Workflow: rnaseq-pt1.cwl
Fetched 2024-04-20 05:57:56 GMT
Verified with cwltool version 3.1.20221201130942
Star/HTSeq RNA Seq Pipeline
- Selected
- |
- Default Values
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- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| reads | File[] |
Sequences to be mapped (e.g. RNA-seq FASTQ files) |
|
| threads | Integer |
Number of threads |
|
| gff_file | File |
Genomic features in the GFF format |
|
| star_genome | Directory |
Genome directory containing STAR genome indices |
|
| ref_gene_model | File |
Reference gene model in bed format |
|
| align_out_prefix | String |
STAR output files name prefix |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| qc |
../tools/fastqc.cwl
(CommandLineTool)
|
||
| trim |
../tools/trim_galore.cwl
(CommandLineTool)
|
||
| align |
../tools/STAR.cwl
(CommandLineTool)
|
||
| index |
../tools/samtools-index.cwl
(CommandLineTool)
|
samtools-index.cwl is developed for CWL consortium |
|
| merge_index |
../tools/merge-secondary-file.cwl
(ExpressionTool)
|
||
| quantification |
../tools/htseq-count.cwl
(CommandLineTool)
|
||
| read_distribution |
../tools/read_distribution.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| align_logs | File[] |
STAR alignment log files |
|
| qc_reports | File[] |
FastQC reports for input sequences |
|
| aligned_read | File |
STAR alignments in SAM format |
|
| trim_reports | File[] |
Trim Galore! summary reports |
|
| trimmed_reads | File[] |
Input reads trimmed by Trim Galore! |
|
| aligned_read_index | File |
BAM files indexed by samtools |
|
| quantification_report | File |
HTSeq feature counts report |
|
| read_distribution_report | File |
RSeQC read distribution report |
Permalink:
https://w3id.org/cwl/view/git/bbe24d8d7fde2e918583b96805909a2867b749d6/workflows/rnaseq-pt1.cwl
