- 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 |
---|---|---|---|
fastq1 | File | ||
fastq2 | File (Optional) | ||
genome | File | ||
adapter1 | String (Optional) | ||
adapter2 | String (Optional) | ||
is_paired_end | Boolean | ||
max_mapping_insert_length | Long (Optional) |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
qc_raw |
../tools/fastqc.cwl
(CommandLineTool)
|
||
mapping |
../tools/bowtie2.cwl
(CommandLineTool)
|
||
sam2bam |
../tools/samtools_view_sam2bam.cwl
(CommandLineTool)
|
||
sort_bam |
../tools/samtools_sort.cwl
(CommandLineTool)
|
Sort a bam file by read names. |
|
adaptor_trimming_and_qc_trimmed |
../tools/trim_galore.cwl
(CommandLineTool)
|
Outputs
ID | Type | Label | Doc |
---|---|---|---|
bam | File | ||
bowtie2_log | File | ||
fastq1_trimmed | File | ||
fastq2_trimmed | File (Optional) | ||
raw_fastqc_zip | File[] | ||
raw_fastqc_html | File[] | ||
trim_galore_log | File[] | ||
trimmed_fastqc_zip | File[] | ||
trimmed_fastqc_html | File[] |
Permalink:
https://w3id.org/cwl/view/git/7828cbb2c596936d386876ff84cb80c25b507713/CWL/workflow_modules/trim_and_map.cwl