Workflow: trim_and_map.cwl
Fetched 2020-02-22 16:18:39 GMT
Verified with cwltool version 1.0.20191022103248
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
https://raw.githubusercontent.com/CompEpigen/ChIPseq_workflows/master/LICENSE
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| max_mapping_insert_length | Long (Optional) | ||
| genome | File | ||
| adapter2 | String (Optional) | ||
| adapter1 | String (Optional) | ||
| fastq2 | File (Optional) | ||
| fastq1 | File | ||
| is_paired_end | Boolean |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| sam2bam |
../tools/samtools_view_sam2bam.cwl
(CommandLineTool)
|
||
| mapping |
../tools/bowtie2.cwl
(CommandLineTool)
|
||
| adaptor_trimming_and_qc_trimmed |
../tools/trim_galore.cwl
(CommandLineTool)
|
||
| qc_raw |
../tools/fastqc.cwl
(CommandLineTool)
|
||
| sort_bam |
../tools/samtools_sort.cwl
(CommandLineTool)
|
Sort a bam file by read names. |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| bowtie2_log | File | ||
| trim_galore_log | File[] | ||
| trimmed_fastqc_zip | File[] | ||
| fastq2_trimmed | File (Optional) | ||
| trimmed_fastqc_html | File[] | ||
| fastq1_trimmed | File | ||
| raw_fastqc_html | File[] | ||
| raw_fastqc_zip | File[] | ||
| bam | File |
Permalink:
https://w3id.org/cwl/view/git/7828cbb2c596936d386876ff84cb80c25b507713/CWL/workflow_modules/trim_and_map.cwl
