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Plant-Food-Research-Open / genepal

A Nextflow pipeline for consensus, phased and pan-genome annotation
MIT License
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RNASeq not forwarded to BRAKER3 #74

Open GallVp opened 2 days ago

GallVp commented 2 days ago

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

No response

System information

plant-food-research-open/genepal: 0.5.0dev (https://github.com/Plant-Food-Research-Open/genepal/commit/9ac400ebbd17df93c7bbd882db588ef4f143852f)

GallVp commented 2 days ago

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

GallVp commented 1 day ago

This bug also does not affect release 0.4.0. It was introduced by an update of STAR_ALIGN by this commit: https://github.com/Plant-Food-Research-Open/genepal/blob/7949b4424b6f40a9537b426d1b13b3bf0d5e755e/modules/nf-core/star/align/main.nf#L26

where bam_sorted_aligned was separated from bam_sorted.