Workflow: rna_seq_workflow_2.cwl
Fetched 2024-11-23 14:42:54 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| fruitfly_gene_model | File | ||
| ref_fruitfly_genome | Directory | ||
| rna_reads_fruitfly_forward | File [FASTQ] | ||
| rna_reads_fruitfly_reverse | File [FASTQ] |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| mapping_reads |
bio-cwl-tools/STAR/STAR-Align.cwl
(CommandLineTool)
|
||
| index_alignment |
bio-cwl-tools/samtools/samtools_index.cwl
(CommandLineTool)
|
Indexing BAM. |
|
| trim_low_quality_bases |
bio-cwl-tools/cutadapt/cutadapt-paired.cwl
(CommandLineTool)
|
||
| quality_control_forward |
bio-cwl-tools/fastqc/fastqc_2.cwl
(CommandLineTool)
|
Tool runs FastQC from Babraham Bioinformatics |
|
| quality_control_reverse |
bio-cwl-tools/fastqc/fastqc_2.cwl
(CommandLineTool)
|
Tool runs FastQC from Babraham Bioinformatics |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| bam_sorted_indexed | File | ||
| quality_report_forward | File | ||
| quality_report_reverse | File |
Permalink:
https://w3id.org/cwl/view/git/dcdce1d1af183b4f908bea685e90fb2d87aeec21/rna_seq_workflow_2.cwl
