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RNASeq not forwarded to BRAKER3 #74

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GallVp opened this issue Oct 26, 2024 · 2 comments · Fixed by #78
Closed

RNASeq not forwarded to BRAKER3 #74

GallVp opened this issue Oct 26, 2024 · 2 comments · Fixed by #78
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bug Something isn't working top-priority
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0.5.0

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GallVp commented Oct 26, 2024

Description of the bug

RNASeq data is mapped but it does not flow to SAMTOOLS_CAT and consequently it is not forwarded to BRAKER3.

Command used and terminal output

No response

Relevant files

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System information

plant-food-research-open/genepal: 0.5.0dev (9ac400e)
@GallVp GallVp added the bug Something isn't working label Oct 26, 2024
@GallVp GallVp added this to the 0.5.0 milestone Oct 26, 2024
@GallVp GallVp self-assigned this Oct 26, 2024
@GallVp GallVp pinned this issue Oct 26, 2024
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GallVp commented Oct 26, 2024

This bug does not affect the test data set. Investigating...

@GallVp GallVp unpinned this issue Oct 27, 2024
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GallVp commented Oct 27, 2024

This bug also does not affect release 0.4.0. It was introduced by an update of STAR_ALIGN by this commit:

genepal/modules/nf-core/star/align/main.nf

Line 26 in 7949b44

tuple val(meta), path("${prefix}.Aligned.sortedByCoord.out.bam") , optional:true, emit: bam_sorted_aligned

where bam_sorted_aligned was separated from bam_sorted.

@GallVp GallVp linked a pull request Oct 29, 2024 that will close this issue
Now using the correct out channel from STAR_ALIGN #78
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@GallVp GallVp mentioned this issue Nov 21, 2024
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@GallVp GallVp closed this as completed Nov 21, 2024
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Now using the correct out channel from STAR_ALIGN Plant-Food-Research-Open/genepal
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