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Issue with using "--retain_unpaired" with the "FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE" module #799

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m3hdad opened this issue Mar 30, 2022 · 1 comment
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Issue with using "--retain_unpaired" with the "FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE" module #799

m3hdad opened this issue Mar 30, 2022 · 1 comment
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bug Something isn't working WIP Work in progress
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3.7

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@m3hdad
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m3hdad commented Mar 30, 2022

Description of the bug

if you pass --retain_unpaired to FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE, then ALIGN_STAR:STAR_ALIGN breaks by returning segmentation fault. I believe the issue is that four files are passed to STAR, two paired and two unpaired! (slack disscussion)

@drpatelh suggested the use of a discriminator in the TrimGalore module to determine the type of read

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@m3hdad m3hdad added the bug Something isn't working label Mar 30, 2022
@drpatelh drpatelh added this to the 3.7 milestone Apr 26, 2022
@drpatelh drpatelh mentioned this issue Apr 26, 2022
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@drpatelh drpatelh changed the title "--retain_unpaired" to "FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE" issue Issue with using "--retain_unpaired" with the "FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE" module Apr 26, 2022
drpatelh added a commit to drpatelh/nf-core-rnaseq that referenced this issue Apr 26, 2022
@drpatelh
Fix nf-core#799
0b9d61a
@drpatelh drpatelh added the WIP Work in progress label Apr 26, 2022
@drpatelh drpatelh mentioned this issue Apr 26, 2022
Merged
drpatelh added a commit that referenced this issue Apr 27, 2022
@drpatelh
Merge pull request #811 from drpatelh/fixes
343e52f 
Fix #798, #799, #802
@drpatelh
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This should be fixed in #811 @m3hdad if you want to give -r dev a test drive.

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