This will generate two subphases (multiple input files), but the output filename construction is based on the value given to '-i'. This means the output filenames will be the same for both subphases and the pipeline will terminate. Add the values supplied to '-s' to build the filenames.
Fix filename construction for temp files. Example:
gkno subset-vcf -i file.vcf.gz -s 1.txt 2.txt -o 1.vcf.gz -o 2.vcf.gz
This will generate two subphases (multiple input files), but the output filename construction is based on the value given to '-i'. This means the output filenames will be the same for both subphases and the pipeline will terminate. Add the values supplied to '-s' to build the filenames.