- Selected
- |
- Default Values
- Nested Workflows
- Tools
- 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 |
../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/e2f3e99deba204a31af06646a8326b41242b07a8/CWL/workflow_modules/merge_filter.cwl