Workflow: FASTQ to BQSR

Fetched 2023-01-10 00:11:28 GMT
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workflow cluster_inputs Workflow Inputs cluster_outputs Workflow Outputs fastq_1s fastq_1s align align with bwa_mem and tag fastq_1s->align fastq_1 bqsr_known_sites bqsr_known_sites bqsr create BQSR table bqsr_known_sites->bqsr known_sites final_name final_name merge Samtools: merge final_name->merge name apply_bqsr apply BQSR final_name->apply_bqsr output_name fastq_2s fastq_2s fastq_2s->align fastq_2 reference reference reference->apply_bqsr reference reference->bqsr reference reference->align reference readgroups readgroups readgroups->align readgroup bqsr_intervals bqsr_intervals bqsr_intervals->bqsr intervals final_bam final_bam mark_duplicates_metrics_file mark_duplicates_metrics_file name_sort sort BAM by name merge->name_sort bam index_bam samtools index apply_bqsr->index_bam bam mark_duplicates_and_sort Mark duplicates and Sort name_sort->mark_duplicates_and_sort bam bqsr->apply_bqsr bqsr_table index_bam->final_bam align->merge bams mark_duplicates_and_sort->mark_duplicates_metrics_file mark_duplicates_and_sort->apply_bqsr bam mark_duplicates_and_sort->bqsr bam
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Inputs

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

One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis.

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/2e0562a5c3cd7aac24af4c622a5ae68a7fb23a71/definitions/subworkflows/fastq_to_bqsr.cwl