Fingerprint

README.md

@@ -6,6 +6,13 @@ CWL files and workflows to accompany the [helix_filters_01](https://github.com/m
 
 # Installation & Setup
 
+Clone this repo with 
+
+```
+git clone --recursive https://github.com/mskcc/pluto-cwl.git
+cd pluto-cwl
+```
+
 Install dependencies for the repo with the command:
 
 ```

cwl/conpair-pileup.cwl

@@ -0,0 +1,86 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+
+class: CommandLineTool
+baseCommand:
+  - python
+  - /usr/bin/conpair/scripts/run_gatk_pileup_for_sample.py
+
+id: conpair-pileup
+
+requirements:
+  InlineJavascriptRequirement: {}
+  ResourceRequirement:
+    ramMin: 16000
+    coresMin: 1
+  DockerRequirement:
+    dockerPull: mskcc/roslin-variant-conpair:0.3.3
+
+doc: |
+  None
+
+inputs:
+
+  ref:
+    type: File
+    inputBinding:
+      prefix: --reference
+    secondaryFiles:
+      - .amb
+      - .ann
+      - .bwt
+      - .pac
+      - .sa
+      - .fai
+      - ^.dict
+  java_xmx:
+    type:
+    - 'null'
+    - type: array
+      items: string
+    doc: set up java -Xmx parameter
+    inputBinding:
+      prefix: --xmx_java
+
+  java_temp:
+    type: ['null', string]
+    doc: temporary directory to set -Djava.io.tmpdir
+    inputBinding:
+      prefix: --temp_dir_java
+
+  gatk:
+    type:
+    - [File, string, "null"]
+    inputBinding:
+      prefix: --gatk
+
+  markers_bed:
+    type:
+    - [File, string]
+    inputBinding:
+      prefix: --markers
+
+  bam:
+    type:
+    - [File, string]
+    inputBinding:
+      prefix: --bam
+    secondaryFiles:
+      - ^.bai
+
+  outfile:
+    type:
+    - string
+    inputBinding:
+      prefix: --outfile
+
+outputs:
+  out_file:
+    type: File
+    outputBinding:
+      glob: |
+        ${
+          if (inputs.outfile)
+            return inputs.outfile;
+          return null;
+        }

cwl/fingerprint.cwl

@@ -0,0 +1,143 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: Workflow
+doc: "
+Workflow to run generate fingerprint search on entire dmp normals and optionally on project normals
+"
+
+requirements:
+  MultipleInputFeatureRequirement: {}
+  ScatterFeatureRequirement: {}
+  StepInputExpressionRequirement: {}
+  InlineJavascriptRequirement: {}
+  SubworkflowFeatureRequirement: {}
+
+hints:
+  cwltool:LoadListingRequirement:
+    loadListing: no_listing
+
+inputs:
+  dmp_dir:
+    type: Directory
+    default:
+      class: Directory
+      path: /work/ci/dmp_finderprint_matching/dummy_pileup
+  conpair_markers_bed:  # conpair_markers_txt
+    type: File
+  conpair_markers_txt:  # conpair_markers_txt
+    type: File
+  tumor_bam: # GATK .pileup or likelihoods .pickle
+    type: File
+    secondaryFiles: ["^.bai"]
+  additional_normal_bams:
+    type: File[]
+    secondaryFiles: ["^.bai"]
+    default: [{class: File, path: /work/ci/dmp_finderprint_matching/dummy_bam/dummy.bam}]
+  ref_fasta:
+    type: File
+    secondaryFiles:
+      - .amb
+      - .ann
+      - .bwt
+      - .pac
+      - .sa
+      - .fai
+      - ^.dict
+
+
+outputs:
+  output_file:
+    type: File
+    outputSource: run_conpair_concordance/output_file
+
+steps:
+  run-pileup-tumor:
+    run: conpair-pileup.cwl
+    in:
+      bam: tumor_bam
+      ref: ref_fasta
+      gatk:
+        valueFrom: ${ return '/usr/bin/gatk.jar'; }
+      markers_bed: conpair_markers_bed
+      java_xmx:
+        valueFrom: ${ return ["24g"]; }
+      outfile:
+        valueFrom: ${ return inputs.bam.basename.replace(".bam", ".pileup"); }
+    out: [out_file]
+######
+  run-pileup-additional_normals:
+    run: conpair-pileup.cwl
+    scatter: bam
+    in:
+        bam: additional_normal_bams
+        ref: ref_fasta
+        gatk:
+          valueFrom: ${ return '/usr/bin/gatk.jar'; }
+        markers_bed: conpair_markers_bed
+        java_xmx:
+          valueFrom: ${ return ["24g"]; }
+        outfile:
+          valueFrom: ${ return inputs.bam.basename.replace(".bam", ".pileup"); }
+    out: [out_file]
+
+  put-in-dir:
+    run: put_in_dir.cwl
+    in:
+      output_directory_name:
+        valueFrom: ${ return "additional_normals"; }
