Workflow wo facets update

cwl/analysis-workflow_wo_facets.cwl

@@ -0,0 +1,199 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: Workflow
+
+requirements:
+  ScatterFeatureRequirement: {}
+  StepInputExpressionRequirement: {}
+  InlineJavascriptRequirement: {}
+  SubworkflowFeatureRequirement: {}
+
+inputs:
+  analysis_segment_cna_filename:
+    type: string
+    doc: "(ANALYSIS_SEGMENT_CNA_FILE; <project_id>.seg.cna.txt)"
+  analysis_sv_filename:
+    type: string
+    doc: "(ANALYSIS_SV_FILE; <project_id>.svs.maf)"
+  analysis_gene_cna_filename:
+    type: string
+    doc: "(ANALYSIS_GENE_CNA_FILENAME; <project_id>.gene.cna.txt)"
+  analysis_mutations_filename:
+    type: string
+    doc: "(ANALYSIS_MUTATIONS_FILENAME; <project_id>.muts.maf)"
+  analysis_mutations_share_filename:
+    type: string
+    doc: "<project_id>.muts.share.maf"
+  mutation_maf_files:
+    type: File[]
+    doc: "analysis_mutations_filename (ANALYSIS_MUTATIONS_FILENAME) cbio_mutation_data_filename (CBIO_MUTATION_DATA_FILENAME): (MAF_DIR)/*.muts.maf"
+  facets_hisens_seg_files:
+    type: File[]
+    doc: "cbio_segment_data_filename (CBIO_SEGMENT_DATA_FILENAME; <project_id>_data_cna_hg19.seg) analysis_segment_cna_filename (ANALYSIS_SEGMENT_CNA_FILE; <project_id>.seg.cna.txt): (FACETS_DIR)/*_hisens.seg"
+  facets_hisens_cncf_files:
+    type: File[]
+    doc: "cbio_cna_data_filename (CBIO_CNA_DATA_FILENAME; data_CNA.txt) analysis_gene_cna_filename (ANALYSIS_GENE_CNA_FILENAME; <project_id>.gene.cna.txt): (FACETS_DIR)/*_hisens.cncf.txt"
+  mutation_svs_maf_files:
+    type: File[]
+    doc: "analysis_sv_filename (ANALYSIS_SV_FILE; <project_id>.svs.maf): (MAF_DIR)/*.svs.pass.vep.maf"
+  targets_list:
+    type: File
+  argos_version_string:
+    type: string
+    doc: "the version label of Roslin / Argos used to run the project analysis (ARGOS_VERSION_STRING)"
+  is_impact:
+    default: true
+    type: boolean
+    doc: "whether or not the project is an IMPACT project; should be the value 'True' if so, otherwise any other value means 'False' (IS_IMPACT)"
+  helix_filter_version:
+    type: string
+    doc: "the version label of this helix filter repo (HELIX_FILTER_VERSION; git describe --all --long)"
+  IMPACT_gene_list:
+    type: File
+    doc: "TSV file with gene labels and corresponding impact assays"
+
+steps:
+  # <project_id>.gene.cna.txt (analysis_gene_cna_filename)
+  # generate_cna_data:
+  #   run: copy_number.cwl
+  #   in:
+  #     output_cna_filename: analysis_gene_cna_filename
+  #     output_cna_ascna_filename:
+  #       valueFrom: ${ return inputs.output_cna_filename.replace(/\.[^/.]+$/, "") + '.ascna.txt'; }
+  #     output_cna_scna_filename:
+  #       valueFrom: ${ return inputs.output_cna_filename.replace(/\.[^/.]+$/, "") + '.scna.txt'; }
+  #     targets_list: targets_list
+  #     hisens_cncfs: facets_hisens_cncf_files
+  #   out:
+  #     [ output_cna_file ]
+
+  # <project_id>.muts.maf (analysis_mutations_filename)
+  # filter each maf file
+  muts_maf_filter:
+    run: maf_filter.cwl
+    scatter: maf_file
+    in:
+      maf_file: mutation_maf_files
+      argos_version_string: argos_version_string
+      is_impact: is_impact
+      analysis_mutations_filename: analysis_mutations_filename # <project_id>.muts.maf
+    out: [ analysis_mutations_file ]
+    # concat all the maf files into a single table
+  concat_analysis_muts_maf:
+    run: concat-tables.cwl
+    in:
+      input_files: muts_maf_filter/analysis_mutations_file
+      output_filename: analysis_mutations_filename # <project_id>.muts.maf
+      comments:
