummy-file--1.0.0/file_name" + } + ], + "outputs": [ + { + "label": "dummy file", + "doc": "Output dummy file\n", + "type": "File", + "outputBinding": { + "glob": "$(inputs.file_name)" + }, + "id": "#custom-touch-file__1.0.0.cwl/custom-create-dummy-file--1.0.0/dummy_file_output" + } + ], + "successCodes": [ + 0 + ], + "https://schema.org/author": { + "class": "https://schema.org/Person", + "https://schema.org/name": "Alexis Lucattini", + "https://schema.org/email": "Alexis.Lucattini@umccr.org", + "https://schema.org/identifier": "https://orcid.org/0000-0001-9754-647X" + } + }, + { + "class": "CommandLineTool", + "id": "#dragen-transcriptome__4.2.4.cwl", + "label": "dragen-transcriptome v(4.2.4)", + "doc": "Documentation for dragen-transcriptome v4.2.4\n", + "hints": [ + { + "dockerPull": "699120554104.dkr.ecr.us-east-1.amazonaws.com/public/dragen:4.2.4", + "class": "DockerRequirement" + }, + { + "coresMin": 16, + "ramMin": 240000, + "class": "ResourceRequirement", + "https://platform.illumina.com/rdf/ica/resources:tier": "standard", + "https://platform.illumina.com/rdf/ica/resources:type": "fpga", + "https://platform.illumina.com/rdf/ica/resources:size": "medium" + } + ], + "requirements": [ + { + "listing": [ + { + "entryname": "$(get_script_path())", + "entry": "#!/usr/bin/env bash\n\n# Fail on non-zero exit of subshell\nset -euo pipefail\n\n# Initialise dragen\n/opt/edico/bin/dragen \\\\\n --partial-reconfig DNA-MAPPER \\\\\n --ignore-version-check true\n\n# Create directories\nmkdir --parents \\\\\n \"$(get_ref_mount())\" \\\\\n \"$(get_intermediate_results_dir())\" \\\\\n \"$(inputs.output_directory)\"\n\n# untar ref data into scratch space\ntar \\\\\n --directory \"$(get_ref_mount())\" \\\\\n --extract \\\\\n --file \"$(inputs.reference_tar.path)\"\n\n# Run dragen command and import options from cli\n\"$(get_dragen_bin_path())\" \"\\${@}\"\n" + }, + "${\n return generate_transcriptome_mount_points(inputs);\n}\n" + ], + "class": "InitialWorkDirRequirement" + }, + { + "expressionLib": [ + "/* Author:Alexis Lucattini */\n/* For assistance on generation of typescript expressions */\n/* In CWL, please visit our wiki page at https://github.com/umccr/cwl-ica/wiki/TypeScript */\n/* Imports */\n/* Functions */\nfunction get_script_path() {\n /*\n Abstract script path, can then be referenced in baseCommand attribute too\n Makes things more readable.\n */\n return \"run-dragen-script.sh\";\n}\nfunction get_scratch_mount() {\n /*\n Return the path of the scratch directory space\n */\n return \"/scratch/\";\n}\nfunction get_intermediate_results_dir() {\n /*\n Get intermediate results directory as /scratch for dragen runs\n */\n return get_scratch_mount() + \"intermediate-results/\";\n}\nfunction get_name_root_from_tarball(basename) {\n var tar_ball_regex = /(\\S+)\\.tar\\.gz/g;\n var tar_ball_expression = tar_ball_regex.exec(basename);\n if (tar_ball_expression === null) {\n throw new Error(\"Could not get nameroot from \".concat(basename));\n }\n return tar_ball_expression[1];\n}\nfunction get_ref_path(reference_input_obj) {\n /*\n Get the reference path\n */\n return get_ref_mount() + get_name_root_from_tarball(reference_input_obj.basename) + \"/\";\n}\nfunction get_ref_mount() {\n /*\n Get the reference mount point\n */\n return get_scratch_mount() + \"ref/\";\n}\nfunction get_dragen_bin_path() {\n /*\n Get dragen bin path\n */\n return \"/opt/edico/bin/dragen\";\n}\nfunction get_dragen_eval_line() {\n /*\n Return string\n */\n return \"eval \\\"\" + get_dragen_bin_path() + \"\\\" '\\\"\\$@\\\"' \\n\";\n}\nfunction get_fastq_list_csv_path() {\n /*\n The fastq list path must be placed in working directory\n */\n return \"fastq_list.csv\";\n}\nfunction get_tumor_fastq_list_csv_path() {\n /*\n The tumor fastq list path must be placed in working directory\n */\n return \"tumor_fastq_list.csv\";\n}\nfunction get_normal_name_from_fastq_list_rows(fastq_list_rows) {\n /*\n Get the normal sample name from the fastq list rows object\n */\n /*\n Check fastq list rows is defined\n */\n if (fastq_list_rows === undefined || fastq_list_rows === null) {\n return null;\n }\n /*\n Get RGSM value and return\n */\n return fastq_list_rows[0].rgsm;\n}\nfunction get_normal_name_from_fastq_list_csv(fastq_list_csv) {\n /*\n Get the normal name from the fastq list csv...\n */\n /*\n Check file is defined\n */\n if (fastq_list_csv === undefined || fastq_list_csv === null) {\n return null;\n }\n /*\n Check contents are defined\n */\n if (fastq_list_csv.contents === null || fastq_list_csv.contents === undefined) {\n return null;\n }\n /*\n Confirm fastq list csv is of type File\n */\n if (fastq_list_csv.class !== \"File\") {\n throw new Error(\"Could not confirm input fastq_list_csv is of type File\");\n }\n /*\n Split contents by line\n */\n var contents_by_line = [];\n fastq_list_csv.contents.split(\"\\n\").forEach(function (line_content) {\n var stripped_line_content = line_content.replace(/(\\r\\n|\\n|\\r)/gm, \"\");\n if (stripped_line_content !== \"\") {\n contents_by_line.push(stripped_line_content);\n }\n });\n var column_names = contents_by_line[0].split(\",\");\n /*\n Get RGSM index value (which column is RGSM at?)\n */\n var rgsm_index = column_names.indexOf(\"RGSM\");\n /*\n RGSM is not in index. Return null\n */\n if (rgsm_index === -1) {\n return null;\n }\n /*\n Get RGSM value of first row and return\n */\n return contents_by_line[1].split(\",\")[rgsm_index];\n}\nfunction get_normal_output_prefix(inputs) {\n var _a;\n /*\n Get the normal RGSM value and then add _normal to it\n */\n var normal_name = null;\n var normal_re_replacement = /_normal$/;\n /*\n Check if bam_input is set\n */\n if (inputs.bam_input !== null && inputs.bam_input !== undefined) {\n /* Remove _normal from nameroot if it already exists */\n /* We dont want _normal_normal as a suffix */\n return \"\".concat((_a = inputs.bam_input.nameroot) === null || _a === void 0 ? void 0 :_a.replace(normal_re_replacement, \"\"), \"_normal\");\n }\n /*\n Check if fastq list file is set\n */\n if (inputs.fastq_list !== null && inputs.fastq_list !== undefined) {\n normal_name = get_normal_name_from_fastq_list_csv(inputs.fastq_list);\n if (normal_name !== null) {\n return \"\".concat(normal_name, \"_normal\");\n }\n }\n /*\n Otherwise collect and return from schema object\n */\n normal_name = get_normal_name_from_fastq_list_rows(inputs.fastq_list_rows);\n return \"\".concat(normal_name, \"_normal\");\n}\nfunction build_fastq_list_csv_header(header_names) {\n /*\n Convert lowercase labels to uppercase values\n i.e\n [ \"rgid\", \"rglb\", \"rgsm\", \"lane\", \"read_1\", \"read_2\" ]\n to\n \"RGID,RGLB,RGSM,Lane,Read1File,Read2File\"\n */\n var modified_header_names = [];\n for (var _i = 0, header_names_1 = header_names; _i < header_names_1.length; _i++) {\n var header_name = header_names_1[_i];\n if (header_name.indexOf(\"rg\") === 0) {\n /*\n rgid -> RGID\n */\n modified_header_names.push(header_name.toUpperCase());\n }\n else if (header_name.indexOf(\"read\") === 0) {\n /*\n read_1 -> Read1File\n */\n modified_header_names.push(\"Read\" + header_name.charAt(header_name.length - 1) + \"File\");\n }\n else {\n /*\n lane to Lane\n */\n modified_header_names.push(header_name[0].toUpperCase() + header_name.substr(1));\n }\n }\n /*\n Convert array to comma separated strings\n */\n return modified_header_names.join(\",\") + \"\\n\";\n}\nfunction get_fastq_list_row_as_csv_row(fastq_list_row, row_order) {\n var fastq_list_row_values_array = [];\n /* This for loop is here to ensure were assigning values in the same order as the header */\n for (var _i = 0, row_order_1 = row_order; _i < row_order_1.length; _i++) {\n var item_index = row_order_1[_i];\n var found_item = false;\n /* Find matching attribute in this row */\n for (var _a = 0, _b = Object.getOwnPropertyNames(fastq_list_row); _a < _b.length; _a++) {\n var fastq_list_row_field_name = _b[_a];\n var fastq_list_row_field_value = fastq_list_row[fastq_list_row_field_name];\n if (fastq_list_row_field_value === null) {\n /*\n Item not found, add an empty attribute for this cell in the csv\n */\n continue;\n }\n /* The header value matches the name in the item */\n if (fastq_list_row_field_name === item_index) {\n /*\n If the field value has a class attribute then it's either read_1 or read_2\n */\n if (fastq_list_row_field_value.hasOwnProperty(\"class\")) {\n var fastq_list_row_field_value_file = fastq_list_row_field_value;\n /*\n Assert that this is actually of class file\n */\n if (fastq_list_row_field_value_file.class !== \"File\") {\n continue;\n }\n if (fastq_list_row_field_value_file.path !== null && fastq_list_row_field_value_file.path !