Bug with design matrix: No such variable: ch_design_reads_csv

[dekan-aleksandr]

Hello! I am trying to run tests for nextflow atac seq, but they fail:

nextflow run nf-core/atacseq -profile test,docker

Output: N E X T F L O W ~ version 22.04.0 Launching https://github.com/nf-core/atacseq [elegant_fermi] DSL2 - revision: 1b3a832db5 [master] Run Name : elegant_fermi Data Type : Paired-End Design File : https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/design.csv Genome : Not supplied Fasta File : https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa GTF File : https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genes.gtf Mitochondrial Contig : MT MACS2 Genome Size : 1.2E+7 Min Consensus Reps : 1 MACS2 Narrow Peaks : No MACS2 Broad Cutoff : 0.1 Trim R1 : 0 bp Trim R2 : 0 bp Trim 3' R1 : 0 bp Trim 3' R2 : 0 bp NextSeq Trim : 0 bp Fingerprint Bins : 100 Save Genome Index : No Max Resources : 6 GB memory, 2 cpus, 12h time per job Container : docker - nfcore/atacseq:1.2.1 Output Dir : ./results Launch Dir : /home/dekan Working Dir : /home/dekan/work Script Dir : /home/dekan/.nextflow/assets/nf-core/atacseq User : dekan Config Profile : test,docker Config Description : Minimal test dataset to check pipeline function

No such variable: ch_design_reads_csv

Check script '.nextflow/assets/nf-core/atacseq/main.nf' at line: 360 or see '.nextflow.log' file for more details

[i-pletenev]

Hi, I'm having the same issue. Downgrading to older nextflow version helps: conda install -c bioconda nextflow=21.10.6.

[JoseEspinosa]

The problem is that nextflow has enabled DSL2 as default from version 22.04.0and the current atacseq version is still a DSL1 pipeline (see this post). The easiest fix is to add the -dsl1 flag at the end of your command when using new nextflow versions, e.g.: NXF_VER=22.04.0 nextflow run nf-core/atacseq -profile test,docker -dsl1

[dekan-aleksandr]

The problem is that nextflow has enabled DSL2 as default from version 22.04.0and the current atacseq version is still a DSL1 pipeline (see this post). The easiest fix is to add the -dsl1 flag at the end of your command when using new nextflow versions, e.g.: NXF_VER=22.04.0 nextflow run nf-core/atacseq -profile test,docker -dsl1

Thank you! This one works! but use two dashes (--) before dsl1

[JoseEspinosa]

Are you sure? This is a Nextflow option and from Nextflow docs: "Nextflow options use a single dash prefix, e.g. -foo. Do not confuse with double dash notation, e.g. --foo, which is instead used for Pipeline parameters." I just tried myself and I can make it work with two dashes :thinking: