User: ttom
ttom • 210
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C: Capture Output files using glob
... Thank you, it worked ...
written 2.1 years ago by
ttom • 210
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Comment:
C: Capture Output files using glob
... One more question on this.
With the given below lines in the code, `splad_outDir` has to be existing for this to work, but will create `splad_outDir/splad`
requirements:
- class: InitialWorkDirRequirement
listing:
- entry: $(inputs.splad_outDir)
writable: true
In ...
written 2.1 years ago by
ttom • 210
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... The issue was the presence of this line
- entry: $(inputs.spladder_bams) ...
written 2.1 years ago by
ttom • 210
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... Yes, I tried the changes mentioned in both the CWL and YAML files. But getting the same error.
I have given File list like below in other YAML files and they seemed to work. Also here when spladder bams is changed to type `File` and given just one `bam` as input, instead of `File[]`, it is working
...
written 2.1 years ago by
ttom • 210
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... Not sure, what I am missing here or doing wrong here
**cat spladder.cwl**
cwlVersion: v1.0
class: CommandLineTool
baseCommand: [python, spladder.py]
requirements:
- class: InitialWorkDirRequirement
listing:
- entry: $(inputs.spladder_outDir)
- ...
written 2.1 years ago by
ttom • 210
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... Ah.... my bad. I thought I removed it, but hadn't.
With that line removed it works. Thank you... ...
written 2.1 years ago by
ttom • 210
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... Yes, makes sense to use the pre-written codes. Thank you !!
By adding `InitialWorkDirRequirement`, the script `index_bam.cwl ` could capture `bam` and `bai` outputs
**cat index_bam.cwl**
requirements:
InitialWorkDirRequirement:
listing: [ $(inputs.bam) ]
inputs:
b ...
written 2.1 years ago by
ttom • 210
1
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1
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... Yes, true. The scatter creates multiple jobs and each job output gets written to different file, although the output file is the same. Each time a file gets created, overwriting the previous one.
As a solution, writing the output of the scatter to different output files and then another step to `ca ...
written 2.1 years ago by
ttom • 210
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... **Option 1**
The script used in `degradation.cwl` does not have an option to give `bai` files as an input explicitly. It rather needs/searches for the `bai` file within the same path where the `bam` file exists. Hence giving `bai` as secondary file worked.
**Option 2 Trial**
`index_bam.cwl` only re ...
written 2.1 years ago by
ttom • 210
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... Using scatter to run `fastqc_check` step in the workflow where input is an array. Trying to capture all the results to one file. When the output file is kept as File, only the results from last file in the input array gets stored in the output file.
fastqc_check_out:
type: File[]
...
written 2.1 years ago by
ttom • 210
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