Create snpEff_build_ann.cwl

snpEff/snpEff_build_ann.cwl

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+class: CommandLineTool
+cwlVersion: v1.0
+baseCommand: [bash, commands.sh]
+doc: 'SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes). Use references genomes or import the genbank file of another genome.'
+
+inputs:
+  - id: importGenome
+    type: boolean
+    doc: 'import your own genome (genbank)'
+  - id: genome_reference
+    type: string
+
+  - id: bankfile
+    type: File?
+    doc: 'import your own genome'
+
+  - id: sequence
+    type: File
+
+  - id: inputFormat
+    type:
+      - 'null'
+      - type: enum
+        symbols:
+          - vcf
+          - bed
+    default: vcf
+  - id: outputFormat
+    type:
+      - 'null'
+      - type: enum
+        symbols:
+          - vcf
+          - bed
+          - gatk
+          - bedAnn
+    default: vcf
+
+  - id: udLength
+    type: int
+    doc: 'Set upstream downstream interval length (in bases). 0 base: No upstream / downstream intervals'
+
+## reports:
+  - id: html_report
+    type: boolean?
+
+  - id: csvFile
+    type: boolean?
+  - id: noStats
+    type: boolean?
+
+## Annotations options:
+  - id: formatEff
+    type: boolean?
+    doc: "Use 'EFF' field compatible with older versions (instead of 'ANN')"
+  - id: classic
+    type: boolean?
+    doc: "Use Classic Effect names and amino acid variant annotations (NON_SYNONYMOUS_CODING vs missense_variant and G180R vs p.Gly180Arg/c.538G>C)"
+  - id: sequenceOntology
+    type: boolean?
+    doc: "Override classic and use Sequence Ontolgy terms for effects (missense_variant vs NON_SYNONYMOUS_CODING)"
+  - id: hgvs
+    type: boolean?
+    default: true
+    doc: "Override classic and use HGVS annotations for amino acid annotations (p.Gly180Arg/c.538G>C vs G180R)"
+  - id: noShiftHgvs
+    type: boolean?
+    doc: "Do not shift variants according to HGVS notation (most 3prime end)"
+  - id: noHgvs
+    type: boolean?
+    doc: "Do not add HGVS annotations"
+  - id: geneId
+    type: boolean?
+    doc: "Use gene ID instead of gene name (VCF output). Default: false"
+  - id: lof
+    type: boolean?
+    doc: "Add loss of function (LOF) and nonsense mediated decay (NMD) tags"
+  - id: noLof
+    type: boolean?
+    doc: "Do not add LOF and NMD annotations"
+  - id: cancer
+    type: boolean?
+    inputBinding:
+      prefix: -cancer
+    doc: "Perform 'cancer' comparisons (somatic vs. germline)"
+  - id: cancerSamples
+    type: File?
+    doc: "<file> : Two column TXT file defining 'oringinal \t derived' samples."
+  - id: oicr
+    type: boolean?
+    doc: "Add OICR tag in VCF file. Default: false"
+
+## Database options:
+
+  - id: canon
+    type: boolean?
+    doc: "Only use canonical transcripts"
+  - id: motif
+    type: boolean?
+    doc: "Annotate using motifs (requires Motif database)."
+  - id: noMotif
+    type: boolean?
+    doc: "Disable motif annotations"
+  - id: noNextProt
+    type: boolean?
+    doc: "Disable NextProt annotations"
+  - id: nextProt
+    type: boolean?
+    doc: "Annotate using NextProt (requires NextProt database)."
+  - id: noGenome
+    type: boolean?
+    doc: "Do not load any genomic database (e.g. annotate using custom files)."
+  - id: onlyProtein
+    type: boolean?
+    doc: "Only use protein coding transcripts. Default: false"
+  - id: transcripts
+    type: File?
+    doc: '<file.txt>   Only use the transcripts in this file. Format: One transcript ID per line.'
+
+  # à rendre facultatif:
+  - id: interval
+    type: File[]?
+      #- type: null
+      #type: array
+      #items: File
+    doc: 'Use a custom intervals in TXT/BED/BigBed/VCF/GFF file (you may use this option many times).'
+  - id: spliceRegionExonSize
+    type: int?
+    default: 3
+  - id: spliceRegionIntronMax
+    type: int?
+    default: 8
+  - id: spliceRegionIntronMin
+    type: int?
+    default: 8
+  - id: spliceSiteSize
+    type: int?
+    default: 2
+  - id: onlyReg
+    type: boolean?
+    doc: "Only use regulation tracks."
+  - id: strict
+    type: boolean?
+    doc: "Only use 'validated' transcripts (i.e. sequence has been checked). Default: false"
+## Results filter options :
+
+  - id: filterInterval
+    type: File[]?
+    doc: "Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)"
+  - id: no_downstream
+    type: boolean?
+    doc: " Do not show DOWNSTREAM changes"
+  - id: no_intergenic
+    type: boolean?
+    doc: "Do not show INTERGENIC changes"
+  - id: no_intron
+    type: boolean?
+    doc: "Do not show INTRON changes"
+  - id: no_upstream
+    type: boolean?
+    doc: "Do not show UPSTREAM changes"
+  - id: no_utr
+    type: boolean?
+    doc: "Do not show 5_PRIME_UTR or 3_PRIME_UTR changes"
+  - id: no_EffectType
+    type: boolean?
