- 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/12aba268a55088a0350b7475a255a9713c78f8ff/CWL/workflow_modules/merge_duprem_filter.cwl