== undefined) {\n /*\n Push the path attribute to the fastq list csv row if it is not null\n */\n fastq_list_row_values_array.push(fastq_list_row_field_value_file.path);\n }\n else {\n /*\n Otherwise push the location attribute\n */\n fastq_list_row_values_array.push(fastq_list_row_field_value_file.location);\n }\n }\n else {\n /*\n Push the string attribute to the fastq list csv row\n */\n fastq_list_row_values_array.push(fastq_list_row_field_value.toString());\n }\n found_item = true;\n break;\n }\n }\n if (!found_item) {\n /*\n Push blank cell if no item found\n */\n fastq_list_row_values_array.push(\"\");\n }\n }\n /*\n Convert to string and return as string\n */\n return fastq_list_row_values_array.join(\",\") + \"\\n\";\n}\nfunction generate_fastq_list_csv(fastq_list_rows) {\n /*\n Fastq list rows generation\n */\n var fastq_csv_file = {\n class:\"File\",\n basename:get_fastq_list_csv_path()\n };\n /*\n Set the row order\n */\n var row_order = [];\n /*\n Set the array order\n Make sure we iterate through all rows of the array\n */\n for (var _i = 0, fastq_list_rows_1 = fastq_list_rows; _i < fastq_list_rows_1.length; _i++) {\n var fastq_list_row = fastq_list_rows_1[_i];\n for (var _a = 0, _b = Object.getOwnPropertyNames(fastq_list_row); _a < _b.length; _a++) {\n var fastq_list_row_field_name = _b[_a];\n if (row_order.indexOf(fastq_list_row_field_name) === -1) {\n row_order.push(fastq_list_row_field_name);\n }\n }\n }\n /*\n Make header\n */\n fastq_csv_file.contents = build_fastq_list_csv_header(row_order);\n /*\n For each fastq list row,\n collect the values of each attribute but in the order of the header\n */\n for (var _c = 0, fastq_list_rows_2 = fastq_list_rows; _c < fastq_list_rows_2.length; _c++) {\n var fastq_list_row = fastq_list_rows_2[_c];\n /* Add csv row to file contents */\n fastq_csv_file.contents += get_fastq_list_row_as_csv_row(fastq_list_row, row_order);\n }\n return fastq_csv_file;\n}\nfunction generate_germline_mount_points(inputs) {\n /*\n Create and add in the fastq list csv for the input fastqs\n */\n var e = [];\n if (inputs.fastq_list_rows !== null) {\n e.push({\n \"entryname\":get_fastq_list_csv_path(),\n \"entry\":generate_fastq_list_csv(inputs.fastq_list_rows)\n });\n }\n if (inputs.fastq_list !== null) {\n e.push({\n \"entryname\":get_fastq_list_csv_path(),\n \"entry\":inputs.fastq_list\n });\n }\n /*\n Return file paths\n */\n /* @ts-ignore Type '{ entryname:string; entry:FileProperties; }[]' is not assignable to type 'DirentProperties[]' */\n return e;\n}\nfunction generate_somatic_mount_points(inputs) {\n /*\n Create and add in the fastq list csv for the input fastqs\n */\n var e = [];\n if (inputs.fastq_list_rows !== null) {\n e.push({\n \"entryname\":get_fastq_list_csv_path(),\n \"entry\":generate_fastq_list_csv(inputs.fastq_list_rows)\n });\n }\n if (inputs.tumor_fastq_list_rows !== null) {\n e.push({\n \"entryname\":get_tumor_fastq_list_csv_path(),\n \"entry\":generate_fastq_list_csv(inputs.tumor_fastq_list_rows)\n });\n }\n if (inputs.fastq_list !== null) {\n e.push({\n \"entryname\":get_fastq_list_csv_path(),\n \"entry\":inputs.fastq_list\n });\n }\n if (inputs.tumor_fastq_list !== null) {\n e.push({\n \"entryname\":get_tumor_fastq_list_csv_path(),\n \"entry\":inputs.tumor_fastq_list\n });\n }\n /*\n Return file paths\n */\n /* @ts-ignore Type '{ entryname:string; entry:FileProperties; }[]' is not assignable to type 'DirentProperties[]' */\n return e;\n}\nfunction generate_transcriptome_mount_points(inputs) {\n /*\n Calls another function that generates mount points\n */\n return generate_germline_mount_points(inputs);\n}\n/* Custom functions for dragen reference tarball build */\nfunction get_liftover_dir() {\n /* Hardcoded liftover directory in dragen 4.2 */\n return \"/opt/edico/liftover/\";\n}\nfunction get_mask_dir() {\n /* Hardcoded mask directory in dragen 4.2 */\n return \"/opt/edico/fasta_mask/\";\n}\nfunction get_ref_scratch_dir(reference_name) {\n /* We get the reference scratch directory as a combination of */\n /* the dragen scratch mount and the reference name */\n return get_scratch_mount() + reference_name + \"/\";\n}\n", + "/* Author:Alexis Lucattini */\n/* For assistance on generation of typescript expressions */\n/* In CWL, please visit our wiki page at https://github.com/umccr/cwl-ica/wiki/TypeScript */\n/* Imports */\n/* Functions */\nfunction is_not_null(input_obj) {\n /*\n Determine if input object is defined and is not null\n */\n return !(input_obj === null || input_obj === undefined);\n}\nfunction get_attribute_from_optional_input(input_object, attribute) {\n /*\n Get attribute from optional input -\n If input is not defined, then return null\n */\n if (input_object === null || input_object === undefined) {\n return null;\n }\n else {\n return get_optional_attribute_from_object(input_object, attribute);\n }\n}\nfunction get_optional_attribute_from_object(input_object, attribute) {\n /*\n Get attribute from object, if attribute is not defined return null\n Assume the input object is an object of key value pairs where we know the key is of type string\n stackoverflow.com/questions/56833469/typescript-error-ts7053-element-implicitly-has-an-any-type\n */\n if (input_object.hasOwnProperty(attribute)) {\n return input_object[attribute];\n }\n else {\n return null;\n }\n}\nfunction get_bool_value_as_str(input_bool) {\n if (is_not_null(input_bool) && input_bool) {\n return \"true\";\n }\n else {\n return \"false\";\n }\n}\nfunction boolean_to_int(input_bool) {\n if (is_not_null(input_bool) && String(input_bool).toLowerCase() === \"true\") {\n return 1;\n }\n else {\n return 0;\n }\n}\nfunction get_optional_attribute_from_multi_type_input_object(object, attribute) {\n /*\n Get attribute from optional input\n */\n if (object === null || object === undefined) {\n return null;\n }\n else if (typeof object === \"object\") {\n /* Get attribute from optional input */\n return get_attribute_from_optional_input(object, attribute);\n }\n else {\n /* Object is likely actually a str */\n return object;\n }\n}\nfunction get_source_a_or_b(input_a, input_b) {\n /*\n Get the first input parameter if it is not null\n Otherwise return the second parameter\n Otherwise return null\n */\n if (is_not_null(input_a)) {\n return input_a;\n }\n else if (is_not_null(input_b)) {\n return input_b;\n }\n else {\n return null;\n }\n}\nfunction get_first_non_null_input(inputs) {\n /*\n Get first element of the array that is not null\n */\n for (var _i = 0, inputs_1 = inputs; _i < inputs_1.length; _i++) {\n var input_element = inputs_1[_i];\n if (is_not_null(input_element)) {\n return input_element;\n }\n }\n return null;\n}\n" + ], + "class": "InlineJavascriptRequirement" + }, + { + "tmpdirMin": "${\n /* 1 Tb */\n return 2 ** 20;\n}\n", + "class": "ResourceRequirement" + }, + { + "types": [ + { + "type": "record", + "name": "#fastq-list-row__1.0.0.yaml/fastq-list-row", + "fields": [ + { + "label": "lane", + "doc": "The lane that the sample was run on\n", + "type": "int", + "name": "#fastq-list-row__1.0.0.yaml/fastq-list-row/lane" + }, + { + "label": "read 1", + "doc": "The path to R1 of a sample\n", + "type": [ + "File", + "string" + ], + "streamable": true, + "name": "#fastq-list-row__1.0.0.yaml/fastq-list-row/read_1" + }, + { + "label": "read 2", + "doc": "The path to R2 of a sample\n", + "type": [ + "null", + "File", + "string" + ], + "streamable": true, + "name": "#fastq-list-row__1.0.0.yaml/fastq-list-row/read_2" + }, + { + "label": "rgid", + "doc": "The read-group id of the sample.\nOften an index\n", + "type": "string", + "name": "#fastq-list-row__1.0.0.yaml/fastq-list-row/rgid" + }, + { + "label": "rglb", + "doc": "The read-group library of the sample.\n", + "type": "string", + "name": "#fastq-list-row__1.0.0.yaml/fastq-list-row/rglb" + }, + { + "label": "rgsm", + "doc": "The read-group sample name\n", + "type": "string", + "name": "#fastq-list-row__1.0.0.yaml/fastq-list-row/rgsm" + } + ] + } + ], + "class": "SchemaDefRequirement" + } + ], + "baseCommand": [ + "bash" + ], + "arguments": [ + { + "valueFrom": "$(get_script_path())", + "position": -1 + }, + { + "prefix": "--intermediate-results-dir=", + "separate": false, + "valueFrom": "$(get_intermediate_results_dir())" + }, + { + "prefix": "--enable-rna=", + "separate": false, + "valueFrom": "true" + } + ], + "inputs": [ + { + "label": "annotation file", + "doc": "Path to annotation transcript file.