outputs:
featurecounts:
type: File
- outputBinding:
+ outputBinding:
glob: featurecounts.tsv
### 6. Running in a container
ResourceRequirement:
ramMin: 500
run: featureCounts.cwl
- in:
- counts_input_bam: samtools/bam_sorted_indexed
- gtf: gtf
- out: [featurecounts]
+ in:
+ counts_input_bam: samtools/bam_sorted_indexed
+ gtf: gtf
+ out: [featurecounts]
outputs:
qc_html:
### 8. Adding it to the workflow
featurecounts:
type: File
- outputSource: featureCounts/featurecounts
+ outputSource: featureCounts/featurecounts
outputs:
featurecounts:
type: File
- outputBinding:
+ outputBinding:
glob: featurecounts.tsv
```
ResourceRequirement:
ramMin: 500
run: featureCounts.cwl
- in:
- counts_input_bam: samtools/bam_sorted_indexed
- gtf: gtf
- out: [featurecounts]
+ in:
+ counts_input_bam: samtools/bam_sorted_indexed
+ gtf: gtf
+ out: [featurecounts]
```
We will add the result from featurecounts to the output:
...
featurecounts:
type: File
- outputSource: featureCounts/featurecounts
+ outputSource: featureCounts/featurecounts
```
You should now be able to re-run the workflow and it will run the
ResourceRequirement:
ramMin: 500
run: featureCounts.cwl
- in:
- counts_input_bam: samtools/bam_sorted_indexed
- gtf: gtf
- out: [featurecounts]
+ in:
+ counts_input_bam: samtools/bam_sorted_indexed
+ gtf: gtf
+ out: [featurecounts]
outputs:
qc_html:
featurecounts:
type: File
- outputSource: featureCounts/featurecounts
+ outputSource: featureCounts/featurecounts
outputs:
featurecounts:
type: File
- outputBinding:
+ outputBinding:
glob: featurecounts.tsv
hints:
ResourceRequirement:
ramMin: 500
run: featureCounts.cwl
- in:
- counts_input_bam: samtools/bam_sorted_indexed
- gtf: gtf
- out: [featurecounts]
+ in:
+ counts_input_bam: samtools/bam_sorted_indexed
+ gtf: gtf
+ out: [featurecounts]
outputs:
qc_html:
featurecounts:
type: File
- outputSource: featureCounts/featurecounts
+ outputSource: featureCounts/featurecounts
outputs:
featurecounts:
type: File
- outputBinding:
+ outputBinding:
glob: featurecounts.tsv
hints:
outputs:
featurecounts:
type: File
- outputBinding:
+ outputBinding:
glob: featurecounts.tsv
hints:
fq: fq
genome: genome
gtf: gtf
- out: [qc_html, bam_sorted_indexed, featurecounts]
+ out: [qc_html, bam_sorted_indexed]
### 4. Combining results
featureCounts:
outputs:
featurecounts:
type: File
- outputBinding:
+ outputBinding:
glob: featurecounts.tsv
hints:
fq: fq
genome: genome
gtf: gtf
- out: [qc_html, bam_sorted_indexed, featurecounts]
+ out: [qc_html, bam_sorted_indexed]
featureCounts:
requirements: