CWL Workflow: varscanW.cwl

Workflow: varscanW.cwl

Fetched 2025-05-23 21:21:31 GMT

Verified with cwltool version 3.1.20221201130942

Author: AMBARISH KUMAR er.ambarish@gmail.com; ambari73_sit@jnu.ac.in This is a proposed standard operating procedure for genomic variant detection using VARSCAN. It is hoped to be effective and useful for getting SARS-CoV-2 genome variants. It uses Illumina RNASEQ reads and genome sequence.

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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	Title	Doc
sample_name	String
rnaseq_left_reads	File [FASTQ]
rnaseq_right_reads	File [FASTQ]
sars_cov_2_reference_genome	File [FASTA]

Steps

ID	Runs	Doc
align_rnaseq_reads_to_genome	bowtie2_align.cwl (CommandLineTool)	Tool runs bowtie aligner to align input FASTQ file(s) to reference genome
snp_calling_using_mpileup2snp	mpileup2snp.cwl (CommandLineTool)
indel_calling_using_mpileup2indel	mpileup2indel.cwl (CommandLineTool)
index_reference_genome_with_bowtie2	bowtie2_build.cwl (CommandLineTool)	Tool runs bowtie2-build to generate indices from input FASTA files
index_bam_files_using_samtools_index	samtools_index.cwl (CommandLineTool)	Indexing BAM.
index_reference_genome_with_samtools	samtools_faidx.cwl (CommandLineTool)
sort_alignment_files_using_samtools_sort	samtools_sort.cwl (CommandLineTool)	Sort a bam file by read names.
sam_to_bam_conversion_using_samtools_view	samtools_view_sam2bam.cwl (CommandLineTool)	Convert SAM to BAM.

Outputs

ID	Type	Label	Doc
snps	File
indels	File