I am trying to write CWL for the tool rMATS. It uses files with list of fastq/BAM as input.
--s1 s1.txt A text file contains FASTQ file(s) for the sample_1.(Only if using fastq)
--s2 s2.txt A text file contains FASTQ file(s) for the sample_2.(Only if using fastq)
Could anyone please show me how to mount these fastq files when using docker?
Yes. This should be what I am looking for. I am not familiar with JavsScript. My temporary solution is to use a bash script to create the input file and then pass the arguments one by one.
Hi @hubentu, the JS is fairly simple and can be copy-pasted from that example. I too am not a JS expert, but what is needed is not so extensive. Best -Kaushik