+        valueFrom: ${ return true; }
+    out:
+      [ output_file ]
+  # Need to add a version label to the maf file as per Nick's request
+  add_maf_comment:
+      run: concat_with_comments.cwl
+      in:
+        some_file: concat_analysis_muts_maf/output_file
+        input_files:
+          valueFrom: ${ return [ inputs.some_file ]; }
+        comment_value: helix_filter_version
+        output_filename: analysis_mutations_filename # <project_id>.muts.maf
+      out:
+        [ output_file ]
+  # add the AF allele frequency column to the maf
+  add_af:
+    run: add_af.cwl
+    in:
+      input_file: add_maf_comment/output_file
+      output_filename: analysis_mutations_filename
+    out:
+      [ output_file ]
+  # label all the mutations that are in a gene covered by an IMPACT assay
+  add_is_in_impact:
+    run: add_is_in_impact.cwl
+    in:
+      input_file: add_af/output_file
+      output_filename: analysis_mutations_filename
+      IMPACT_file: IMPACT_gene_list
+    out:
+      [ IMPACT_col_added_file ]
+  # create a version of the maf with fewer columns; shareable maf <project_id>.muts.share.maf
+  filter_maf_cols:
+    run: maf_col_filter.cwl
+    in:
+      input_file: add_is_in_impact/IMPACT_col_added_file
+      output_filename: analysis_mutations_share_filename # <project_id>.muts.share.maf
+    out:
+      [ output_file ]
+
+  # <project_id>.seg.cna.txt (analysis_segment_cna_filename)
+  # need to reduce the number of significant figures in the hisens_segs files
+  reduce_sig_figs_hisens_segs:
+    run: reduce_sig_figs.cwl
+    scatter: input_file
+    in:
+      input_file: facets_hisens_seg_files
+    out:
+      [output_file]
+  # concatenate all of the hisens_segs files
+  concat_hisens_segs:
+    run: concat.cwl
+    in:
+      input_files: reduce_sig_figs_hisens_segs/output_file
+    out:
+      [output_file]
+  # rename the output file
+  rename_analysis_hisens_segs:
+    run: cp.cwl
+    in:
+      input_file: concat_hisens_segs/output_file
+      output_filename: analysis_segment_cna_filename # <project_id>.seg.cna.txt
+    out:
+      [output_file]
+
+  # <project_id>.svs.maf (analysis_sv_filename)
+  # (MAF_DIR)/*.svs.pass.vep.maf (mutation_svs_maf_files)
+  generate_analysis_svs_maf:
+    run: concat_with_comments.cwl
+    in:
+      input_files: mutation_svs_maf_files
+      comment_value: helix_filter_version
+    out:
+      [output_file]
+  rename_analysis_svs_maf:
+    run: cp.cwl
+    in:
+      input_file: generate_analysis_svs_maf/output_file
+      output_filename: analysis_sv_filename # <project_id>.svs.maf
+    out:
+      [output_file]
+
+  # create the 'analysis' directory and put some files in it
+  make_analysis_dir:
+    run: put_in_dir.cwl
+    in:
+
+
+      #gene_cna_file: #generate_cna_data/output_cna_file # <project_id>.gene.cna.txt
+
+
+      muts_maf_file: add_is_in_impact/IMPACT_col_added_file # <project_id>.muts.maf
+      muts_share_maf_file: filter_maf_cols/output_file
+      hisens_segs: rename_analysis_hisens_segs/output_file # <project_id>.seg.cna.txt
+      svs_maf_file: rename_analysis_svs_maf/output_file # <project_id>.svs.maf
+      output_directory_name:
+        valueFrom: ${ return "analysis"; }
+      files:
+        valueFrom: ${ return [
+          inputs.gene_cna_file,
+          inputs.muts_maf_file,
+          inputs.muts_share_maf_file,
+          inputs.hisens_segs,
+          inputs.svs_maf_file
+          ]}
+    out: [ directory ]
+
+outputs:
+  analysis_dir:
+    type: Directory
+    outputSource: make_analysis_dir/directory