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nf-core / rnavar

gatk4 RNA variant calling pipeline
https://nf-co.re/rnavar
MIT License
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Paired end files are being classified as single_end: true #129

Closed nschcolnicov closed 7 months ago

nschcolnicov commented 7 months ago

Description of the bug

The ch_input definition classifies all samples as single end: image The println statement in this part of the rnavar.nf workflow prints a nested list, so it will always be of size 1: image Adding a flatten() before checking the size should fix it

Command used and terminal output

nextflow run ../../main.nf -profile bi,cluster --outdir . --annotate_tools vep --input https://raw.githubusercontent.com/nf-core/test-datasets/rnavar/samplesheet/v1.0/samplesheet_full.csv -c ../config.config -resume

Relevant files

No response

System information

No response

nschcolnicov commented 7 months ago

Nevermind, I see that this is used to concatenate reads for samples with replicates, I think that the meta key should be replaced for something like "has_replicates" instead, to avoid confusion, but this doesn't impact the pipeline's execution