\n", + "type": "File", + "inputBinding": { + "prefix": "--annotation-file=", + "separate": false + }, + "id": "#dragen-transcriptome__4.2.4.cwl/dragen-transcriptome--4.2.4/annotation_file" + }, + { + "label": "bam input", + "doc": "Input a BAM file for the Dragen RNA options\n", + "type": [ + "null", + "File" + ], + "inputBinding": { + "prefix": "--bam-input=", + "separate": false + }, + "secondaryFiles": [ + { + "pattern": ".bai", + "required": true + } + ], + "id": "#dragen-transcriptome__4.2.4.cwl/dragen-transcriptome--4.2.4/bam_input" + }, + { + "label": "enable duplicate marking", + "doc": "Mark identical alignments as duplicates\n", + "type": "boolean", + "inputBinding": { + "prefix": "--enable-duplicate-marking=", + "separate": false, + "valueFrom": "$(self.toString())" + }, + "id": "#dragen-transcriptome__4.2.4.cwl/dragen-transcriptome--4.2.4/enable_duplicate_marking" + }, + { + "label": "enable map align", + "doc": "Enabled by default.\nSet this value to false if using bam_input\n", + "type": [ + "null", + "boolean" + ], + "inputBinding": { + "prefix": "--enable-map-align=", + "separate": false, + "valueFrom": "$(self.toString())" + }, + "id": "#dragen-transcriptome__4.2.4.cwl/dragen-transcriptome--4.2.4/enable_map_align" + }, + { + "label": "enable map align output", + "doc": "Do you wish to have the output bam files present\n", + "type": "boolean", + "inputBinding": { + "prefix": "--enable-map-align-output=", + "separate": false, + "valueFrom": "$(self.toString())" + }, + "id": "#dragen-transcriptome__4.2.4.cwl/dragen-transcriptome--4.2.4/enable_map_align_output" + }, + { + "label": "enable rna gene fusion", + "type": [ + "null", + "boolean" + ], + "default": true, + "doc": "Enable the DRAGEN Gene Fusion module. The default value is true.\n", + "inputBinding": { + "prefix": "--enable-rna-gene-fusion=", + "separate": false, + "valueFrom": "$(self.toString())" + }, + "id": "#dragen-transcriptome__4.2.4.cwl/dragen-transcriptome--4.2.4/enable_rna_gene_fusion" + }, + { + "label": "enable rna quantification", + "type": [ + "null", + "boolean" + ], + "default": true, + "doc": "Enable the quantification module. The default value is true.\n", + "inputBinding": { + "prefix": "--enable-rna-quantification=", + "separate": false, + "valueFrom": "$(self.toString())" + }, + "id": "#dragen-transcriptome__4.2.4.cwl/dragen-transcriptome--4.2.4/enable_rna_quantification" + }, + { + "label": "enable rrna filtering", + "type": [ + "null", + "boolean" + ], + "default": true, + "doc": "Use the DRAGEN RNA pipeline to filter rRNA reads during alignment. The default value is false.\n", + "inputBinding": { + "prefix": "--rrna-filter-enable=", + "separate": false, + "valueFrom": "$(self.toString())" + }, + "id": "#dragen-transcriptome__4.2.4.cwl/dragen-transcriptome--4.2.4/enable_rrna_filter" + }, + { + "label": "enable sort", + "doc": "True by default, only set this to false if using --bam-input parameters\n", + "type": [ + "null", + "boolean" + ], + "inputBinding": { + "prefix": "--enable-sort=", + "separate": false, + "valueFrom": "$(self.toString())" + }, + "id": "#dragen-transcriptome__4.2.4.cwl/dragen-transcriptome--4.2.4/enable_sort" + }, + { + "label": "fastq list", + "doc": "CSV file that contains a list of FASTQ files\nto process. read_1 and read_2 components in the CSV file must be presigned urls.\n", + "type": [ + "null", + "File" + ], + "inputBinding": { + "loadContents": true, + "prefix": "--fastq-list=", + "separate": false, + "valueFrom": "$(get_fastq_list_csv_path())" + }, + "id": "#dragen-transcriptome__4.2.4.cwl/dragen-transcriptome--4.2.4/fastq_list" + }, + { + "label": "fastq list rows", + "doc": "Alternative to providing a file, one can instead provide a list of 'fastq-list-row' objects\n", + "type": [ + "null", + { + "type": "array", + "items": "#fastq-list-row__1.0.0.yaml/fastq-list-row" + } + ], + "inputBinding": { + "prefix": "--fastq-list=", + "separate": false, + "valueFrom": "$(get_fastq_list_csv_path())" + }, + "id": "#dragen-transcriptome__4.2.4.cwl/dragen-transcriptome--4.2.4/fastq_list_rows" + }, + { + "label": "license instance id location", + "doc": "You may wish to place your own in.\nOptional value, default set to /opt/instance-identity\nwhich is a path inside the dragen container\n", + "type": [ + "null", + "File", + "string" + ], + "default": "/opt/instance-identity", + "inputBinding": { + "prefix": "--lic-instance-id-location=", + "separate": false + }, + "id": "#dragen-transcriptome__4.2.4.cwl/dragen-transcriptome--4.2.4/lic_instance_id_location" + }, + { + "label": "output directory", + "doc": "The directory where all output files are placed.\n", + "type": "string", + "inputBinding": { + "prefix": "--output-directory=", + "separate": false + }, + "id": "#dragen-transcriptome__4.2.4.cwl/dragen-transcriptome--4.2.4/output_directory" + }, + { + "label": "output file prefix", + "doc": "The prefix given to all output files.\n", + "type": "string", + "inputBinding": { + "prefix": "--output-file-prefix=", + "separate": false + }, + "id": "#dragen-transcriptome__4.2.4.cwl/dragen-transcriptome--4.2.4/output_file_prefix" + }, + { + "label": "read trimming", + "type": [ + "null", + "string" + ], + "doc": "To enable trimming filters in hard-trimming mode, set to a comma-separated list of the trimmer tools\nyou would like to use. To disable trimming, set to none. During mapping, artifacts are removed from all reads.\nRead trimming is disabled by default.\n", + "inputBinding": { + "prefix": "--read-trimmers=", + "separate": false + }, + "id": "#dragen-transcriptome__4.2.4.cwl/dragen-transcriptome--4.2.4/read_trimmers" + }, + { + "label": "reference tar", + "doc": "Path to ref data tarball.\n", + "type": "File", + "inputBinding": { + "prefix": "--ref-dir=", + "separate": false, + "valueFrom": "$(get_ref_path(self))" + }, + "id": "#dragen-transcriptome__4.2.4.cwl/dragen-transcriptome--4.2.4/reference_tar" + }, + { + "label": "name of the rRNA sequences to use for filtering", + "type": [ + "null", + "string" + ], + "doc": "Specify the name of the rRNA sequences to use for filtering.\n", + "inputBinding": { + "prefix": "--rrna-filter-contig=", + "separate": false + }, + "id": "#dragen-transcriptome__4.2.4.cwl/dragen-transcriptome--4.2.4/rrna_filter_contig" + }, + { + "label": "soft read trimming", + "type": [ + "null", + "string" + ], + "doc": "To enable trimming filters in soft-trimming mode, set to a comma-separated list of the trimmer tools\nyou would like to use. To disable soft trimming, set to none. During mapping, reads are aligned as if trimmed,\nand bases are not removed from the reads. Soft-trimming is enabled for the polyg filter by default.\n", + "inputBinding": { + "prefix": "--soft-read-trimmers=", + "separate": false + }, + "id": "#dragen-transcriptome__4.2.4.cwl/dragen-transcriptome--4.2.4/soft_read_trimmers" + }, + { + "label": "trim adapter r1 5prime", + "type": [ + "null", + "File" + ], + "doc": "Specify the FASTA file that contains adapter sequences to trim from the 5' end of Read 1.\nNB: the sequences should be in reverse order (with respect to their appearance in the FASTQ) but not complemented.\n", + "inputBinding": { + "prefix": "--trim-adapter-r1-5prime=", + "separate": false + }, + "id": "#dragen-transcriptome__4.2.4.cwl/dragen-transcriptome--4.2.4/trim_adapter_r1_5prime" + }, + { + "label": "trim adapter r2 5prime", + "type": [ + "null", + "File" + ], + "doc": "Specify the FASTA file that contains adapter sequences to trim from the 5' end of Read 2.\nNB: the sequences should be in reverse order (with respect to their appearance in the FASTQ) but not complemented.\n", + "inputBinding": { + "prefix": "--trim-adapter-r2-5prime=", + "separate": false + }, + "id": "#dragen-transcriptome__4.2.4.cwl/dragen-transcriptome--4.2.4/trim_adapter_r2_5prime" + }, + { + "label": "trim adapter read1", + "type": [ + "null", + "File" + ], + "doc": "Specify the FASTA file that contains adapter sequences to trim from the 3' end of Read 1.\n", + "inputBinding": { + "prefix": "--trim-adapter-read1=", + "separate": false + }, + "id": "#dragen-transcriptome__4.2.4.cwl/dragen-transcriptome--4.2.4/trim_adapter_read1" + }, + { + "label": "trim adapter read2", + "type": [ + "null", + "File" + ], + "doc": "Specify the FASTA file that contains adapter sequences to trim from the 3' end of Read 2.\n", + "inputBinding": { + "prefix": "--trim_adapter_read2=", + "separate": false + }, + "id": "#dragen-transcriptome__4.2.4.cwl/dragen-transcriptome--4.2.4/trim_adapter_read2" + }, + { + "label": "trim adapter stringency", + "type": [ + "null", + "int" + ], + "doc": "Specify the minimum number of adapter bases required for trimming\n", + "inputBinding": { + "prefix": "--trim-adapter-stringency=", + "separate": false + }, + "id": "#dragen-transcriptome__4.2.4.cwl/dragen-transcriptome--4.2.4/trim_adapter_stringency" + }, + { + "label": "trim r1 3prime", + "type": [ + "null", + "int" + ], + "doc": "Specify the minimum number of bases to trim from the 3' end of Read 1 (default: 0).