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Running test profile fails #1510

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bounlu opened this issue Mar 12, 2025 · 2 comments
Closed

Running test profile fails #1510

bounlu opened this issue Mar 12, 2025 · 2 comments
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@bounlu
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bounlu commented Mar 12, 2025

Description of the bug

Run with test data fails.

Command used and terminal output

$ nextflow run nf-core/rnaseq \
-latest \
-profile docker,test \
--genome GRCh38 \
--outdir './results/' \
-work-dir './work/' \
-r master \
-resume

ERROR ~ Error executing process > 'NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)'

Caused by:
  Directive `process.shell` cannot contain new-line characters - offending value: [bash
  
  set -e # Exit if a tool returns a non-zero status/exit code
  set -u # Treat unset variables and parameters as an error
  set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
  ]



 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

 -- Check '.nextflow.log' file for details
-[nf-core/rnaseq] Pipeline completed with errors-

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@bounlu bounlu added the bug Something isn't working label Mar 12, 2025
@pinin4fjords
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I believe this should be fixed by the imminent template update

@pinin4fjords pinin4fjords added this to the 3.19.0 milestone May 27, 2025
@pinin4fjords
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Fixed in dev

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