How mount paths in file argument when using docker?

CWL Questions
1

Hi all,

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?

Thanks!

2

Hi @hubentu!

I’m interpreting what you posted as “The tool requires a manifest file with a list of input files”. You can do this by creating the manifest file on the fly using Javascript. It is this cwl-pattern: https://github.com/common-workflow-library/cwl-patterns#manifest-file-via-javascript

3

Hi @kaushik-work

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.

Thanks!

4

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