\n", + "inputBinding": { + "prefix": "--trim-min-r1-3prime=", + "separate": false + }, + "id": "#dragen-transcriptome__4.2.4.cwl/dragen-transcriptome--4.2.4/trim_r1_3prime" + }, + { + "label": "trim r1 5prime", + "type": [ + "null", + "int" + ], + "doc": "Specify the minimum number of bases to trim from the 5' end of Read 1 (default: 0).\n", + "inputBinding": { + "prefix": "--trim-min-r1-5prime=", + "separate": false + }, + "id": "#dragen-transcriptome__4.2.4.cwl/dragen-transcriptome--4.2.4/trim_r1_5prime" + }, + { + "label": "trim r2 3prime", + "type": [ + "null", + "int" + ], + "doc": "Specify the minimum number of bases to trim from the 3' end of Read 2 (default: 0).\n", + "inputBinding": { + "prefix": "--trim-min-r2-3prime=", + "separate": false + }, + "id": "#dragen-transcriptome__4.2.4.cwl/dragen-transcriptome--4.2.4/trim_r2_3prime" + }, + { + "label": "trim r2 5prime", + "type": [ + "null", + "int" + ], + "doc": "Specify the minimum number of bases to trim from the 5' end of Read 2 (default: 0).\n", + "inputBinding": { + "prefix": "--trim-min-r2-5prime=", + "separate": false + }, + "id": "#dragen-transcriptome__4.2.4.cwl/dragen-transcriptome--4.2.4/trim_r2_5prime" + } + ], + "outputs": [ + { + "label": "dragen bam out", + "doc": "The output bam file, exists only if --enable-map-align-output is set to true\n", + "type": [ + "null", + "File" + ], + "outputBinding": { + "glob": "$(inputs.output_directory)/$(inputs.output_file_prefix).bam" + }, + "secondaryFiles": [ + { + "pattern": ".bai", + "required": null + } + ], + "id": "#dragen-transcriptome__4.2.4.cwl/dragen-transcriptome--4.2.4/dragen_bam_out" + }, + { + "label": "dragen transcriptome output directory", + "doc": "The output directory containing all wts analysis output files\n", + "type": "Directory", + "outputBinding": { + "glob": "$(inputs.output_directory)" + }, + "id": "#dragen-transcriptome__4.2.4.cwl/dragen-transcriptome--4.2.4/dragen_transcriptome_directory" + } + ], + "successCodes": [ + 0 + ], + "https://schema.org/author": { + "class": "https://schema.org/Person", + "https://schema.org/name": "Sehrish Kanwal", + "https://schema.org/email": "sehrish.kanwal@umccr.org" + } + }, + { + "class": "CommandLineTool", + "id": "#multiqc__1.15.0.cwl", + "label": "multiqc v(1.15.0)", + "doc": "Documentation for multiqc v1.15.0\nUse patch that includes https://github.com/ewels/MultiQC/pull/1969\n", + "hints": [ + { + "dockerPull": "quay.io/umccr/multiqc:1.15-dev--eb98188", + "class": "DockerRequirement" + }, + { + "coresMin": 2, + "ramMin": 4000, + "class": "ResourceRequirement", + "https://platform.illumina.com/rdf/ica/resources:tier": "standard", + "https://platform.illumina.com/rdf/ica/resources:type": "standard", + "https://platform.illumina.com/rdf/ica/resources:size": "small" + } + ], + "requirements": [ + { + "class": "InlineJavascriptRequirement" + } + ], + "baseCommand": [ + "multiqc" + ], + "inputs": [ + { + "label": "cl config", + "doc": "Override config from the cli\n", + "type": [ + "null", + "string" + ], + "inputBinding": { + "prefix": "--cl-config" + }, + "id": "#multiqc__1.15.0.cwl/multiqc--1.15.0/cl_config" + }, + { + "label": "comment", + "doc": "Custom comment, will be printed at the top of the report.\n", + "type": [ + "null", + "string" + ], + "inputBinding": { + "prefix": "--comment" + }, + "id": "#multiqc__1.15.0.cwl/multiqc--1.15.0/comment" + }, + { + "label": "config", + "doc": "Configuration file for bclconvert\n", + "type": [ + "null", + "File" + ], + "streamable": true, + "inputBinding": { + "prefix": "--config" + }, + "id": "#multiqc__1.15.0.cwl/multiqc--1.15.0/config" + }, + { + "label": "dummy file", + "doc": "testing inputs stream logic\nIf used will set input mode to stream on ICA which\nsaves having to download the entire input folder\n", + "type": [ + "null", + "File" + ], + "streamable": true, + "id": "#multiqc__1.15.0.cwl/multiqc--1.15.0/dummy_file" + }, + { + "label": "input directories", + "doc": "The list of directories to place in the analysis\n", + "type": { + "type": "array", + "items": "Directory" + }, + "inputBinding": { + "position": 100 + }, + "id": "#multiqc__1.15.0.cwl/multiqc--1.15.0/input_directories" + }, + { + "label": "output directory", + "doc": "The output directory\n", + "type": "string", + "inputBinding": { + "prefix": "--outdir", + "valueFrom": "$(runtime.outdir)/$(self)" + }, + "id": "#multiqc__1.15.0.cwl/multiqc--1.15.0/output_directory_name" + }, + { + "label": "output filename", + "doc": "Report filename in html format.\nDefaults to 'multiqc-report.html\"\n", + "type": "string", + "inputBinding": { + "prefix": "--filename" + }, + "id": "#multiqc__1.15.0.cwl/multiqc--1.15.0/output_filename" + }, + { + "label": "title", + "doc": "Report title.\nPrinted as page header, used for filename if not otherwise specified.\n", + "type": "string", + "inputBinding": { + "prefix": "--title" + }, + "id": "#multiqc__1.15.0.cwl/multiqc--1.15.0/title" + } + ], + "outputs": [ + { + "label": "output directory", + "doc": "Directory that contains all multiqc analysis data\n", + "type": "Directory", + "outputBinding": { + "glob": "$(inputs.output_directory_name)" + }, + "id": "#multiqc__1.15.0.cwl/multiqc--1.15.0/output_directory" + }, + { + "label": "output file", + "doc": "Output html file\n", + "type": "File", + "outputBinding": { + "glob": "$(inputs.output_directory_name)/$(inputs.output_filename)" + }, + "id": "#multiqc__1.15.0.cwl/multiqc--1.15.0/output_file" + } + ], + "successCodes": [ + 0 + ], + "https://schema.org/author": { + "class": "https://schema.org/Person", + "https://schema.org/name": "Alexis Lucattini", + "https://schema.org/email": "Alexis.Lucattini@umccr.org", + "https://schema.org/identifier": "https://orcid.org/0000-0001-9754-647X" + } + }, + { + "class": "CommandLineTool", + "id": "#qualimap__2.2.2.cwl", + "label": "qualimap v(2.2.2)", + "doc": "It perform RNA-seq QC analysis on paired-end data http://qualimap.bioinfo.cipf.es/doc_html/command_line.html.\n", + "hints": [ + { + "dockerPull": "public.ecr.aws/biocontainers/qualimap:2.2.2d--hdfd78af_2", + "class": "DockerRequirement" + }, + { + "coresMin": 8, + "ramMin": 32000, + "class": "ResourceRequirement", + "https://platform.illumina.com/rdf/ica/resources:tier": "standard", + "https://platform.illumina.com/rdf/ica/resources:type": "standard", + "https://platform.illumina.com/rdf/ica/resources:size": "large" + } + ], + "requirements": [ + { + "listing": [ + { + "entryname": "run_qualimap.sh", + "entry": "#!/usr/bin/env bash\n\n# Set to fail\nset -euo pipefail\n\n# Set java opts\nif [[ ! -z \"$(inputs.tmp_dir)\" ]]\nthen\n export JAVA_OPTS=-Djava.io.tmpdir=\"$(inputs.tmp_dir)\"\nfi\n# Run qualimap\nqualimap rnaseq --paired \"\\${@}\"\n" + } + ], + "class": "InitialWorkDirRequirement" + }, + { + "class": "InlineJavascriptRequirement" + } + ], + "baseCommand": [ + "bash", + "run_qualimap.sh" + ], + "inputs": [ + { + "label": "algorithm", + "doc": "Counting algorithm:\nuniquely-mapped-reads(default) or proportional.\n", + "type": [ + "null", + "string" + ], + "inputBinding": { + "prefix": "--algorithm" + }, + "id": "#qualimap__2.2.2.cwl/qualimap--2.2.2/algorithm" + }, + { + "label": "gtf", + "doc": "Region file in GTF, GFF or BED format.\nIf GTF format is provided, counting is based on\nattributes, otherwise based on feature name.\n", + "type": "File", + "inputBinding": { + "prefix": "-gtf" + }, + "id": "#qualimap__2.2.2.cwl/qualimap--2.2.2/gtf" + }, + { + "label": "input bam", + "doc": "Input mapping file in BAM format.\n", + "type": "File", + "inputBinding": { + "prefix": "-bam" + }, + "id": "#qualimap__2.2.2.cwl/qualimap--2.2.2/input_bam" + }, + { + "label": "java mem", + "doc": "Set desired Java heap memory size\n", + "type": "string", + "inputBinding": { + "prefix": "--java-mem-size=", + "separate": false + }, + "id": "#qualimap__2.2.2.cwl/qualimap--2.2.2/java_mem" + }, + { + "label": "out dir", + "doc": "Output folder for HTML report and raw data.\n", + "type": "string", + "inputBinding": { + "prefix": "-outdir" + }, + "id": "#qualimap__2.2.2.cwl/qualimap--2.2.2/out_dir" + }, + { + "label": "seq protocol", + "type": [ + "null", + { + "type": "enum", + "symbols": [ + "#qualimap__2.2.2.cwl/qualimap--2.2.2/seq_protocol/strand-specific-forward", + "#qualimap__2.2.2.cwl/qualimap--2.2.2/seq_protocol/strand-specific-reverse", + "#qualimap__2.2.2.cwl/qualimap--2.2.2/seq_protocol/non-strand-specific" + ] + } + ], + "doc": "Sequencing library protocol:\nstrand-specific-forward, strand-specific-reverse or\nnon-strand-specific (default).\n", + "inputBinding": { + "prefix": "--sequencing-protocol" + }, + "id": "#qualimap__2.2.2.cwl/qualimap--2.2.2/seq_protocol" + }, + { + "label": "tmp dir", + "doc": "Qualimap creates temporary bam files when sorting by name, which takes up space in the system tmp dir (usually /tmp).