--outdir

[portah]

I did not find a way to put file into ./test-files and do not have a cwltool error. I can either output it into the dir but have workflow error or have it in current dir and no errors.

When I run command cwltool --outdir ./test-files/ ./samtools-index.cwl ./jobs/samtools-index-job.json file .bai created in ./test-files but I have an error from cwltool

Error while running job: Did not find output file with glob pattern: '[u'SRR1031972.Aligned.sortedByCoord.out.bam.bai']'
[job 4463785808] completed permanentFail
Final process status is permanentFail
Workflow error:
  Process status is ['permanentFail']

Or I can run cwltool ./samtools-index.cwl ./jobs/samtools-index-job.json but then file in current directory :(

[portah]

Sorry found a way
cwltool --basedir ./ --outdir ./test-files ./samtools-index.cwl ./jobs/samtools-index-job.json