Snpeff hocine

test/snpEff-job.yml

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+genome: hg19
+
+variant_calling_file:
+  class: File
+  path: "/data_small/small_vcf/NA12878.sorted.vcf"
+
+nodownload: true
+
+output_format: vcf
+
+data_dir:
+  class: Directory
+  location: "/data_small/snpEff_hg19/data"
+

tools/snpEff.cwl

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+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: CommandLineTool
+
+hints:
+  DockerRequirement:
+    dockerPull: quay.io/snpeff:4.3
+
+requirements:
+  - class: InlineJavascriptRequirement
+
+inputs:
+
+  data_dir:
+    type: Directory
+    inputBinding:
+      prefix: "-dataDir"
+      position: 1
+
+  no_stats:
+    type: boolean?
+    inputBinding:
+      prefix: "-noStats"
+      position: 2
+
+  csvStats:
+    type: boolean?
+    inputBinding:
+      prefix: "-csvStats"
+      position: 3
+
+  output_format:
+    type:
+      type: enum
+      symbols: [ vcf, gatk, bed, bedAnn ]
+    default: vcf
+    inputBinding:
+      prefix: -o
+      position: 4
+
+  nodownload:
+    type: boolean?
+    inputBinding:
+      prefix: -nodownload
+      position: 5
+
+  verbose:
+    type: boolean?
+    inputBinding:
+      prefix: -v
+      position: 6
+
+  genome:
+    type: string
+    inputBinding:
+      position: 7
+
+  variant_calling_file:
+    type: File
+    format: "http://edamontology.org/format_3016"
+    inputBinding:
+      position: 8
+
+stdout: $(inputs.variant_calling_file.path.replace(/^.*[\\\/]/, '').replace(/\.[^/.]+$/, '') + '.ann.vcf')
+
+outputs:
+  annotated_vcf:
+    type: stdout
+
+  summary_html:
+    type: File?
+    outputBinding:
+      glob: "snpEff_summary.html"
+
+  summary_txt:
+    type: File?
+    outputBinding:
+      glob: "snpEff_genes.txt"
+
+baseCommand: [ snpEff ]
+arguments: [ "ann", "-stats", "snpEff_summary.html" ]

tools/snpEff_Dockerfile

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+FROM java:8-jdk
+
+RUN apt-get update && apt-get install -y unzip wget
+
+WORKDIR /usr/local
+RUN wget https://sourceforge.net/projects/snpeff/files/snpEff_v4_3_core.zip
+RUN unzip snpEff_v4_3_core.zip
+RUN rm snpEff_v4_3_core.zip
+
+RUN chmod a+x /usr/local/snpEff/scripts/snpEff
+
+ENV PATH /usr/local/snpEff/scripts:$PATH
+
+RUN mkdir /data
+WORKDIR /data
+
+RUN groupadd -r -g 1000 ubuntu && useradd -r -g ubuntu -u 1000 ubuntu
+USER ubuntu
+
+CMD ["/bin/bash"]