nf-core
test run TRIMGALORE error
Description of the bug
Hello! I'm trying to install and test the pipeline. nextflow run nf-core/cutandrun -profile test,singularity --outdir ~/test but I get the following error
ERROR ~ Cannot invoke method optional() on null object
-- Check script '.nextflow/assets/nf-core/cutandrun/modules/local/for_patch/trimgalore/main.nf' at line: 18 or see '.nextflow.log' file for more details
Command used and terminal output
Relevant files
No response
System information
Nextflow 25.10.0 cutandrun 3.2.2 Singularity Linux
Hello, also getting this error on Nextflow 25.10.0. Same error if forcing to cutandrun 3.0. Traceback to '.nextflow/assets/nf-core/cutandrun/modules/local/for_patch/trimgalore/main.nf at line 18 yields this command:
tuple val(meta), path("*.html"), emit: html optional true
Not sure how to interpret this error, some google suggests Groovy might have issues with hyphens in html addresss?
Same here, same versions. This is true if I try a test run (-profile test,apptainer) or a real run. Also doesn't matter if I run using nf-core pipelines ... or nextflow run. I tried using my own yml, as well as one put together with the builder.
Here is my terminal output from a test, and attached is my .nextflow.log
nextflow run nf-core/cutandrun -r 3.2.2 -profile test,singularity
N E X T F L O W ~ version 25.10.0
Launching `https://github.com/nf-core/cutandrun` [irreverent_crick] DSL2 - revision: 6e1125d4fe [3.2.2]
WARN: =========================================================================================================
dt_calc_all_matrix is switched on which will calculate a deeptools matrix for all samples.
If you have a large sample count, this may affect pipeline performance and result in errors.
Set this option to false to disable this feature and only calculate deeptools heatmaps for single samples
===============================================================================================================
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,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/cutandrun v3.2.2-g6e1125d
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Core Nextflow options
revision : 3.2.2
runName : irreverent_crick
containerEngine : singularity
launchDir : /projects/standard/swernimo/shared/RI/2025_cutntag/scripts
workDir : /projects/standard/swernimo/shared/RI/2025_cutntag/scripts/work
projectDir : /users/4/chaco001/.nextflow/assets/nf-core/cutandrun
userName : chaco001
profile : test,singularity
configFiles :
Input/output options
input : https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-small.csv
Reference data options
bowtie2 : https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-bowtie2.tar.gz
gtf : https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.gtf.gz
gene_bed : https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.bed.gz
blacklist : /users/4/chaco001/.nextflow/assets/nf-core/cutandrun/assets/blacklists/hg38-blacklist.bed
spikein_bowtie2 : https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz
spikein_fasta : https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.fa.gz
fasta : https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20.fa.gz
Pipeline Options
remove_mitochondrial_reads: true
mito_name : chrM
remove_linear_duplicates : true
macs_gsize : 2700000000.0
replicate_threshold : 1.0
Institutional config options
config_profile_name : Test profile
config_profile_description: Minimal test dataset to check pipeline function
Max job request options
max_cpus : 2
max_memory : 6.GB
max_time : 6.h
!! Only displaying parameters that differ from the pipeline defaults !!
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If you use nf-core/cutandrun for your analysis please cite:
https://doi.org/10.5281/zenodo.5653535
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/cutandrun/blob/master/CITATIONS.md
ERROR ~ Cannot invoke method optional() on null object
-- Check script '/users/4/chaco001/.nextflow/assets/nf-core/cutandrun/modules/local/for_patch/trimgalore/main.nf' at line: 18 or see '.nextflow.log' file for more details
I had the same issue earlier and after lots of digging, I found that Nextflow 25 rewired the channel emit syntax so modifiers (like optional, collect, saveAs, etc.) have to use the key: value form now. So you actually have to either use an earlier version or set NXF_ENABLE_STRICT=false to allow the old syntax until they make the necessary changes.
I wanted to report that if I reverted to Nextflow 24, I was able to pull and run the cutandrun pipeline without issue if anybody is still looking for a (hopefully temporary) solution.
the two lines: https://github.com/nf-core/cutandrun/blob/3.2.2/modules/local/for_patch/trimgalore/main.nf#L18-L19, are wrong with missing commas. you also need to remove the empty line, see follows.
output: tuple val(meta), path("trimmed.fastq.gz") , emit: reads tuple val(meta), path("report.txt") , emit: log path "versions.yml" , emit: versions tuple val(meta), path(".html"), emit: html, optional: true tuple val(meta), path(".zip") , emit: zip, optional: true
I wanted to report that if I reverted to Nextflow 24, I was able to pull and run the cutandrun pipeline without issue if anybody is still looking for a (hopefully temporary) solution.
same here