\nThis can be avoided by sorting the bam file by name before running Qualimap.\n", + "type": [ + "null", + "string" + ], + "id": "#qualimap__2.2.2.cwl/qualimap--2.2.2/tmp_dir" + } + ], + "outputs": [ + { + "label": "qualimap qc", + "doc": "Output directory with qc files and report\n", + "type": "Directory", + "outputBinding": { + "glob": "$(inputs.out_dir)" + }, + "id": "#qualimap__2.2.2.cwl/qualimap--2.2.2/qualimap_qc" + } + ], + "successCodes": [ + 0 + ], + "https://schema.org/author": { + "class": "https://schema.org/Person", + "https://schema.org/name": "Sehrish Kanwal", + "https://schema.org/email": "sehrish.kanwal@umccr.org" + } + }, + { + "class": "Workflow", + "id": "#main", + "label": "dragen-transcriptome-pipeline v(4.2.4)", + "doc": "Documentation for dragen-transcriptome-pipeline v4.2.4\n", + "requirements": [ + { + "expressionLib": [ + "/* Author:Alexis Lucattini */\n/* For assistance on generation of typescript expressions */\n/* In CWL, please visit our wiki page at https://github.com/umccr/cwl-ica/wiki/TypeScript */\n/* Imports */\n/* Functions */\nfunction add_sample_to_sample_name_replace_in_multiqc_cl_config(multiqc_cl_config, sample_name_old, sample_name_new) {\n /*\n Get the normal RGSM value and then add _normal to it\n */\n if (multiqc_cl_config === undefined || multiqc_cl_config === null || multiqc_cl_config == \"\") {\n multiqc_cl_config = \"{}\";\n }\n var multiqc_cl_config_json = JSON.parse(multiqc_cl_config);\n if (multiqc_cl_config_json[\"sample_names_replace\"] !== null && multiqc_cl_config_json[\"sample_names_replace\"] !== undefined) {\n multiqc_cl_config_json[\"sample_names_replace\"][sample_name_old] = sample_name_new;\n }\n else {\n multiqc_cl_config_json[\"sample_names_replace\"] = {};\n multiqc_cl_config_json[\"sample_names_replace\"][sample_name_old] = sample_name_new;\n }\n return JSON.stringify(multiqc_cl_config_json);\n}\n" + ], + "class": "InlineJavascriptRequirement" + }, + { + "class": "MultipleInputFeatureRequirement" + }, + { + "class": "ScatterFeatureRequirement" + }, + { + "types": [ + { + "$import": "#fastq-list-row__1.0.0.yaml/fastq-list-row" + } + ], + "class": "SchemaDefRequirement" + }, + { + "class": "StepInputExpressionRequirement" + } + ], + "inputs": [ + { + "label": "algorithm", + "type": [ + "null", + "string" + ], + "doc": "Counting algorithm:\nuniquely-mapped-reads(default) or proportional.\n", + "default": "proportional", + "id": "#main/algorithm" + }, + { + "label": "annotation file", + "doc": "Path to annotation transcript file.\n", + "type": "File", + "id": "#main/annotation_file" + }, + { + "label": "bam input", + "doc": "Input a BAM file for WTS analysis\n", + "type": [ + "null", + "File" + ], + "secondaryFiles": [ + { + "pattern": ".bai", + "required": true + } + ], + "id": "#main/bam_input" + }, + { + "label": "blacklist", + "type": "File", + "doc": "File with blacklist range\n", + "id": "#main/blacklist" + }, + { + "label": "cl config", + "doc": "command line config to supply additional config values on the command line.\n", + "type": [ + "null", + "string" + ], + "id": "#main/cl_config" + }, + { + "label": "contigs", + "type": [ + "null", + "string" + ], + "doc": "Optional - List of interesting contigs\nIf not specified, defaults to 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y\n", + "id": "#main/contigs" + }, + { + "label": "cytobands", + "type": "File", + "doc": "Coordinates of the Giemsa staining bands.\n", + "id": "#main/cytobands" + }, + { + "label": "enable duplicate marking", + "doc": "Mark identical alignments as duplicates\n", + "type": "boolean", + "id": "#main/enable_duplicate_marking" + }, + { + "label": "enable map align", + "doc": "Enabled by default.\nSet this value to false if using bam_input AND tumor_bam_input\n", + "type": [ + "null", + "boolean" + ], + "id": "#main/enable_map_align" + }, + { + "label": "enable map align output", + "doc": "Do you wish to have the output bam files present\n", + "type": "boolean", + "id": "#main/enable_map_align_output" + }, + { + "label": "enable rna gene fusion", + "type": [ + "null", + "boolean" + ], + "doc": "Optional - Enable the DRAGEN Gene Fusion module - defaults to true\n", + "id": "#main/enable_rna_gene_fusion" + }, + { + "label": "enable rna quantification", + "type": [ + "null", + "boolean" + ], + "doc": "Optional - Enable the quantification module - defaults to true\n", + "id": "#main/enable_rna_quantification" + }, + { + "label": "enable sort", + "doc": "True by default, only set this to false if using --bam-input as input parameter\n", + "type": [ + "null", + "boolean" + ], + "id": "#main/enable_sort" + }, + { + "label": "fastq list", + "doc": "CSV file that contains a list of FASTQ files\nto process. read_1 and read_2 components in the CSV file must be presigned urls.\n", + "type": [ + "null", + "File" + ], + "id": "#main/fastq_list" + }, + { + "label": "Row of fastq lists", + "doc": "The row of fastq lists.\nEach row has the following attributes:\n * RGID\n * RGLB\n * RGSM\n * Lane\n * Read1File\n * Read2File (optional)\n", + "type": [ + "null", + { + "type": "array", + "items": "#fastq-list-row__1.0.0.yaml/fastq-list-row" + } + ], + "id": "#main/fastq_list_rows" + }, + { + "label": "java mem", + "type": "string", + "doc": "Set desired Java heap memory size\n", + "default": "20G", + "id": "#main/java_mem" + }, + { + "label": "license instance id location", + "doc": "You may wish to place your own in.\nOptional value, default set to /opt/instance-identity\nwhich is a path inside the dragen container\n", + "type": [ + "null", + "File", + "string" + ], + "id": "#main/lic_instance_id_location" + }, + { + "label": "output directory", + "doc": "The directory where all output files are placed\n", + "type": "string", + "id": "#main/output_directory" + }, + { + "label": "output directory name arriba", + "type": [ + "null", + "string" + ], + "doc": "Name of the directory to collect arriba outputs in.\n", + "default": "arriba", + "id": "#main/output_directory_name_arriba" + }, + { + "label": "output file prefix", + "doc": "The prefix given to all output files\n", + "type": "string", + "id": "#main/output_file_prefix" + }, + { + "label": "protein domains", + "type": "File", + "doc": "GFF3 file containing the genomic coordinates of protein domains.\n", + "id": "#main/protein_domains" + }, + { + "label": "qc reference samples", + "type": { + "type": "array", + "items": "Directory" + }, + "doc": "Reference samples for multiQC report\n", + "id": "#main/qc_reference_samples" + }, + { + "label": "read trimming", + "type": [ + "null", + "string" + ], + "doc": "To enable trimming filters in hard-trimming mode, set to a comma-separated list of the trimmer tools\nyou would like to use. To disable trimming, set to none. During mapping, artifacts are removed from all reads.\nRead trimming is disabled by default.\n", + "id": "#main/read_trimmers" + }, + { + "label": "reference Fasta", + "type": "File", + "doc": "FastA file with genome sequence\n", + "secondaryFiles": [ + { + "pattern": ".fai", + "required": true + } + ], + "id": "#main/reference_fasta" + }, + { + "label": "reference tar", + "doc": "Path to ref data tarball\n", + "type": "File", + "id": "#main/reference_tar" + }, + { + "label": "soft read trimming", + "type": [ + "null", + "string" + ], + "doc": "To enable trimming filters in soft-trimming mode, set to a comma-separated list of the trimmer tools\nyou would like to use. To disable soft trimming, set to none. During mapping, reads are aligned as if trimmed,\nand bases are not removed from the reads. Soft-trimming is enabled for the polyg filter by default.\n", + "id": "#main/soft_read_trimmers" + }, + { + "label": "tmp dir", + "type": [ + "null", + "string" + ], + "doc": "Qualimap creates temporary bam files when sorting by name, which takes up space in the system tmp dir (usually /tmp).\nThis can be avoided by sorting the bam file by name before running Qualimap.\n", + "default": "/scratch", + "id": "#main/tmp_dir" + }, + { + "label": "trim adapter r1 5prime", + "type": [ + "null", + "File" + ], + "doc": "Specify the FASTA file that contains adapter sequences to trim from the 5' end of Read 1.\nNB: the sequences should be in reverse order (with respect to their appearance in the FASTQ) but not complemented.\n", + "id": "#main/trim_adapter_r1_5prime" + }, + { + "label": "trim adapter read1", + "type": [ + "null", + "File" + ], + "doc": "Specify the FASTA file that contains adapter sequences to trim from the 3' end of Read 1.\n", + "id": "#main/trim_adapter_read1" + }, + { + "label": "trim adapter read2", + "type": [ + "null", + "File" + ], + "doc": "Specify the FASTA file that contains adapter sequences to trim from the 3' end of Read 2.