From f49b9fe601e8c68e4d59d4b8fb819c879fb26b1c Mon Sep 17 00:00:00 2001 From: gschang Date: Tue, 2 Mar 2021 18:45:29 -0600 Subject: [PATCH] Fix cgpbigwig_bamcoverage step and update workflow example of rnaseq.cwl --- definitions/tools/bam_to_bigwig.cwl | 4 +- example_data/rnaseq/workflow.yaml | 88 ++++++++++++++++------------- 2 files changed, 51 insertions(+), 41 deletions(-) mode change 100644 => 100755 definitions/tools/bam_to_bigwig.cwl mode change 100644 => 100755 example_data/rnaseq/workflow.yaml diff --git a/definitions/tools/bam_to_bigwig.cwl b/definitions/tools/bam_to_bigwig.cwl old mode 100644 new mode 100755 index 1ba8e5b72..67dcc055d --- a/definitions/tools/bam_to_bigwig.cwl +++ b/definitions/tools/bam_to_bigwig.cwl @@ -3,7 +3,7 @@ cwlVersion: v1.0 class: CommandLineTool label: 'cgpBigWig Converting BAM to BigWig' -baseCommand: ["bam2bw", "-a -F", "1024"] +baseCommand: ["bam2bw", "-a", "-F", "1024"] arguments: ["-o", { valueFrom: $(inputs.bam.nameroot).bw}] requirements: - class: DockerRequirement @@ -16,7 +16,7 @@ inputs: inputBinding: position: 1 prefix: '-i' - secondaryFiles: [^.bai, .bai] + secondaryFiles: [.bai] reference: type: - string diff --git a/example_data/rnaseq/workflow.yaml b/example_data/rnaseq/workflow.yaml old mode 100644 new mode 100755 index e133266d0..39f7a7b8a --- a/example_data/rnaseq/workflow.yaml +++ b/example_data/rnaseq/workflow.yaml @@ -1,39 +1,49 @@ -instrument_data_bams: - - class: File - path: gerald_H3MYFBBXX_4_GCCAAT_1k.bam - - class: File - path: gerald_H3MYFBBXX_5_GCCAAT_1k.bam -reference_index: - class: File - path: /gscmnt/gc2560/core/GRC-human-build38_human_90_38/rna_seq_annotation/hisat2.1.0_index/GRCh38DH -reference_annotation: - class: File - path: /gscmnt/gc2560/core/GRC-human-build38_human_90_38/rna_seq_annotation/Homo_sapiens.GRCh38DH.90.gtf -kallisto_index: - class: File - path: /gscmnt/gc2560/core/GRC-human-build38_human_90_38/rna_seq_annotation/Homo_sapiens.GRCh38.cdna.all.fa.kallisto.idx -gene_transcript_lookup_table: - class: File - path: /gscmnt/gc2560/core/GRC-human-build38_human_90_38/rna_seq_annotation/ensembl90.transcriptToGene.tsv -read_group_id: - - '2895626107' - - '2895626112' -read_group_fields: - - ['PU:H3MYFBBXX5.4.GCCAAT', 'SM:H_NJ-HCC1395-HCC1395_RNA', 'LB:Pooled_RNA_2891007020-cD1-lib1', 'PL:Illumina', 'CN:WUGSC'] - - ['PU:H3MYFBBXX5.5.GCCAAT', 'SM:H_NJ-HCC1395-HCC1395_RNA', 'LB:Pooled_RNA_2891007020-cD1-lib1', 'PL:Illumina', 'CN:WUGSC'] -trimming_adapters: - class: File - path: illumina_multiplex.fa -trimming_adapter_trim_end: 'RIGHT' -trimming_adapter_min_overlap: 7 -trimming_max_uncalled: 300 -trimming_min_readlength: 25 -sample_name: H_NJ-HCC1395-HCC1395_RNA -firststrand: TRUE -refFlat: - class: File - path: /gscmnt/gc2560/core/GRC-human-build38_human_90_38_U2AF1_fix/rna_seq_annotation/Homo_sapiens.GRCh38.90.refFlat.txt -ribosomal_intervals: - class: File - path: /gscmnt/gc2560/core/GRC-human-build38_human_90_38_U2AF1_fix/rna_seq_annotation/Homo_sapiens.GRCh38.90.rRNA.interval_list -strand: "second" +instrument_data_bams: + - class: File + path: gerald_H3MYFBBXX_4_GCCAAT_1k.bam + - class: File + path: gerald_H3MYFBBXX_5_GCCAAT_1k.bam +reference: /gscmnt/gc2560/core/model_data/2887491634/build21f22873ebe0486c8e6f69c15435aa96/all_sequences.fa +reference_index: + class: File + path: /gscmnt/gc2560/core/GRC-human-build38_human_95_38_U2AF1_fix/rna_seq_annotation/hisat2.1.0_index/GRCh38DH +reference_annotation: + class: File + path: /gscmnt/gc2560/core/GRC-human-build38_human_95_38_U2AF1_fix/rna_seq_annotation/Homo_sapiens.GRCh38.95.gtf +kallisto_index: + class: File + path: /gscmnt/gc2560/core/GRC-human-build38_human_95_38_U2AF1_fix/rna_seq_annotation/Homo_sapiens.GRCh38.cdna.all.fa.kallisto.idx +gene_transcript_lookup_table: + class: File + path: /gscmnt/gc2560/core/GRC-human-build38_human_95_38_U2AF1_fix/rna_seq_annotation/ensembl95.transcriptToGene.tsv +read_group_id: + - '2895626107' + - '2895626112' +read_group_fields: +- - PU:H3MYFBBXX.4 + - SM:H_NJ-HCC1395-HCC1395_RNA + - LB:Pooled_RNA_2891007020-cD1-lib1 + - PL:Illumina + - CN:WUGSC +- - PU:H3MYFBBXX.5 + - SM:H_NJ-HCC1395-HCC1395_RNA + - LB:Pooled_RNA_2891007020-cD1-lib1 + - PL:Illumina + - CN:WUGSC +trimming_adapters: + class: File + path: illumina_multiplex.fa +trimming_adapter_trim_end: 'RIGHT' +trimming_adapter_min_overlap: 7 +trimming_max_uncalled: 300 +trimming_min_readlength: 25 +sample_name: H_NJ-HCC1395-HCC1395_RNA +strand: first +refFlat: + class: File + path: /gscmnt/gc2560/core/GRC-human-build38_human_95_38_U2AF1_fix/rna_seq_annotation/Homo_sapiens.GRCh38.95.refFlat.txt +ribosomal_intervals: + class: File + path: /gscmnt/gc2560/core/GRC-human-build38_human_95_38_U2AF1_fix/rna_seq_annotation/Homo_sapiens.GRCh38.95.ribo_intervals +species: homo_sapiens +assembly: GRCh38