Workflow: FASTQ to BQSR

Fetched 2023-01-04 09:41:44 GMT
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Workflow as SVG
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Inputs

ID Type Title Doc
mills File
fastq_1s File[]
fastq_2s File[]
dbsnp_vcf File
reference String
final_name String
readgroups String[]
known_indels File
bqsr_intervals String[] (Optional)

Steps

ID Runs Label Doc
bqsr
../tools/bqsr.cwl (CommandLineTool)
create BQSR table
align
../tools/fastq_align_and_tag.cwl (CommandLineTool)
align with bwa_mem and tag
merge
../tools/merge_bams_samtools.cwl (CommandLineTool)
Samtools: merge
index_bam
../tools/index_bam.cwl (CommandLineTool)
samtools index
name_sort
../tools/name_sort.cwl (CommandLineTool)
sort BAM by name
apply_bqsr
../tools/apply_bqsr.cwl (CommandLineTool)
apply BQSR
mark_duplicates_and_sort
../tools/mark_duplicates_and_sort.cwl (CommandLineTool)
Mark duplicates and Sort

Outputs

ID Type Label Doc
final_bam File
mark_duplicates_metrics_file File
Permalink: https://w3id.org/cwl/view/git/9143dc4ebacb9e1df36a712b0be6fa5d982b0c4f/definitions/subworkflows/fastq_to_bqsr.cwl