Workflow: Unaligned BAM to BQSR

Fetched 2023-01-05 07:47:15 GMT
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workflow cluster_inputs Workflow Inputs cluster_outputs Workflow Outputs reference reference apply_bqsr apply BQSR reference->apply_bqsr reference bqsr create BQSR table reference->bqsr reference align Unaligned to aligned BAM reference->align reference mills mills mills->bqsr known_sites bams bams bams->align bam final_name final_name final_name->apply_bqsr output_name merge Samtools: merge final_name->merge name readgroups readgroups readgroups->align readgroup known_indels known_indels known_indels->bqsr known_sites dbsnp_vcf dbsnp_vcf dbsnp_vcf->bqsr known_sites bqsr_intervals bqsr_intervals bqsr_intervals->bqsr intervals mark_duplicates_metrics_file mark_duplicates_metrics_file final_bam final_bam name_sort sort BAM by name mark_duplicates_and_sort Mark duplicates and Sort name_sort->mark_duplicates_and_sort bam index_bam samtools index apply_bqsr->index_bam bam bqsr->apply_bqsr bqsr_table align->merge bams index_bam->final_bam merge->name_sort bam mark_duplicates_and_sort->mark_duplicates_metrics_file mark_duplicates_and_sort->apply_bqsr bam mark_duplicates_and_sort->bqsr bam
Workflow as SVG
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Inputs

ID Type Title Doc
bams File[]
mills 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
align.cwl (Workflow)
Unaligned to aligned BAM
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/06d2440d115b446c299b4ce96e8812d2f8df86ec/definitions/subworkflows/bam_to_bqsr.cwl