+    doc: "Do not show 'EffectType'. This option can be used several times."
+
+outputs:
+  - id: snpeff_output
+    type: File?
+    # format $(inputs.outputFormat)
+    outputBinding:
+      glob: "*.$(inputs.outputFormat)"
+  - id: statsFile
+    type: File?
+    outputBinding:
+      glob: "*.html"
+  - id: csvFile
+    type: File?
+    outputBinding:
+      glob: '*.csv'
+  - id: genes
+    type: File?
+    outputBinding:
+      glob: '*.txt'
+requirements:
+  - class: DockerRequirement
+    dockerPull: biocontainers/snpeff:v4.1k_cv3
+  - class: InlineJavascriptRequirement
+  - class: InitialWorkDirRequirement
+    listing:
+      - entry: "$({class: 'Directory', listing: []})"
+        entryname: $(inputs.genome_reference)
+        writable: true
+      - entryname: $(inputs.genome_reference)/genes.gbk
+        entry: $(inputs.bankfile)
+      - entryname: commands.sh
+        entry: |-
+          #!/bin/bash
+          ###########################
+          #cd /home/biodocker/bin/snpEff
+          cp /home/biodocker/bin/snpEff/snpEff.config .
+          ls -R
+
+          if [ $(inputs.importGenome) ]
+          then
+              echo $(inputs.genome_reference).genome=$(inputs.genome_reference) >> snpEff.config
+              snpEff build -v -c snpEff.config -dataDir . -configOption $(inputs.genome_reference).genome=$(inputs.genome_reference) -genbank $(inputs.genome_reference)
+              grep covid19 snpEff.config
+          fi
+
+          ${
+          var command=
+          "snpEff ann -v -c snpEff.config -dataDir .  -i "+ (inputs.inputFormat)+" -o "+(inputs.outputFormat)+" -upDownStreamLen "+(inputs.udLength)+" -spliceRegionExonSize "+(inputs.spliceRegionExonSize)+" -spliceRegionIntronMax  "+(inputs.spliceRegionIntronMax)+" -spliceRegionIntronMin "+(inputs.spliceRegionIntronMin)+" -spliceSiteSize "+(inputs.spliceSiteSize)
+
+          if (inputs.csvFile){
+            command+= " -csvFile "
+          }
+          if (inputs.html_report){
+            command+=" -s "
+          }
+          if (inputs.noStats){
+            command+=" -noStats "
+          }
+          if (inputs.formatEff){
+            command+=" -formatEff "
+          }
+          if (inputs.classic){
+            command+=" -classic "
+          }
+          if (inputs.sequenceOntology){
+            command+=" -sequenceOntology "
+          }
+          if (inputs.hgvs){
+            command+=" -hgvs "
+          }
+          if (inputs.noShiftHgvs){
+            command+=" -noShiftHgvs "
+          }
+          if (inputs.noHgvs){
+            command+=" -noHgvs "
+          }
+          if (inputs.geneId){
+            command+= " -geneId"
+          }
+          if (inputs.lof){
+            command+=" -lof "
+          }
+          if (inputs.noLof){
+            command+=" -noLof "
+          }
+          if (inputs.cancer){
+            command+=" -cancer "
+          }
+          if (inputs.oicr){
+            command+=" -oicr "
+          }
+          if (inputs.cancerSamples!=null){
+            command+= " -cancerSamples "+(inputs.cancerSamples.path)
+          }
+          if (inputs.canon){
+            command+= " -canon "
+          }
+          if (inputs.motif){
+            command+= " -motif "
+          }
+          if (inputs.noMotif){
+            command+= " -noMotif "
+          }
+          if (inputs.noNextProt){
+            command+=" -noNextProt "
+          }
+          if (inputs.nextProt){
+            command+=" -nextProt "
+          }
+          if (inputs.noGenome){
+            command+=" -noGenome "
+          }
+          if (inputs.onlyProtein){
+            command+=" -onlyProtein "
+          }
+          if (inputs.onlyReg){
+            command+=" -onlyReg "
+          }
+          if (inputs.strict){
+            command+=" -strict "
+          }
+          if (inputs.no_downstream){
+            command+= " -no-downstream "
+          }
+          if (inputs.no_intergenic){
+            command+= " -no-intergenic "
+          }
+          if (inputs.no_intron){
+            command+= " -no-intron "
+          }
+          if (inputs.no_upstream){
+            command+= " -no-upstream "
+          }
+          if (inputs.no_utr){
+            command+= " -no-utr "
+          }
+          if (inputs.no_EffectType){
+            command+= " -no EffectType "
+          }
+          if (inputs.transcripts!=null){
+           for (var i=0; i< inputs.transcripts.length; i++){
+             command+= " -onlyTr "+inputs.transcripts[i].path
+           }
+          }
+          if (inputs.filterInterval!=null){
+           for (var i=0; i< inputs.filterInterval.length; i++){
+             command+= " -filterInterval "+inputs.filterInterval[i].path
+           }
+          }
+          if (inputs.interval!=null){
+           for (var i=0; i< inputs.interval.length; i++){
+             command+= " -interval "+inputs.interval[i].path
+           }
+          }
+          command+=(inputs.genome_reference)+" "+(inputs.sequence.path)+" > "+(inputs.sequence.nameroot)+".ann."+(inputs.outputFormat)
+
+          return command;
+          }