removing src code not in use

Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

diff --git a/src/preprocessing/cwl/createSingleBam-wf.cwl b/src/preprocessing/cwl/createSingleBam-wf.cwl
deleted file mode 100644 (file)
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 (file)
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 (file)
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 (file)
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 (file)
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 (file)
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 (file)
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 (file)
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 (file)
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
-
-~