- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
ID | Type | Title | Doc |
---|---|---|---|
fastq1 | File | ||
fastq2 | File | ||
genome | String | ||
adapter | String | ||
tmp_dir | String | ||
adapter2 | String | ||
add_rg_CN | String | ||
add_rg_ID | String | ||
add_rg_LB | String | ||
add_rg_PL | String | ||
add_rg_PU | String | ||
add_rg_SM | String | ||
md_output | String | ||
bwa_output | String | ||
add_rg_output | String | ||
md_metrics_output | String |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
cmo-bwa-mem |
cmo-bwa-mem/0.7.5a/cmo-bwa-mem.cwl
(CommandLineTool)
|
cmo-bwa-mem |
run bwa mem |
cmo-trimgalore |
cmo-trimgalore/0.2.5.mod/cmo-trimgalore.cwl
(CommandLineTool)
|
cmo-trimgalore |
None |
cmo-picard.MarkDuplicates |
cmo-picard.MarkDuplicates/2.9/cmo-picard.MarkDuplicates.cwl
(CommandLineTool)
|
cmo-picard-MarkDuplicates |
None |
cmo-picard.AddOrReplaceReadGroups |
cmo-picard.AddOrReplaceReadGroups/2.9/cmo-picard.AddOrReplaceReadGroups.cwl
(CommandLineTool)
|
cmo-picard-AddOrReplaceReadGroups |
None |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
bai | File | ||
bam | File | ||
clstats1 | File | ||
clstats2 | File | ||
md_metrics | File |
Permalink:
https://w3id.org/cwl/view/git/425970cb18efb69b42edf26f92c07b7683a62576/setup/cwl/module-1.cwl