Workflow: merge_filter.cwl

Fetched 2023-01-30 18:04:43 GMT
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Inputs

ID Type Title Doc
bams File[]
sample_id String
is_paired_end Boolean

Steps

ID Runs Label Doc
qc
../tools/fastqc.cwl (CommandLineTool)
filter_by_mapq
../tools/samtools_view_filter.cwl (CommandLineTool)
sorting_merged_bam
../tools/samtools_sort.cwl (CommandLineTool)

Sort a bam file by read names.

sorting_filtered_bam
../tools/samtools_sort.cwl (CommandLineTool)

Sort a bam file by read names.

indexing_filtered_bam
../tools/samtools_index_hack.cwl (CommandLineTool)
lane_replicate_merging
../tools/samtools_merge.cwl (CommandLineTool)

Outputs

ID Type Label Doc
bam File
fastqc_zip File[]
fastqc_html File[]
Permalink: https://w3id.org/cwl/view/git/8526687739a6802eeb08e97b27c20010225d5eb5/CWL/workflow_modules/merge_filter.cwl