+      files: run-pileup-additional_normals/out_file
+    out: [ directory ]
+#######
+  run_conpair_concordance:
+    in:
+      dmp_dir: dmp_dir
+      markers: conpair_markers_txt
+      tumor_file: run-pileup-tumor/out_file
+      additional_normal_pickles: put-in-dir/directory
+
+    out: [output_file]
+
+    run:
+      class: CommandLineTool
+      baseCommand: ['bash', 'run.sh']
+      requirements:
+        DockerRequirement:
+          dockerPull: mskcc/conpair:1.0.1
+        InitialWorkDirRequirement:
+          listing:
+            # NOTE: might need dos2unix for some that give errors ERROR: Your MAF uses CR line breaks, which we can't support. Please use LF or CRLF.
+            # NOTE: might also need sanity check that maf has >1 line
+            - entryname: run.sh
+              entry: |-
+                set -eu
+                path="${ return inputs.dmp_dir.path; }"
+                find "\$path"/ -type f > normal_dmp_pickles_file_list.txt
+
+                path="${ return inputs.additional_normal_pickles.path; }"
+                find "\$path"/ -type f >> normal_dmp_pickles_file_list.txt
+
+                tumor_pickle="${ return inputs.tumor_file.path; }"
+                markers="${ return inputs.markers.path; }"
+                run.py \\
+                  concordance \\
+                  \$tumor_pickle \\
+                  --normals-list normal_dmp_pickles_file_list.txt \\
+                  --markers \$markers \\
+                  --threads 10 \\
+                  --output-file "${ return inputs.tumor_file.nameroot + '.concordance.tsv' }"
+      inputs:
+        dmp_dir: Directory
+        additional_normal_pickles: Directory
+        markers: File
+        tumor_file: File
+
+      outputs:
+        output_file:
+          type: File
+          outputBinding:
+            glob: ${ return inputs.tumor_file.nameroot + '.concordance.tsv' }
+
+
+
+$namespaces:
+  cwltool: "http://commonwl.org/cwltool#"

tests/test_fingerprint_cwl.py

@@ -0,0 +1,74 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+unit tests for the fingerprint.cwl
+"""
+import os
+import sys
+import unittest
+# import json
+# from tempfile import TemporaryDirectory
+
+THIS_DIR = os.path.dirname(os.path.realpath(__file__))
+PARENT_DIR = os.path.dirname(THIS_DIR)
+sys.path.insert(0, PARENT_DIR)
+from pluto.tools import PlutoTestCase, CWLFile
+from pluto.serializer import OFile
+sys.path.pop(0)
+
+
+class TestFingerprint(PlutoTestCase):
+    cwl_file = CWLFile('fingerprint.cwl')
+
+
+    def test_fingerprint_1(self):
+        """
+        """
+
+        self.preserve = True
+
+        self.input = {
+            "conpair_markers_txt": {
+                "path": "/juno/work/ci/concordance-workflow/markers/IMPACT468/FP_tiling_genotypes_for_Conpair.txt",
+                "class": "File"
+                },
+            "conpair_markers_bed": {
+                "path": "/juno/work/ci/concordance-workflow/markers/IMPACT468/FP_tiling_genotypes_for_Conpair.bed",
+                "class": "File"
+                },
+            "ref_fasta": {
+                "path": "/juno/work/ci/resources/genomes/GRCh37/fasta/b37.fasta",
+                "class": "File"
+                },
+            "runparams": {
+                "tmp_dir": "/scratch",
+                "gatk_jar_path": "/usr/bin/gatk.jar"
+                },
+            "tumor_bam": {
+                "path": "/work/ci/dmp_finderprint_matching/dummy_bam/dummy.bam",
+                "class": "File"
+                },
+            "dmp_dir": {
+                "class": "Directory",
+                "path": "/work/ci/dmp_finderprint_matching/dummy_pickle"
+                }
+            }
+
+
+
+##"/work/ci/dmp/likelihoods"
+
+        output_json, output_dir = self.run_cwl()
+
+        expected_output = {
+            'output_file': OFile(name = 'dummy.concordance.tsv', hash = "sha1$6b1a5ef498be9c15c842033ba7b5cc970397b5f5", size = 487, dir = output_dir)
+            }
+
+
+        self.assertCWLDictEqual(expected_output, output_json)
+
+
+
+
+if __name__ == "__main__":
+    unittest.main()