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