Issue running nf-core/rnaseq on SLURM via Seqera Platform — tools not found (exit code 127)

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Hi!

I’m trying to run the nf-core/rnaseq pipeline on my SLURM cluster using the Seqera Platform. I successfully created the compute environment, added the pipeline to Launchpad, and provided all required inputs. However, when I start the run, I get errors like the following:

Error executing process > ‘NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_UNINDUCED_REP1)’

Caused by:

Process … terminated with an error exit status (127)

Command error:

.command.sh: line 7: fastqc: command not found

This suggests that tools like fastqc aren’t available in the environment.

When I run the same pipeline directly via Nextflow, everything works fine and all tools are resolved automatically.

Could you please clarify:

* Do I need to install these tools manually on the SLURM, or should the Seqera platform automatically pull the required containers (as Nextflow does locally)?

* Is there a specific configuration I might have missed in my compute environment or pipeline setup?

Thank you for your help!

Best regards,

Arseniy Sokolov

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Hi Arseniy

When you say

When I run the same pipeline directly via Nextflow

are you running the Nextflow on the same SLURM cluster? Is there any configuration that you’re applying when running on the CLI that is not being provided when running on Seqera Platform? For example:
docker.enabled = true