Crosslinks and peaks are not produced for all samples in the samplesheet

[kkuret]

Crosslink files missing from results folder for ungrouped samples

When I run the pipeline (version corresponding to this PR: #166 -> https://github.com/iraiosub/clipseq/tree/feat-2-0-canonical) on ungrouped samples, crosslinks of only one sample are reported in the 04_crosslinks results folder and used further in peak calling and PEKA analysis.

I can see in the /work folder, that genomic crosslink files are produced also for other samples, but these are not published in the results folder and don't proceed to peak calling. I checked in case the crosslink files would have too few crosslinks (less than 10k), but they don't.

Pipeline run "completes successfully" and doesn't throw errors. If you resume the run, the next sample will get published in the results folder, that wasn't there previously. The log file wanst helpful in deciphering why only one sample proceeds.

I don't know where te bug stems from. I would really appreciate insights on this.

Steps to reproduce

Steps to reproduce the behaviour:
nextflow run ../clipseq/main.nf
-profile docker
--input samplesheet_ungrouped.csv
--source "fastq"
--fasta chr21.GRCh38.primary_assembly.genome.fa.gz
--gtf chr21_main.v39.gencode.gtf
--ncrna_fasta homosapiens_smallRNA.fa.gz
--ncrna_genome_index bowtie.tar.gz
--umitools_bc_pattern 'NNNNNNNNN'

Samplesheet used

sample_name,group_name,input_name,fastq
sample_1,,,https://raw.githubusercontent.com/nf-core/test-datasets/clipseq/reads/prpf8-hela-eif4a3-sirna-20190611-ju_trimmed_chr20_0_64444167.fq.gz
sample_2,,,https://raw.githubusercontent.com/nf-core/test-datasets/clipseq/reads/prpf8-hela-eif4a3-sirna-20190611-ju-2_trimmed_chr20_0_64444167.fq.gz
sample_3,,,https://raw.githubusercontent.com/nf-core/test-datasets/clipseq/reads/prpf8-hela-eif4a3-sirna-20190611-ju_trimmed_chr20_0_64444167.fq.gz

Expected behaviour

Expected: if samples are ungrouped, all xl files should be published to the results folder.

System

• Hardware: PC and HPC
• Executor: local and slurm
• OS: CentOS Linux

Nextflow Installation

• Version: 24.10.5.5935

Container engine

Docker and singularity

[iraiosub]

This issue isn’t limited to PR #166 — it also occurs when running the same settings and samplesheet on the feat-2-0 branch. A fix for this has been implemented in this PR on my fork. Once merged, it will be incorporated into PR #166.