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

**URL:** <https://community.seqera.io/t/issue-running-nf-core-rnaseq-on-slurm-via-seqera-platform-tools-not-found-exit-code-127/2431>\
**Category:** Ask for help\
**Tags:** nextflow, nf-core, platform, seqera\
**Created:** [October 27, 2025, 3:41pm UTC](https://community.seqera.io/t/issue-running-nf-core-rnaseq-on-slurm-via-seqera-platform-tools-not-found-exit-code-127/2431 "2025-10-27T15:41:11Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Arseniy\_Sokolov](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/arseniy_sokolov/32/2113_2.png) [@Arseniy\_Sokolov](https://community.seqera.io/u/Arseniy_Sokolov)\
**Post date:** [October 27, 2025, 3:41pm UTC](https://community.seqera.io/t/issue-running-nf-core-rnaseq-on-slurm-via-seqera-platform-tools-not-found-exit-code-127/2431/1 "2025-10-27T15:41:11Z")

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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:

```auto
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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<div class="post-metadata">

**Author:** ![robsyme](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/robsyme/32/342_2.png) [@robsyme](https://community.seqera.io/u/robsyme)\
**Post date:** [October 27, 2025, 8:57pm UTC](https://community.seqera.io/t/issue-running-nf-core-rnaseq-on-slurm-via-seqera-platform-tools-not-found-exit-code-127/2431/2 "2025-10-27T20:57:23Z")

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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`