Workflow: merge_duprem_filter.cwl
Fetched 2025-02-18 06:56:50 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
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- Inputs/Outputs
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 |
|---|---|---|---|
| bams | File[] | ||
| sample_id | String | ||
| is_paired_end | Boolean |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| qc_duprem |
../tools/fastqc.cwl
(CommandLineTool)
|
||
| filter_by_mapq |
../tools/samtools_view_filter.cwl
(CommandLineTool)
|
||
| remove_duplicates |
../tools/picard_markdup.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 | ||
| duprem_fastqc_zip | File[] | ||
| duprem_fastqc_html | File[] | ||
| picard_markdup_log | File |
Permalink:
https://w3id.org/cwl/view/git/8526687739a6802eeb08e97b27c20010225d5eb5/CWL/workflow_modules/merge_duprem_filter.cwl