\n", + "id": "#main/trim_adapter_read2" + }, + { + "label": "trim adapter stringency", + "type": [ + "null", + "int" + ], + "doc": "Specify the minimum number of adapter bases required for trimming\n", + "id": "#main/trim_adapter_stringency" + }, + { + "label": "trim adapter r2 5prime", + "type": [ + "null", + "File" + ], + "doc": "Specify the FASTA file that contains adapter sequences to trim from the 5' end of Read 2.\nNB: the sequences should be in reverse order (with respect to their appearance in the FASTQ) but not complemented.\n", + "id": "#main/trim_dapter_r2_5prime" + }, + { + "label": "trim r1 3prime", + "type": [ + "null", + "int" + ], + "doc": "Specify the minimum number of bases to trim from the 3' end of Read 1 (default: 0).\n", + "id": "#main/trim_r1_3prime" + }, + { + "label": "trim r1 5prime", + "type": [ + "null", + "int" + ], + "doc": "Specify the minimum number of bases to trim from the 5' end of Read 1 (default: 0).\n", + "id": "#main/trim_r1_5prime" + }, + { + "label": "trim r2 3prime", + "type": [ + "null", + "int" + ], + "doc": "Specify the minimum number of bases to trim from the 3' end of Read 2 (default: 0).\n", + "id": "#main/trim_r2_3prime" + }, + { + "label": "trim r2 5prime", + "type": [ + "null", + "int" + ], + "doc": "Specify the minimum number of bases to trim from the 5' end of Read 2 (default: 0).\n", + "id": "#main/trim_r2_5prime" + } + ], + "steps": [ + { + "label": "arriba drawing step", + "doc": "Run Arriba drawing script for fusions predicted by previous step.\n", + "in": [ + { + "source": "#main/annotation_file", + "id": "#main/arriba_drawing_step/annotation" + }, + { + "source": "#main/run_dragen_transcriptome_step/dragen_bam_out", + "id": "#main/arriba_drawing_step/bam_file" + }, + { + "source": "#main/cytobands", + "id": "#main/arriba_drawing_step/cytobands" + }, + { + "source": "#main/arriba_fusion_step/fusions", + "id": "#main/arriba_drawing_step/fusions" + }, + { + "source": "#main/protein_domains", + "id": "#main/arriba_drawing_step/protein_domains" + } + ], + "out": [ + { + "id": "#main/arriba_drawing_step/output_pdf" + } + ], + "run": "#arriba-drawing__2.4.0.cwl", + "id": "#main/arriba_drawing_step" + }, + { + "label": "arriba fusion step", + "doc": "Runs Arriba fusion calling on the bam file produced by Dragen.\n", + "in": [ + { + "source": "#main/annotation_file", + "id": "#main/arriba_fusion_step/annotation" + }, + { + "source": "#main/run_dragen_transcriptome_step/dragen_bam_out", + "id": "#main/arriba_fusion_step/bam_file" + }, + { + "source": "#main/blacklist", + "id": "#main/arriba_fusion_step/blacklist" + }, + { + "source": "#main/contigs", + "id": "#main/arriba_fusion_step/contigs" + }, + { + "source": "#main/reference_fasta", + "id": "#main/arriba_fusion_step/reference" + } + ], + "out": [ + { + "id": "#main/arriba_fusion_step/fusions" + }, + { + "id": "#main/arriba_fusion_step/discarded_fusions" + } + ], + "run": "#arriba-fusion-calling__2.4.0.cwl", + "id": "#main/arriba_fusion_step" + }, + { + "label": "create arriba output directory", + "doc": "Create an output directory to contain the arriba files\n", + "in": [ + { + "source": [ + "#main/arriba_fusion_step/fusions", + "#main/arriba_fusion_step/discarded_fusions", + "#main/arriba_drawing_step/output_pdf" + ], + "id": "#main/create_arriba_output_directory/input_files" + }, + { + "source": "#main/output_directory_name_arriba", + "id": "#main/create_arriba_output_directory/output_directory_name" + } + ], + "out": [ + "#main/create_arriba_output_directory/output_directory" + ], + "run": "#custom-create-directory__1.0.0.cwl", + "id": "#main/create_arriba_output_directory" + }, + { + "label": "Create dummy file", + "doc": "Intermediate step for letting multiqc-interop be placed in stream mode\n", + "in": [], + "out": [ + { + "id": "#main/create_dummy_file_step/dummy_file_output" + } + ], + "run": "#custom-touch-file__1.0.0.cwl", + "id": "#main/create_dummy_file_step" + }, + { + "label": "dragen qc step", + "doc": "The dragen qc step - this takes in an array of dirs\n", + "in": [ + { + "source": [ + "#main/cl_config", + "#main/output_file_prefix" + ], + "valueFrom": "${\n return add_sample_to_sample_name_replace_in_multiqc_cl_config(self[0], self[1] + \"_qualimap\", self[1]);\n}\n", + "id": "#main/dragen_qc_step/cl_config" + }, + { + "source": "#main/create_dummy_file_step/dummy_file_output", + "id": "#main/dragen_qc_step/dummy_file" + }, + { + "source": [ + "#main/run_dragen_transcriptome_step/dragen_transcriptome_directory", + "#main/run_qualimap_step/qualimap_qc", + "#main/qc_reference_samples" + ], + "linkMerge": "merge_flattened", + "id": "#main/dragen_qc_step/input_directories" + }, + { + "source": "#main/output_file_prefix", + "valueFrom": "$(self)_dragen_transcriptome_multiqc", + "id": "#main/dragen_qc_step/output_directory_name" + }, + { + "source": "#main/output_file_prefix", + "valueFrom": "$(self)_dragen_transcriptome_multiqc.html", + "id": "#main/dragen_qc_step/output_filename" + }, + { + "source": "#main/output_file_prefix", + "valueFrom": "UMCCR MultiQC Dragen Transcriptome Report for $(self)", + "id": "#main/dragen_qc_step/title" + } + ], + "out": [ + { + "id": "#main/dragen_qc_step/output_directory" + }, + { + "id": "#main/dragen_qc_step/output_file" + } + ], + "run": "#multiqc__1.15.0.cwl", + "id": "#main/dragen_qc_step" + }, + { + "label": "run dragen transcriptome step", + "doc": "Runs the dragen transcriptome workflow on the FPGA.\nTakes in a fastq list and corresponding mount paths from the predefined_mount_paths.\nAll other options avaiable at the top of the workflow\n", + "in": [ + { + "source": "#main/annotation_file", + "id": "#main/run_dragen_transcriptome_step/annotation_file" + }, + { + "source": "#main/bam_input", + "id": "#main/run_dragen_transcriptome_step/bam_input" + }, + { + "source": "#main/enable_duplicate_marking", + "id": "#main/run_dragen_transcriptome_step/enable_duplicate_marking" + }, + { + "source": "#main/enable_map_align", + "id": "#main/run_dragen_transcriptome_step/enable_map_align" + }, + { + "source": "#main/enable_map_align_output", + "id": "#main/run_dragen_transcriptome_step/enable_map_align_output" + }, + { + "source": "#main/enable_rna_gene_fusion", + "id": "#main/run_dragen_transcriptome_step/enable_rna_gene_fusion" + }, + { + "source": "#main/enable_rna_quantification", + "id": "#main/run_dragen_transcriptome_step/enable_rna_quantification" + }, + { + "source": "#main/enable_sort", + "id": "#main/run_dragen_transcriptome_step/enable_sort" + }, + { + "source": "#main/fastq_list", + "id": "#main/run_dragen_transcriptome_step/fastq_list" + }, + { + "source": "#main/fastq_list_rows", + "id": "#main/run_dragen_transcriptome_step/fastq_list_rows" + }, + { + "source": "#main/lic_instance_id_location", + "id": "#main/run_dragen_transcriptome_step/lic_instance_id_location" + }, + { + "source": "#main/output_directory", + "id": "#main/run_dragen_transcriptome_step/output_directory" + }, + { + "source": "#main/output_file_prefix", + "id": "#main/run_dragen_transcriptome_step/output_file_prefix" + }, + { + "source": "#main/read_trimmers", + "id": "#main/run_dragen_transcriptome_step/read_trimmers" + }, + { + "source": "#main/reference_tar", + "id": "#main/run_dragen_transcriptome_step/reference_tar" + }, + { + "source": "#main/soft_read_trimmers", + "id": "#main/run_dragen_transcriptome_step/soft_read_trimmers" + }, + { + "source": "#main/trim_adapter_r1_5prime", + "id": "#main/run_dragen_transcriptome_step/trim_adapter_r1_5prime" + }, + { + "source": "#main/trim_dapter_r2_5prime", + "id": "#main/run_dragen_transcriptome_step/trim_adapter_r2_5prime" + }, + { + "source": "#main/trim_adapter_read1", + "id": "#main/run_dragen_transcriptome_step/trim_adapter_read1" + }, + { + "source": "#main/trim_adapter_read2", + "id": "#main/run_dragen_transcriptome_step/trim_adapter_read2" + }, + { + "source": "#main/trim_adapter_stringency", + "id": "#main/run_dragen_transcriptome_step/trim_adapter_stringency" + }, + { + "source": "#main/trim_r1_3prime", + "id": "#main/run_dragen_transcriptome_step/trim_r1_3prime" + }, + { + "source": "#main/trim_r1_5prime", + "id": "#main/run_dragen_transcriptome_step/trim_r1_5prime" + }, + { + "source": "#main/trim_r2_3prime", + "id": "#main/run_dragen_transcriptome_step/trim_r2_3prime" + }, + { + "source": "#main/trim_r2_5prime", + "id": "#main/run_dragen_transcriptome_step/trim_r2_5prime" + } + ], + "out": [ + { + "id": "#main/run_dragen_transcriptome_step/dragen_transcriptome_directory" + }, + { + "id": "#main/run_dragen_transcriptome_step/dragen_bam_out" + } + ], + "run": "#dragen-transcriptome__4.2.4.cwl", + "id": "#main/run_dragen_transcriptome_step" + }, + { + "label": "run qualimap step", + "doc": "Run qualimap step