Write out a software_versions file

[silviamorins]

Hi,

I see that a file containing information about all the versions of all the tools used by the pipeline is also generated:

rnaseq/main.nf

Line 306 in 37f260d

file 'software_versions_mqc.yaml' into software_versions_yaml

Can this information also be made part of nextflow's (MultiQC's) output? I need these numbers as well often for reporting and copying them down from the MultiQC report is doable but requires a little time.

Best,
Silvia

[ewels]

Yup, that's what the file is already used for 😉 See later on in the MultiQC process:

rnaseq/main.nf

Line 1092 in 37f260d

file ('software_versions/*') from software_versions_yaml

It should show up as a section right at the bottom of the report. Is this not the case?

Phil

[silviamorins]

Yes it is the case, I see this session at the bottom of the MultiQC report - the question was if it can be written out as stand alone file in the rnaseq's pipeline results.

But I just chatted about it with @apeltzer and found out that a software_versions.yaml file already exists in the work directory, so I am just going to take it from there. Thank you for your answer :)

[ewels]

Ah I see, I misunderstood the question sorry. It would be pretty trivial to also output a csv / similar from that process and save it to the results folder if you think it would be useful. Just add to this file at the end, to print the dictionary to a csv file too. Then pick up that output from the process and use a conditional publishdir directive to only save this output file to the results.

Feel free to make a pull-request if you fancy it :)

Phil