Bug introduced in 3.4.1 causes premature stop of the pipeline

[bounlu]

Description of the bug

The pipeline prematurely stops with the error:

Missing process or function Channel.empty([[]])

The log file says:
Caused by: groovy.lang.MissingMethodException: No signature of method: java.lang.Object.Channel.empty() is applicable for argument types: (ArrayList) values: [[]]

It's hard to debug where it comes from but I confirm it was introduced in bfec02f

When I run the pipeline with the sha before than that it works fine.

Command used and terminal output

#!/bin/bash

nextflow run nf-core/sarek \
-latest \
-profile docker \
--aligner 'bwa-mem2' \
--step mapping \
--tools freebayes,mutect2,strelka,manta,tiddit,cnvkit,controlfreec,snpeff,vep,merge \
--wes \
--intervals 'chip.hg38.bed' \
--igenomes_base 's3://ngi-igenomes/igenomes' \
--snpeff_cache '/data/snpeff_cache' \
--snpeff_genome 'GRCh38' \
--snpeff_db '105' \
--vep_cache '/data/vep_cache' \
--vep_species 'homo_sapiens' \
--vep_genome 'GRCh38' \
--vep_cache_version '111' \
--input 'samplesheet.csv' \
--outdir 'results/' \
-work-dir 'work/' \
-c 'custom_local.config' \
-r bfec02fcda0bfcdb3ce1ced5792bcc9552d8b26f \
-resume

Relevant files

No response

System information

Nextflow version 24.07.0-edge
Ubuntu Server 22.04
local executor
Docker

[oghzzang]

I have same issue, too!

[asp8200]

Try reverting to Nextflow v24.04.4. It can be done like this:

NXF_VER=24.04.4 nextflow run … <your parameters here>

The problem seems to first have appeared with NF 24.07.0-edge.

[dbarras2]

Thanks so much to all!!

Reverting the version doing :

NXF_VER=24.04.4 nextflow run …

Seems to work fine (at least the pipeline as started!)

Thanks again to all,

David

[asp8200]

It seems that the problem is about to be solved by this PR :-)

[benilton]

Thank you, @asp8200 ....

I've been trying to fix this for days.... and it was great to find your recommendation here...

NXF_VER=24.04.4 nextflow run …

did the trick.

thanks

[asp8200]

@maxulysse : This issue also popped up when I tried to run

nf-test test
-profile singularity
--verbose
-debug modules/nf-core/bcftools/consensus
--updateSnapshot

with NF v21.10.1.

[tm4zza]

Thank you, @asp8200 ....

I've been trying to fix this for days.... and it was great to find your recommendation here...

NXF_VER=24.04.4 nextflow run …

did the trick.

thanks

yes this works also for me