Workflow: merge_duprem_filter.cwl
Fetched 2023-01-04 04:32:13 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| bams | File[] | ||
| sample_id | String | ||
| is_paired_end | Boolean |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| filter_by_mapq |
../tools/samtools_view_filter.cwl
(CommandLineTool)
|
||
| qc_post_filtering |
../tools/fastqc.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 | ||
| picard_markdup_stdout | File | ||
| post_filter_fastqc_zip | File[] | ||
| post_filter_fastqc_html | File[] |
Permalink:
https://w3id.org/cwl/view/git/57f0e832ce1488ba0e4c8345554940e7b2472287/CWL/workflow_modules/merge_duprem_filter.cwl
