CWL Workflow: CNV_pipeline

Workflow: CNV_pipeline

Fetched 2025-12-13 20:59:22 GMT

Verified with cwltool version 3.1.20221201130942

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This workflow is Open Source and may be reused according to the terms of: Apache License 2.0

Note that the tools invoked by the workflow may have separate licenses.

Inputs

ID	Type	Doc
bed	File	capture kit
fastq1	File[]	FASTQ 1 list of files
fastq2	File[]	FASTQ 2 list of files
samples	File	TXT file mapping cases ID, samples ID and batch
bits_set	Integer	skip output alignments with this bits set
blacklist	File (Optional)	BED file containing regions to ignore
chromosome	String	chromosome for targeted sequencing for CODEX
read_group	String (Optional)	FASTA read group (used to fix BAM files)
manta_exome	Boolean	provide appropriate settings for WES
manta_min_q	String	minimum CNV quality for MANTA
enable_codex	Boolean	execute CODEX predictions
enable_manta	Boolean	execute MANTA predictions
gridss_min_q	String	minimum CNV quality for GRIDSS
reference_sa	File (Optional)	sa index reference genome
bwt_algorithm	String (Optional)	BWT construction algorithm: bwtsw or is (Default: auto)
codex_max_len	String	maximum CNV lenght for CODEX
codex_min_len	String	minimum CNV lenght for CODEX
enable_gridss	Boolean	execute GRIDSS predictions
manta_max_len	String	maximum CNV lenght for MANTA
manta_min_len	String	minimum CNV lenght for MANTA
reference_amb	File (Optional)	amb index for reference genome
reference_ann	File (Optional)	ann index for reference genome
reference_bwt	File (Optional)	bwt index for reference genome
reference_fai	File (Optional)	fai index for reference genome
reference_pac	File (Optional)	pac index reference genome
threads_fastp	Integer (Optional)	number of threads for fastp
gridss_max_len	String	maximum CNV lenght for GRIDSS
gridss_min_len	String	minimum CNV lenght for GRIDSS
threads_fastqc	Integer (Optional)	number of threads for fastqc
threads_gridss	Integer (Optional)	number of threads for GRIDSS
reference_fasta	File	reference genome
threads_bwa_mem	Integer (Optional)	number of threads for bwa-mem
codex_min_lratio	String	minimum CNV lratio for CODEX
threads_samtools	Integer (Optional)	number of threads for samtools
enable_exomeDepth	Boolean	execute EXOME_DEPTH predictions
exomeDepth_min_bf	String	minimum CNV Bayes factor for EXOME_DEPTH
exomeDepth_max_len	String	maximum CNV lenght for EXOME_DEPTH
exomeDepth_min_len	String	minimum CNV lenght for EXOME_DEPTH
min_mapping_quality	Integer	skip alignments with MAPQ smaller than this minimum
generate_bwa_indexes	Boolean (Optional)	enable generation of reference genome indexes

Steps

ID	Runs	Label	Doc
bwa_mem	subworkflows/bwa_mem.cwl (Workflow)	bwa_mem
bwa_index	subworkflows/bwa_index.cwl (Workflow)	bwa_index	Modified from https://github.com/kids-first/kf-somatic-workflow/blob/master/sub_workflows/prepare_reference.cwl
cnv_codex	subworkflows/cnv_codex.cwl (Workflow)	cnv_codex	CNV CODEX calling
cnv_manta	subworkflows/cnv_manta.cwl (Workflow)	cnv_manta	CNV Manta calling
cnv_gridss	subworkflows/cnv_gridss.cwl (Workflow)	cnv_gridss	CNV GRIDSS calling
bam_filtering	subworkflows/bam_filtering.cwl (Workflow)	bam_filtering	BAM filtering
samtools_sort	subworkflows/samtools_sort.cwl (Workflow)	samtools_sort
trimmed_fastq	subworkflows/trimmed_fastq.cwl (Workflow)	trimmed_fastq	Quality Control (raw data), Raw Data trimming and Quality Control (pre-processed)
cnv_exomedepth	subworkflows/cnv_exome_depth.cwl (Workflow)	cnv_exomedepth	CNV ExomeDepth calling
final_filtering	subworkflows/final_filtering.cwl (Workflow)	final_filtering	Final filtering
picard_markduplicates	subworkflows/picard_markduplicates.cwl (Workflow)	picard_markduplicates	Mark duplicates
samtools_view_sam2bam	subworkflows/samtools_view_sam2bam.cwl (Workflow)	samtools_view_sam2bam

Outputs

ID	Type	Label	Doc
output_all	File
html_report	File[]
json_report	File[]
output_codex	File (Optional)
output_manta	File (Optional)
output_gridss	File (Optional)
fastqc_raw_zip	File[]
fastqc_raw_html	File[]
fastqc_paired_zip	File[]
output_exomedepth	File (Optional)
fastqc_paired_html	File[]
output_bam_filtering	File[]

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