Open Brilator opened 1 week ago
Also, for the fusions output (l 146), it should probably say glob: "out/fusion.txt"
instead of glob: "fusion.txt"
Thank you @Brilator for reporting this!
If you are running with cwltool
, try cwtool --cachedir cache Kallisto-Quant.cwl my_inputs.yml
or similar, then check the directory cache
and there will be all the files; maybe that will help you suggest a better glob
line for quantification_h5
Thanks, I did that.
For me, adding another input string for the output folder and completely yielding that as output worked.
QuantOutfolder:
type: string
outputs:
# quantification_h5:
# type: File
# outputBinding:
# glob: out/abundances.h5
# # Long form method for defining optional outputs
# quantification_tsv:
# type: File
# outputBinding:
# glob: out/abundances.tsv
# bam:
# type: ["null", File]
# outputBinding:
# glob: "out/*.bam"
# fusions:
# type: ["null", File]
# outputBinding:
# glob: "fusion.txt"
outFolder:
type: Directory
outputBinding:
glob: $(runtime.outdir)/$(inputs.QuantOutfolder)
Hi, I've tested the Kallisto-Quant.cwl with
Unfortunately the output is not wired properly.
I am new to CWL, so not sure how to fix and PR.