to generate additional QC metrics\n", + "in": [ + { + "source": "#main/algorithm", + "id": "#main/run_qualimap_step/algorithm" + }, + { + "source": "#main/annotation_file", + "id": "#main/run_qualimap_step/gtf" + }, + { + "source": "#main/run_dragen_transcriptome_step/dragen_bam_out", + "id": "#main/run_qualimap_step/input_bam" + }, + { + "source": "#main/java_mem", + "id": "#main/run_qualimap_step/java_mem" + }, + { + "source": "#main/output_file_prefix", + "valueFrom": "$(self)_qualimap", + "id": "#main/run_qualimap_step/out_dir" + }, + { + "source": "#main/tmp_dir", + "id": "#main/run_qualimap_step/tmp_dir" + } + ], + "out": [ + { + "id": "#main/run_qualimap_step/qualimap_qc" + } + ], + "run": "#qualimap__2.2.2.cwl", + "id": "#main/run_qualimap_step" + } + ], + "outputs": [ + { + "label": "arriba output directory", + "doc": "The directory containing output files from arriba\n", + "type": "Directory", + "outputSource": "#main/create_arriba_output_directory/output_directory", + "id": "#main/arriba_output_directory" + }, + { + "label": "dragen transcriptome output directory", + "doc": "The output directory containing all transcriptome output files\n", + "type": "Directory", + "outputSource": "#main/run_dragen_transcriptome_step/dragen_transcriptome_directory", + "id": "#main/dragen_transcriptome_output_directory" + }, + { + "label": "multiqc output directory", + "doc": "The output directory for multiqc\n", + "type": "Directory", + "outputSource": "#main/dragen_qc_step/output_directory", + "id": "#main/multiqc_output_directory" + }, + { + "label": "dragen transcriptome output directory", + "doc": "The output directory containing all transcriptome output files\n", + "type": "Directory", + "outputSource": "#main/run_qualimap_step/qualimap_qc", + "id": "#main/qualimap_output_directory" + } + ], + "https://schema.org/author": { + "class": "https://schema.org/Person", + "https://schema.org/name": "Sehrish Kanwal", + "https://schema.org/email": "sehrish.kanwal@umccr.org" + } + } + ], + "cwlVersion": "v1.1", + "$schemas": [ + "https://schema.org/version/latest/schemaorg-current-http.rdf" + ], + "$namespaces": { + "s": "https://schema.org/" + } +} \ No newline at end of file From 504f20ff1ba1262e10878a9e7659d9ecd6b579c3 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Thu, 27 Jun 2024 04:04:48 +0000 Subject: [PATCH 2/3] Uploading visual images for dragen-transcriptome-pipeline__4.2.4__20240627040250 release --- .../workflow.svg | 653 ++++++++++++++++++ 1 file changed, 653 insertions(+) create mode 100644 .github/releases/dragen-transcriptome-pipeline__4.2.4__20240627040250/workflow.svg diff --git a/.github/releases/dragen-transcriptome-pipeline__4.2.4__20240627040250/workflow.svg b/.github/releases/dragen-transcriptome-pipeline__4.2.4__20240627040250/workflow.svg new file mode 100644 index 00000000..35fe1152 --- /dev/null +++ b/.github/releases/dragen-transcriptome-pipeline__4.2.4__20240627040250/workflow.svg @@ -0,0 +1,653 @@ + + + + + + +G + + +cluster_inputs + +Workflow Inputs + + +cluster_outputs + +Workflow Outputs + + + +arriba_fusion_step + +arriba-fusion-calling v(2.4.0) + + + +arriba_drawing_step + +arriba-drawing v(2.4.0) + + + +arriba_fusion_step->arriba_drawing_step + + + + + +create_arriba_output_directory + +custom-create-directory v(1.0.0) + + + +arriba_fusion_step->create_arriba_output_directory + + + + + +arriba_fusion_step->create_arriba_output_directory + + + + + +arriba_drawing_step->create_arriba_output_directory + + + + + +run_dragen_transcriptome_step + +dragen-transcriptome v(4.2.4) + + + +run_dragen_transcriptome_step->arriba_fusion_step + + + + + +run_dragen_transcriptome_step->arriba_drawing_step + + + + + +dragen_qc_step + +multiqc v(1.15.0) + + + +run_dragen_transcriptome_step->dragen_qc_step + + + + + +run_qualimap_step + +qualimap v(2.2.2) + + + +run_dragen_transcriptome_step->run_qualimap_step + + + + + +dragen_transcriptome_output_directory + +dragen_transcriptome_output_directory + + + +run_dragen_transcriptome_step->dragen_transcriptome_output_directory + + + + + +arriba_output_directory + +arriba_output_directory + + + +create_arriba_output_directory->arriba_output_directory + + + + + +multiqc_output_directory + +multiqc_output_directory + + + +dragen_qc_step->multiqc_output_directory + + + + + +create_dummy_file_step + +custom-create-dummy-file v(1.0.0) + + + +create_dummy_file_step->dragen_qc_step + + + + + +run_qualimap_step->dragen_qc_step + + + + + +qualimap_output_directory + +qualimap_output_directory + + + +run_qualimap_step->qualimap_output_directory + + + + + +annotation_file + +annotation_file + + + +annotation_file->arriba_fusion_step + + + + + +annotation_file->arriba_drawing_step + + + + + +annotation_file->run_dragen_transcriptome_step + + + + + +annotation_file->run_qualimap_step + + + + + +cytobands + +cytobands + + + +cytobands->arriba_drawing_step + + + + + +protein_domains + +protein_domains + + + +protein_domains->arriba_drawing_step + + + + + +blacklist + +blacklist + + + +blacklist->arriba_fusion_step + + + + + +contigs + +contigs + + + +contigs->arriba_fusion_step + + + + + +reference_fasta + +reference_fasta + + + +reference_fasta->arriba_fusion_step + + + + + +output_directory_name_arriba + +output_directory_name_arriba + + + +output_directory_name_arriba->create_arriba_output_directory + + + + + +cl_config + +cl_config + + + +cl_config->dragen_qc_step + + + + + +output_file_prefix + +output_file_prefix + + + +output_file_prefix->run_dragen_transcriptome_step + + + + + +output_file_prefix->dragen_qc_step + + + + + +output_file_prefix->dragen_qc_step + + + + + +output_file_prefix->dragen_qc_step + + + + + +output_file_prefix->dragen_qc_step + + + + + +output_file_prefix->run_qualimap_step + + + + + +qc_reference_samples + +qc_reference_samples + + + +qc_reference_samples->dragen_qc_step + + + + + +bam_input + +bam_input + + + +bam_input->run_dragen_transcriptome_step + + + + + +enable_duplicate_marking + +enable_duplicate_marking + + + +enable_duplicate_marking->run_dragen_transcriptome_step + + + + + +enable_map_align + +enable_map_align + + + +enable_map_align->run_dragen_transcriptome_step + + + + + +enable_map_align_output + +enable_map_align_output + + + +enable_map_align_output->run_dragen_transcriptome_step + + + + + +enable_rna_gene_fusion + +enable_rna_gene_fusion + + + +enable_rna_gene_fusion->run_dragen_transcriptome_step + + + + + +enable_rna_quantification + +enable_rna_quantification + + + +enable_rna_quantification->run_dragen_transcriptome_step + + + + + +enable_sort + +enable_sort + + + +enable_sort->run_dragen_transcriptome_step + + + + + +fastq_list + +fastq_list + + + +fastq_list->run_dragen_transcriptome_step + + + + + +fastq_list_rows + +fastq_list_rows + + + +fastq_list_rows->run_dragen_transcriptome_step + + + + + +lic_instance_id_location + +lic_instance_id_location + + + +lic_instance_id_location->run_dragen_transcriptome_step + + + + + +output_directory + +output_directory + + + +output_directory->run_dragen_transcriptome_step + + + + + +read_trimmers + +read_trimmers + + + +read_trimmers->run_dragen_transcriptome_step + + + + + +reference_tar + +reference_tar + + + +reference_tar->run_dragen_transcriptome_step + + + + + +soft_read_trimmers + +soft_read_trimmers + + + +soft_read_trimmers->run_dragen_transcriptome_step + + + + + +trim_adapter_r1_5prime + +trim_adapter_r1_5prime + + + +trim_adapter_r1_5prime->run_dragen_transcriptome_step + + + + + +trim_dapter_r2_5prime + +trim_dapter_r2_5prime + + + +trim_dapter_r2_5prime->run_dragen_transcriptome_step + + + + + +trim_adapter_read1 + +trim_adapter_read1 + + + +trim_adapter_read1->run_dragen_transcriptome_step + + + + + +trim_adapter_read2 + +trim_adapter_read2 + + + +trim_adapter_read2->run_dragen_transcriptome_step + + + + + +trim_adapter_stringency + +trim_adapter_stringency + + + +trim_adapter_stringency->run_dragen_transcriptome_step + + + + + +trim_r1_3prime + +trim_r1_3prime + + + +trim_r1_3prime->run_dragen_transcriptome_step + + + + + +trim_r1_5prime + +trim_r1_5prime + + + +trim_r1_5prime->run_dragen_transcriptome_step + + + + + +trim_r2_3prime + +trim_r2_3prime + + + +trim_r2_3prime->run_dragen_transcriptome_step + + + + + +trim_r2_5prime + +trim_r2_5prime + + + +trim_r2_5prime->run_dragen_transcriptome_step + + + + + +algorithm + +algorithm + + + +algorithm->run_qualimap_step + + + + + +java_mem + +java_mem + + + +java_mem->run_qualimap_step + + + + + +tmp_dir + +tmp_dir + + + +tmp_dir->run_qualimap_step + + + + + From e09762aa93a8d58ba2e42c399964061dc6757f06 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Thu, 27 Jun 2024 04:10:39 +0000 Subject: [PATCH 3/3] Updated config/icav2.yaml to include new bundles --- config/icav2.yaml | 179 