can't find bbsplit.sh

[LinsenHou]

Description of the bug

I met the error ".command.sh: line 3: bbsplit.sh: command not found" when try to run the pipline using test profile
and I checked the workdir:

Command used and terminal output

nextflow run nf-core/rnaseq --outdir output --genome GRCh37 -profile test

Relevant files

No response

System information

No response

[drpatelh]

Hi @LinsenHou ! It looks like you haven't provided a containerisation profile to run with the pipeline e..g Docker or Singularity. You also don't need to provide a genome when running -profile test as this has already been created.

If you are using Docker, the correct way to run the test profile of the pipeline would be:

nextflow run nf-core/rnaseq --outdir output -profile test,docker

If you are using Singularity, the correct way to run the test profile of the pipeline would be:

nextflow run nf-core/rnaseq --outdir output -profile test,singularity

Will close this issue then. Please feel free to join the nf-core Slack Workspace for any future questions/issues. We have an #rnaseq channel where you can get more real-time help.

[LinsenHou]

Got it, thanks @drpatelh