File name collision due to "." in the file name

[hoelzer]

We run poreCov directly on some provided FASTQ files w/o checking the file names in detail. The pipeline failed then because of

Process `create_summary_report_wf:plot_coverages` input file name collision -- There are multiple input files for each of the following file names

The issue is very likely the FASTQ file names:

• foobar_25.fastq.gz
• foobar_26.fastq.gz
• foobar2.4_2_27.fastq.gz
• foobar2.4_2_28.fastq.gz

and it seems that in the pipeline everything after the first "." gets removed. And then we end up with a channel that has non-unique entries foobar2.

Can we fix this, or include something to test the file names before the pipeline really starts?

[MarieLataretu]

see also #192

[hoelzer]

ah, nice @MarieLataretu , thx ;)

[replikation]

We can do basename instead of simplename. But then every sample name has still the .fastq at the end. There is also a filename collision if we have the same fasta headers.

Martin Hölzer @.***> schrieb am Do., 13. Jan. 2022, 14:40:

ah, nice @MarieLataretu https://github.com/MarieLataretu , thx ;)

— Reply to this email directly, view it on GitHub https://github.com/replikation/poreCov/issues/193#issuecomment-1012145842, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIQSLLXD4B75C6AV5CXJZL3UV3I3FANCNFSM5L33M7KQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you were assigned.Message ID: @.***>

[replikation]

closing this as its referenced in #192

[hoelzer]

Yes thx for closing, we just opened the issues simultaneously ;) lets continue the discussion in #192