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SAMURAI incompatible with Nextflow 26.04+ #69
Description
Description of the bug
Description
Running SAMURAI v1.4.0 with Nextflow 26.04.3 fails at script compilation
with the following errors:
Error subworkflows/local/solid_biopsy/main.nf:130:13: Incorrect number of call arguments, expected 9 but received 2
│ 130 | BUILD_PON(ponfiles, caller)
Error modules/nf-core/ichorcna/createpon/main.nf:31:9: exons is already declared
│ 31 | def exons = exons ? "exons.bed='${exons}',"
ERROR ~ Script compilation failed
Check '.nextflow.log' file for details
Command used and terminal output
##Command used:
nextflow run dincalcilab/samurai -profile test,singularity -c /mnt/data/samurai/samurai.config --outdir /mnt/data/samurai/results/test -r v1.4.0
##Terminal output:
Nextflow 26.04.6 is available - Please consider updating your version to it
N E X T F L O W ~ version 26.04.3
NOTE: Your local project version looks outdated - a different revision is available in the remote repository [e9e69e7579]
Launching `https://github.com/dincalcilab/samurai` [desperate_pike] revision: 6a90194028 [v1.4.0]
WARN: Unrecognized config option 'validation.defaultIgnoreParams'
WARN: Unrecognized config option 'validation.monochromeLogs'
WARN: Unrecognized config option 'validation.help.enabled'
WARN: Unrecognized config option 'validation.help.command'
WARN: Unrecognized config option 'validation.help.fullParameter'
WARN: Unrecognized config option 'validation.help.showHiddenParameter'
Error subworkflows/local/solid_biopsy/main.nf:130:13: Incorrect number of call arguments, expected 9 but received 2
│ 130 | BUILD_PON(ponfiles, caller)
╰ | ^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error modules/nf-core/ichorcna/createpon/main.nf:31:9: `exons` is already declared
│ 31 | def exons = exons ? "exons.bed='${exons}',"
╰ | ^^^^^
ERROR ~ Script compilation failed
-- Check '.nextflow.log' file for detailsRelevant files
.nextflow.log
samurai.config.txt
System information
##Environment:
- OS: Ubuntu 24.04 LTS on GARR server; 32 cores, 128 Gb of RAM and 1.8 Tb of free disk space;
- GNU bash, version 5.2.21(1)-release (x86_64-pc-linux-gnu);
- singularity-ce version 3.10.5-focal
- Nextflow version 26.04.3 build 12259;
- nf-core, version 4.0.2.
Activity
lbeltrame commentedon Jul 13, 2026
Hello,
SAMURAI is not (yet!) compatible with the newer Nextflow versions. I think anything below 26.04 would work. Can you file an issue mentioning this so it doesn't get forgotten?
alepolak2512 commentedon Jul 13, 2026
Hello Luca,
Many thanks for the advice. I tried to downversion to 25.10.2 and the test command completed successfully!
Do I need to create a reference in a new issue, or can we close this one?
Thank you again for the help,
Alessio
[-]Script compilation error with Nextflow 26.04.3: error in solid_biopsy subworkflows and ichorcna modules[/-][+]SAMURAI incompatible with Nextflow 26.04+[/+]lbeltrame commentedon Jul 13, 2026
I adjusted the issue title, we'll keep this open.