<commit_before>#!/usr/bin/env cwl-runner

cwlVersion: v1.0

class: Workflow

inputs:

  - id: "#input_bam_path"
    type: File
  - id: "#validation_stringency"
    default: "SILENT"
    type: string
  - id: "#reference_seq"
    type: File
  - id: "#reference_indel_path"
    type: File
  - id: "#reference_snp_path"
    type: File

outputs:

  - id: "#duplicate_removed_output_bam"
    type: File
    source: "#LLDR_SLDR-tool.duplicate_removed_output_bam"
  - id: "#duplicate_removed_output_metrics"
    type: File
    source: "#LLDR_SLDR-tool.duplicate_removed_output_metrics"
  - id: "#duplicate_removed_output_bai"
    type: File
    source: "#LLDR_SLDR-tool.duplicate_removed_output_bai"
  - id: "#left_aligned_bam"
    type: File
    source: "#LeftAlignIndels.left_aligned_bam"
  - id: "#output_target"
    type: File
    source: "#RealignerTargetCreator.output_target"
  - id: "#output_bqsr_bam"
    type: File
    source: "#IndelRealigner.output_bqsr_bam"

steps:

  - id: "#LLDR_SLDR-tool"
    run: ../tools/primary_analysis/LLDR_SLDR.cwl.yaml
    inputs:
       - id: "#LLDR_SLDR-tool.input_bam_path"
         source: "#input_bam_path"
       - id: "#LLDR_SLDR-tool.validation_stringency"
         source: "#validation_stringency"

    outputs:
       - id: "#LLDR_SLDR-tool.duplicate_removed_output_bam"
       - id: "#LLDR_SLDR-tool.duplicate_removed_output_metrics"
       - id: "#LLDR_SLDR-tool.duplicate_removed_output_bai"

  - id: "#LeftAlignIndels"
    run: ../tools/secondary_analysis/LeftAlignIndels.cwl.yaml
    inputs:
       - id: "#LeftAlignIndels.input_bam_path"
         source: "#LLDR_SLDR-tool.duplicate_removed_output_bam"
       - id: "#LeftAlignIndels.reference_fasta_path"
         source: "#reference_seq"

    outputs:
       - id: "#LeftAlignIndels.left_aligned_bam"


  - id: "#RealignerTargetCreator"
    run: ../tools/secondary_analysis/RealignerTargetCreator.cwl.yaml
    inputs:
       - id: "#RealignerTargetCreator.input_bam_path"
         source: "#LeftAlignIndels.left_aligned_bam"
       - id: "#RealignerTargetCreator.reference_fasta_path"
         source: "#reference_seq"
       - id: "#RealignerTargetCreator.reference_indel_path"
         source: "#reference_indel_path"
       - id: "#RealignerTargetCreator.reference_snp_path"
         source: "#reference_snp_path"

    outputs:
       - id: "#RealignerTargetCreator.output_target"

  - id: "#IndelRealigner"
    run: ../tools/secondary_analysis/IndelRealigner.cwl.yaml
    inputs:
       - id: "#IndelRealigner.input_bam_path"
         source: "#LeftAlignIndels.left_aligned_bam"
       - id: "#IndelRealigner.reference_fasta_path"
         source: "#reference_seq"
       - id: "#IndelRealigner.reference_indel_path"
         source: "#reference_indel_path"
       - id: "#IndelRealigner.reference_snp_path"
         source: "#reference_snp_path"
       - id: "#IndelRealigner.target_intervals"
         source: "#RealignerTargetCreator.output_target"

    outputs:
       - id: "#IndelRealigner.output_bqsr_bam"<commit_msg>chore(workflows): update to cwlversion v1.0<commit_after>#!/usr/bin/env cwl-runner

cwlVersion: v1.0

class: Workflow

inputs:

  - id: input_bam_path
    type: File
  - id: validation_stringency
    default: "SILENT"
    type: string
  - id: reference_seq
    type: File
  - id: reference_indel_path
    type: File
  - id: reference_snp_path
    type: File

outputs:

  - id: duplicate_removed_output_bam
    type: File
    outputSource: LLDR_SLDR-tool/duplicate_removed_output_bam
  - id: duplicate_removed_output_metrics
    type: File
    outputSource: LLDR_SLDR-tool/duplicate_removed_output_metrics
  - id: duplicate_removed_output_bai
    type: File
    outputSource: LLDR_SLDR-tool/duplicate_removed_output_bai
  - id: left_aligned_bam
    type: File
    outputSource: LeftAlignIndels/left_aligned_bam
  - id: output_target
    type: File
    outputSource: RealignerTargetCreator/output_target
  - id: output_bqsr_bam
    type: File
    outputSource: IndelRealigner/output_bqsr_bam

steps:

  - id: LLDR_SLDR-tool
    run: ../tools/primary_analysis/LLDR_SLDR.cwl.yaml
    in:
       - id: input_bam_path
         source: input_bam_path
       - id: validation_stringency
         source: validation_stringency

    out:
       - id: duplicate_removed_output_bam
       - id: duplicate_removed_output_metrics
       - id: duplicate_removed_output_bai

  - id: LeftAlignIndels
    run: ../tools/secondary_analysis/LeftAlignIndels.cwl.yaml
    in:
       - id: LeftAlignIndels.input_bam_path
         source: LLDR_SLDR-tool/duplicate_removed_output_bam
       - id: LeftAlignIndels.reference_fasta_path
         source: reference_seq

    out:
       - id: left_aligned_bam


  - id: RealignerTargetCreator
    run: ../tools/secondary_analysis/RealignerTargetCreator.cwl.yaml
    in:
       - id: input_bam_path
         source: LeftAlignIndels/left_aligned_bam
       - id: reference_fasta_path
         source: reference_seq
       - id: reference_indel_path
         source: reference_indel_path
       - id: reference_snp_path
         source: reference_snp_path

    out:
       - id: output_target

  - id: IndelRealigner
    run: ../tools/secondary_analysis/IndelRealigner.cwl.yaml
    in:
       - id: input_bam_path
         source: LeftAlignIndels/left_aligned_bam
       - id: reference_fasta_path
         source: reference_seq
       - id: reference_indel_path
         source: reference_indel_path
       - id: reference_snp_path
         source: reference_snp_path
       - id: target_intervals
         source: RealignerTargetCreator/output_target

    out:
       - id: output_bqsr_bam
{'fraction_non_alphanumeric': 0.09423247559893523, 'fraction_numerical': 0.001064773735581189, 'mean_word_length': 3.0142450142450143, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '121966', 'n_tokens_mistral': 2004, 'n_tokens_neox': 1991, 'n_words': 313}