wholegenome.interval_list not recognized by CreateIntervalsBed process

[klmr]

I may be overlooking something but Sarek does not seem to document the input file formats/purposes of the genome files. For most files, the purpose is obvious but some, at least for me, aren’t. And for others it isn’t clear what file format is expected.

For instance, I had assumed that the wholegenome.interval_list Picard-formatted file from the GATK resource bundle would be valid as a genomes.intervals file, but the result is a cryptic error message, as well as a work directory full of weird BED files:

java.lang.NumberFormatException: For input string: "VN" […]

It turns out that the relevant Sarek process only supports two out of the three formats described by the GATK documentation, and notably does not support the Picard-format file, which is included in the official GATK bundle.

[maxulysse]

Hi,
Thanks a lot for your issue.
We did not notice before that particular problem, which should of course be fixed.
There is some documentation about the interval file:
https://github.com/nf-core/sarek/blob/master/docs/reference.md#intervals
But I do understand if you feel like it's not enough.
I'll make sure to explain more about the expected format.
But this wholegenome.intervals_list should have been working.
I'll look more into it.
Thanks again,
Maxime

[klmr]

Hi @maxulysse, thanks for the prompt reply, I indeed missed that particular documentation file, my bad. To clarify, the .interval_list file format is distinct from the .list format. See my GATK documentation link for a complete description, but for example the file will contain the following entries:

@SQ     SN:chr1 LN:248956422    M5:6aef897c3d6ff0c78aff06ac189178dd     AS:20   UR:/seq/references/kendrix/v0/kendrix.fasta     SP:Homo sapiens
…
chr1    1       248956422       +       .

[maxulysse]

Thanks a lot for the link @klmr, I'll look more into this format to make sur that it works with sarek.

[maxulysse]

By the way with which genome are you working?

[klmr]

I’m using GRCh38, and the file in question can be found in the GATK resource bundle on GCP (requires login) or as a download via HTTP.

[maxulysse]

I do think it's the file that we used to create the intervals file that we host on AWS iGenomes.

[maxulysse]

I think I have a solution.
Any chance you can try out https://github.com/MaxUlysse/sarek/tree/Intervals?
It's adding this small snippet in the CreateIntervalsBed process

     else if (hasExtension(intervals, "interval_list"))
        """
        cat ${intervals} | grep -v "@" > intervals.temp
        awk -vFS="\t" '{
          name = sprintf("%s_%d-%d", \$1, \$2, \$3);
          printf("%s\\t%d\\t%d\\n", \$1, \$2-1, \$3) > name ".bed"
        }' intervals.temp
        """ 

[klmr]

Yes, that works, thanks! I’ve added a review comment on your changeset.

[maxulysse]

PR has been created ;-)
Thanks for your help