From aa289173560cd4466d890f3a63927650e37d8aa7 Mon Sep 17 00:00:00 2001 From: Sarah Wait Zaranek Date: Tue, 16 Jun 2020 01:42:38 +0000 Subject: [PATCH 1/1] removing src code not in use Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek no issue # --- src/preprocessing/cwl/createSingleBam-wf.cwl | 38 ----------------- src/preprocessing/cwl/createSingleBam.cwl | 45 -------------------- src/preprocessing/cwl/getfiles.cwl | 40 ----------------- src/preprocessing/runcommand | 6 --- src/preprocessing/yml/createSingleBam-wf.yml | 3 -- src/preprocessing/yml/createSingleBam.yml | 5 --- src/preprocessing/yml/getfiles.yml | 3 -- src/variantcalling/checksex.sh | 10 ----- src/variantcalling/sample-files.list | 4 -- 9 files changed, 154 deletions(-) delete mode 100644 src/preprocessing/cwl/createSingleBam-wf.cwl delete mode 100644 src/preprocessing/cwl/createSingleBam.cwl delete mode 100644 src/preprocessing/cwl/getfiles.cwl delete mode 100644 src/preprocessing/runcommand delete mode 100644 src/preprocessing/yml/createSingleBam-wf.yml delete mode 100644 src/preprocessing/yml/createSingleBam.yml delete mode 100644 src/preprocessing/yml/getfiles.yml delete mode 100644 src/variantcalling/checksex.sh delete mode 100644 src/variantcalling/sample-files.list diff --git a/src/preprocessing/cwl/createSingleBam-wf.cwl b/src/preprocessing/cwl/createSingleBam-wf.cwl deleted file mode 100644 index c539025..0000000 --- a/src/preprocessing/cwl/createSingleBam-wf.cwl +++ /dev/null @@ -1,38 +0,0 @@ -cwlVersion: v1.1 -class: Workflow -$namespaces: - arv: "http://arvados.org/cwl#" - cwltool: "http://commonwl.org/cwltool#" - -requirements: - ScatterFeatureRequirement: {} - -inputs: - bamdir: - type: Directory - label: Directory of zipped bam files - -outputs: - fastqs: - type: - type: array - items: - type: array - items: File - outputSource: convert-bams/fastqs - -steps: - get-bams: - run: getfiles.cwl - in: - bamdir: bamdir - out: [tarzipbams,samplenames] - - convert-bams: - run: createSingleBam.cwl - scatter: [tarzipbam,samplename] - scatterMethod: dotproduct - in: - tarzipbam: get-bams/tarzipbams - samplename: get-bams/samplenames - out: [fastqs] diff --git a/src/preprocessing/cwl/createSingleBam.cwl b/src/preprocessing/cwl/createSingleBam.cwl deleted file mode 100644 index 15994b2..0000000 --- a/src/preprocessing/cwl/createSingleBam.cwl +++ /dev/null @@ -1,45 +0,0 @@ -cwlVersion: v1.1 -class: CommandLineTool -$namespaces: - arv: "http://arvados.org/cwl#" - cwltool: "http://commonwl.org/cwltool#" - -requirements: - - class: DockerRequirement - dockerPull: curii/bam2fastq - - class: ShellCommandRequirement - -hints: - ResourceRequirement: - ramMin: 4000 - coresMin: 1 - tmpdirMin: 150000 - arv:RuntimeConstraints: - outputDirType: keep_output_dir - -inputs: - tarzipbam: File - samplename: string - -outputs: - fastqs: - type: File[] - outputBinding: - glob: "*fastq" - -arguments: - - tar - - prefix: "-xvf" - valueFrom: $(inputs.tarzipbam.path) - - prefix: "-C" - valueFrom: $(runtime.tmpdir) - - {valueFrom: '&&', shellQuote: false} - - samtools - - merge - - {valueFrom: $(runtime.tmpdir)/$(inputs.samplename).bam, shellQuote: false} - - {valueFrom: $(runtime.tmpdir)/*.bam, shellQuote: false} - - {valueFrom: '&&', shellQuote: false} - - /bam2fastq/bam2fastq - - {valueFrom: $(runtime.tmpdir)/$(inputs.samplename).bam, shellQuote: false} - - prefix: "-o" - valueFrom: $(inputs.samplename)_R#.fastq diff --git a/src/preprocessing/cwl/getfiles.cwl b/src/preprocessing/cwl/getfiles.cwl deleted file mode 100644 index 3d8d3fd..0000000 --- a/src/preprocessing/cwl/getfiles.cwl +++ /dev/null @@ -1,40 +0,0 @@ -$namespaces: - cwltool: "http://commonwl.org/cwltool#" -class: ExpressionTool -label: Create list of bams from directory -cwlVersion: v1.1 -requirements: - InlineJavascriptRequirement: {} - -inputs: - bamdir: - type: Directory - label: Directory of input bams - loadListing: shallow_listing - -outputs: - tarzipbams: - type: File[] - label: Array of bams - samplenames: - type: string[] - label: Array of sample names - -expression: | - ${ - var tarzipbams = []; - var samplenames = []; - - for (var i = 0; i < inputs.bamdir.listing.length; i++) { - var file = inputs.bamdir.listing[i]; - if (file.nameext == '.tgz') { - var main = file; - var sample = file.nameroot; - sample = sample.replace(".bam","") - tarzipbams.push(main); - samplenames.push(sample); - } - } - return {"tarzipbams": tarzipbams, "samplenames": samplenames}; - } - diff --git a/src/preprocessing/runcommand b/src/preprocessing/runcommand deleted file mode 100644 index 659c7aa..0000000 --- a/src/preprocessing/runcommand +++ /dev/null @@ -1,6 +0,0 @@ -tar -xvf ./keep/by_id/d25f1c7905d1b16ab8c799a37fc96d56+1805224/hu007B82_1YB27IM.bam.tgz - -samtools merge WGC071838D.bam WGC071838D_combined.chr*bam -docker run -ti -v=/home/bcosca2/issues/15996/bam/7HL58AX:/7HL58AX curii/bam2fastq -/bam2fastq/bam2fastq WGC071838D.bam - diff --git a/src/preprocessing/yml/createSingleBam-wf.yml b/src/preprocessing/yml/createSingleBam-wf.yml deleted file mode 100644 index 32cb9ef..0000000 --- a/src/preprocessing/yml/createSingleBam-wf.yml +++ /dev/null @@ -1,3 +0,0 @@ -bamdir: - class: Directory - location: keep:d25f1c7905d1b16ab8c799a37fc96d56+1805224 diff --git a/src/preprocessing/yml/createSingleBam.yml b/src/preprocessing/yml/createSingleBam.yml deleted file mode 100644 index 57bfb13..0000000 --- a/src/preprocessing/yml/createSingleBam.yml +++ /dev/null @@ -1,5 +0,0 @@ -tarzipbam: - class: File - location: keep:d25f1c7905d1b16ab8c799a37fc96d56+1805224/hu007B82_1YB27IM.bam.tgz - -samplename: hu007B82_1YB27IM diff --git a/src/preprocessing/yml/getfiles.yml b/src/preprocessing/yml/getfiles.yml deleted file mode 100644 index 32cb9ef..0000000 --- a/src/preprocessing/yml/getfiles.yml +++ /dev/null @@ -1,3 +0,0 @@ -bamdir: - class: Directory - location: keep:d25f1c7905d1b16ab8c799a37fc96d56+1805224 diff --git a/src/variantcalling/checksex.sh b/src/variantcalling/checksex.sh deleted file mode 100644 index 407111e..0000000 --- a/src/variantcalling/checksex.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/bash - -xcov=$(echo "scale=4; $(samtools idxstats $1 | grep 'chrX[^_]' | cut -f 3)/$(samtools idxstats $1 | grep 'chrX[^_]' | cut -f 2)" | bc) -echo $xcov -ycov=$(echo "scale=4; $(samtools idxstats $1 | grep "chrY[^_]" | cut -f 3)/$(samtools idxstats $1 | grep "chrY[^_]" | cut -f 2)" | bc) -echo $ycov - -rat=$(echo "scale=4; ${xcov}/${ycov}" | bc) - -echo $rat diff --git a/src/variantcalling/sample-files.list b/src/variantcalling/sample-files.list deleted file mode 100644 index d290f5b..0000000 --- a/src/variantcalling/sample-files.list +++ /dev/null @@ -1,4 +0,0 @@ -ERR1726424.gatk.g.vcf.gz -ERR1726424.gatk.g.vcf_2.gz - -~ -- 2.30.2