dev branch works only on the first sample

[loipf]

Description of the bug

I know it is still work in progress, but the new version of this pipeline https://github.com/nf-core/rnavar/tree/dev seems really promising. However, it only takes the first sample in a sample sheet and ignores the rest for alignment with STAR.

FASTQC is still done on both samples, but STAR_ALIGN only takes the first sample, probably due to some multichannel conflict? I don't know exactly, what fixed it for me was setting the ch_star_index and ch_gtf to values using .first()? but you probably know a smoother and better way to solve this. just wanted to let you know. thanks for the nice pipeline. can be closed if you already know it.

https://github.com/nf-core/rnavar/blob/0b2c66e5b49eb25be3ce9014534be56a8955ec2b/workflows/rnavar/main.nf#L138

FASTQ_ALIGN_STAR(ch_cat_fastq,
            ch_star_index.first(),
            ch_gtf.first(),
            params.star_ignore_sjdbgtf,
            seq_platform,
            seq_center,
            ch_fasta,
            [[:],[]]) //ch_transcripts_fasta)

Command used and terminal output

nextflow run nf-core/rnavar -r dev -profile docker,test --outdir test2 --input input_sample_sheet.csv

Relevant files

input_sample_sheet.csv (your example with a second row):

sample,fastq_1,fastq_2,strandedness
GM12878,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz,reverse
s2,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz,reverse

System information

N E X T F L O W version 24.04.2 build 5914

[maxulysse]

@loipf Thanks a lot, I'm in the middle of refactoring, and I need to handle the references properly. sorry about that, I'll try to fix it ASAP

[loipf]

yes dont worry and no hurry, its a great pipeline

[maxulysse]

let's keep open until it's fixed

[KristinaGagalova]

Interestingly, some of my runs got stacked at the first sample, while others ran for all of them. I will relate my issue to this since using the dev branch solved my problems. - #150

[fmalmeida]

Hi @maxulysse , I created a branch to propose a fix, converting the two channels from queue to value channel. --> https://github.com/nf-core/rnavar/pull/154

I know you are in the middle of refactoring, but think that maybe would help having this integrated in parallel.

Let me know your thoughts. If this is something you want to integrate now, or prefer handling in a different way.

[nvnieuwk]

This has been fixed!