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 179 insertions(+) diff --git a/config/icav2.yaml b/config/icav2.yaml index 2040b372..8cb5322e 100644 --- a/config/icav2.yaml +++ b/config/icav2.yaml @@ -1911,3 +1911,182 @@ bundles: - secondary-analysis projects: - production + - bundle_name: dragen_transcriptome_pipeline_with_validation_data__4_2_4__20240627040250 + bundle_description: 'This bundle has been generated by the release of workflows/dragen-transcriptome-pipeline/4.2.4/dragen-transcriptome-pipeline__4.2.4.cwl. + The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-transcriptome-pipeline/4.2.4__20240627040250. ' + bundle_version: v9_r3__20240627040250 + bundle_version_description: Bundle version description is currently redundant + while we cannot append versions to bundles. Regardless - the bunch version is + v9_r3 + bundle_region_id: 1efd315d-6309-4d7e-826b-d3824b0b5acb + bundle_region_city_name: Sydney + tenant_name: umccr-prod + pipeline_path: + workflows/dragen-transcriptome-pipeline/4.2.4/dragen-transcriptome-pipeline__4.2.4.cwl + pipeline_name: dragen-transcriptome-pipeline + pipeline_version: 4.2.4 + pipeline_release_url: + https://github.com/umccr/cwl-ica/releases/tag/dragen-transcriptome-pipeline/4.2.4__20240627040250 + pipeline_commit_id: dragen-transcriptome-pipeline/4.2.4__20240627040250 + pipeline_checksum: 7ae80f7cb086f5c300d86f82e07b8593 + pipeline_project_id: 5844391a-69db-4b52-86b5-6a0d55c2386f + bundle_creation_time: '2024-06-27T04:04:55Z' + bundle_release_status: draft + bunch_name: dragen_transcriptome_pipeline_with_validation_data__4_2_4 + bunch_version: v9_r3 + bunch_datasets: + - dataset_name: dragen_hash_table_v9_r3_alt_masked_cnv_hla_rna + dataset_creation_time: '2024-06-21T09:21:42Z' + dataset_id_hash: a5fe1d2e2fe35737bdbc0871d46878e1 + - dataset_name: hg38_fasta + dataset_creation_time: '2024-06-21T11:31:50Z' + dataset_id_hash: 5f129b14aca5b4a7fda902590b15abc2 + - dataset_name: arriba_2_4_0 + dataset_creation_time: '2024-06-21T11:31:26Z' + dataset_id_hash: 8695cf0a98c5cda5726f67d4922da67f + - dataset_name: wts_validation_fastq__SBJ00480 + dataset_creation_time: '2024-06-21T09:41:15Z' + dataset_id_hash: c8b8bdc7e384aaa470b12992ce196693 + - dataset_name: wts_validation_fastq__SBJ00028 + dataset_creation_time: '2024-06-21T09:42:31Z' + dataset_id_hash: fa76e6ca3a0fb0be2bf41840a7aeeb01 + - dataset_name: wts_validation_fastq__SBJ00061 + dataset_creation_time: '2024-06-21T09:42:54Z' + dataset_id_hash: 63ee438354c347b05218b9bddc53d936 + - dataset_name: wts_validation_fastq__SBJ00188 + dataset_creation_time: '2024-06-21T09:43:11Z' + dataset_id_hash: 401d12d90e00db19918e5c9ce13a3da0 + - dataset_name: wts_validation_fastq__SBJ00199 + dataset_creation_time: '2024-06-21T09:49:27Z' + dataset_id_hash: b95ac04c7e3c03a8b1868a4571d23d5f + - dataset_name: wts_validation_fastq__SBJ00236 + dataset_creation_time: '2024-06-21T09:49:54Z' + dataset_id_hash: f084081c52ddda14328294d7bb7f13f4 + - dataset_name: wts_validation_fastq__SBJ00238 + dataset_creation_time: '2024-06-21T09:50:29Z' + dataset_id_hash: ba04ff08acbfbd1c17f1aadc0e8b3cf5 + - dataset_name: wts_multiqc__2023_07_21__4_2_4__Ref_1_Good__SBJ01563 + dataset_creation_time: '2024-06-21T11:33:06Z' + dataset_id_hash: 8de637be95f6ded72f61103bc842da45 + - dataset_name: wts_multiqc__2023_07_21__4_2_4__Ref_2_Good__SBJ01147 + dataset_creation_time: '2024-06-21T11:34:05Z' + dataset_id_hash: e11d32cd8efced32065a52eea33b06d1 + - dataset_name: wts_multiqc__2023_07_21__4_2_4__Ref_3_Good__SBJ01620 + dataset_creation_time: '2024-06-21T11:34:29Z' + dataset_id_hash: 0f0fee1a6b1f7b46978643839ffc0e88 + - dataset_name: wts_multiqc__2023_07_21__4_2_4__Ref_4_Bad__SBJ01286 + dataset_creation_time: '2024-06-21T11:34:51Z' + dataset_id_hash: 3d9dae1be84d29848f24df81d1ab4219 + - dataset_name: wts_multiqc__2023_07_21__4_2_4__Ref_5_Bad__SBJ01673 + dataset_creation_time: '2024-06-21T11:35:25Z' + dataset_id_hash: 42a9396b3f5d7e919e30a0f59f2401b7 + bundle_id: c6693421-03ce-472d-b2e0-7a793a2d3bff + bundle_data_ids: + - fil.2082d35d90fb4b9e126a08dc7a0472f4 + - fil.33b0c303aa2a44efda7008dc8578d1bb + - fil.8ab696eccee945064fe608dc9159afed + - fil.8950646b2bcf4137dac908dc8578d1bb + - fil.361af4dcff7840b5dab808dc8578d1bb + - fil.e956bc1d6e124433503f08dc9159afed + - fil.00db7f575e3c4741766608dc8682e79a + - fil.848678f252004cae726508dc8578d1b7 + - fil.e47895b2674b40cf727508dc8578d1b7 + - fil.f7b97fcf876b4409727608dc8578d1b7 + - fil.ad6640db600e44e1727a08dc8578d1b7 + - fil.6e3e68b7fc8b48ef76a908dc8682e79a + - fil.25ae81b4f33146b2769708dc8682e79a + - fil.dc806da29f02402076aa08dc8682e79a + - fil.8ed5724bce234ff276ad08dc8682e79a + - fil.2c3073bee29c47ea76ae08dc8682e79a + - fil.a191c268b58b414972ae08dc8578d1b7 + - fil.f4d61a69d418416a76af08dc8682e79a + - fil.554ab8b39c49488a76b208dc8682e79a + - fil.728b7d6332dd4d2e72af08dc8578d1b7 + - fol.4bfb05e08c2c46e7927908dc8578d1b7 + - fol.a3f65803908c4f29969508dc8682e79a + - fol.841783fe78e64b7e96cd08dc8682e79a + - fol.0dcfcd90b98d4b58925408dc8578d1b7 + - fol.7ff6b53c0f0148b7970c08dc8682e79a + bundle_pipeline_id: cdd9d473-8ce1-493d-bae6-687b03c5e869 + bundle_url: + https://ica.illumina.com/ica/bundles/c6693421-03ce-472d-b2e0-7a793a2d3bff/bundleDetails + bundle_categories: + - wts + - somatic + - validation + - secondary-analysis + projects: + - development + - staging + - bundle_name: dragen_transcriptome_pipeline_prod__4_2_4__20240627040250 + bundle_description: 'This bundle has been generated by the release of workflows/dragen-transcriptome-pipeline/4.2.4/dragen-transcriptome-pipeline__4.2.4.cwl. + The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-transcriptome-pipeline/4.2.4__20240627040250. ' + bundle_version: v9_r3__20240627040250 + bundle_version_description: Bundle version description is currently redundant + while we cannot append versions to bundles. Regardless - the bunch version is + v9_r3 + bundle_region_id: 1efd315d-6309-4d7e-826b-d3824b0b5acb + bundle_region_city_name: Sydney + tenant_name: umccr-prod + pipeline_path: + workflows/dragen-transcriptome-pipeline/4.2.4/dragen-transcriptome-pipeline__4.2.4.cwl + pipeline_name: dragen-transcriptome-pipeline + pipeline_version: 4.2.4 + pipeline_release_url: + https://github.com/umccr/cwl-ica/releases/tag/dragen-transcriptome-pipeline/4.2.4__20240627040250 + pipeline_commit_id: dragen-transcriptome-pipeline/4.2.4__20240627040250 + pipeline_checksum: 7ae80f7cb086f5c300d86f82e07b8593 + pipeline_project_id: 5844391a-69db-4b52-86b5-6a0d55c2386f + bundle_creation_time: '2024-06-27T04:08:45Z' + bundle_release_status: draft + bunch_name: dragen_transcriptome_pipeline_prod__4_2_4 + bunch_version: v9_r3 + bunch_datasets: + - dataset_name: dragen_hash_table_v9_r3_alt_masked_cnv_hla_rna + dataset_creation_time: '2024-06-21T09:21:42Z' + dataset_id_hash: a5fe1d2e2fe35737bdbc0871d46878e1 + - dataset_name: hg38_fasta + dataset_creation_time: '2024-06-21T11:31:50Z' + dataset_id_hash: 5f129b14aca5b4a7fda902590b15abc2 + - dataset_name: arriba_2_4_0 + dataset_creation_time: '2024-06-21T11:31:26Z' + dataset_id_hash: 8695cf0a98c5cda5726f67d4922da67f + - dataset_name: wts_multiqc__2023_07_21__4_2_4__Ref_1_Good__SBJ01563 + dataset_creation_time: '2024-06-21T11:33:06Z' + dataset_id_hash: 8de637be95f6ded72f61103bc842da45 + - dataset_name: wts_multiqc__2023_07_21__4_2_4__Ref_2_Good__SBJ01147 + dataset_creation_time: '2024-06-21T11:34:05Z' + dataset_id_hash: e11d32cd8efced32065a52eea33b06d1 + - dataset_name: wts_multiqc__2023_07_21__4_2_4__Ref_3_Good__SBJ01620 + dataset_creation_time: '2024-06-21T11:34:29Z' + dataset_id_hash: 0f0fee1a6b1f7b46978643839ffc0e88 + - dataset_name: wts_multiqc__2023_07_21__4_2_4__Ref_4_Bad__SBJ01286 + dataset_creation_time: '2024-06-21T11:34:51Z' + dataset_id_hash: 3d9dae1be84d29848f24df81d1ab4219 + - dataset_name: wts_multiqc__2023_07_21__4_2_4__Ref_5_Bad__SBJ01673 + dataset_creation_time: '2024-06-21T11:35:25Z' + dataset_id_hash: 42a9396b3f5d7e919e30a0f59f2401b7 + bundle_id: a5a60e54-be4e-4df2-a6e1-255e05a78d11 + bundle_data_ids: + - fil.2082d35d90fb4b9e126a08dc7a0472f4 + - fil.33b0c303aa2a44efda7008dc8578d1bb + - fil.8ab696eccee945064fe608dc9159afed + - fil.8950646b2bcf4137dac908dc8578d1bb + - fil.361af4dcff7840b5dab808dc8578d1bb + - fil.e956bc1d6e124433503f08dc9159afed + - fol.4bfb05e08c2c46e7927908dc8578d1b7 + - fol.a3f65803908c4f29969508dc8682e79a + - fol.841783fe78e64b7e96cd08dc8682e79a + - fol.0dcfcd90b98d4b58925408dc8578d1b7 + - fol.7ff6b53c0f0148b7970c08dc8682e79a + bundle_pipeline_id: cdd9d473-8ce1-493d-bae6-687b03c5e869 + bundle_url: + https://ica.illumina.com/ica/bundles/a5a60e54-be4e-4df2-a6e1-255e05a78d11/bundleDetails + bundle_categories: + - wts + - somatic + - production + - secondary-analysis + projects: + - development + - staging