SAMURAI incompatible with Nextflow 26.04+

[alepolak2512]

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NOTE: Your local project version looks outdated - a different revision is available in the remote repository [e9e69e7579]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 details

Relevant 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.

[lbeltrame]

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]

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

[lbeltrame]

I adjusted the issue title, we'll keep this open.