Trim_galore not found

[andrebolerbarros]

nextflow.log

Description of the bug

Hey everyone,

I have just installed locally in my pc (Windows 11) nextflow and was trying to run the test for the rnaseq pipeline, using the test command. However, I got an error message, saying trim_galore cannot be found:

Cheers!

Command used and terminal output

nextflow run nf-core/rnaseq -profile test --outdir out_test/

ERROR ~ Error executing process > 'NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_UNINDUCED_REP1)'

Caused by:
  Process `NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_UNINDUCED_REP1)` terminated with an error exit status (127)

Command executed:

  [ ! -f  RAP1_UNINDUCED_REP1.fastq.gz ] && ln -s SRR6357073_1.fastq.gz RAP1_UNINDUCED_REP1.fastq.gz
  trim_galore \
      --fastqc_args '-t 2' \
      --cores 1 \
      --gzip \
      RAP1_UNINDUCED_REP1.fastq.gz

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE":
      trimgalore: $(echo $(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*$//')
      cutadapt: $(cutadapt --version)
  END_VERSIONS

Command exit status:
  127

Command output:
  (empty)

Command error:
  .command.sh: line 4: trim_galore: command no
[nextflow.log](https://github.com/nf-core/rnaseq/files/13936673/nextflow.log)
t found

Work dir:
  /home/asbarros/work/1c/eb86e409f0c99003e235a805324de0

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

 -- Check '.nextflow.log' file for details

Relevant files

nextflow.log file

System information

Windows 11

[MatthiasZepper]

This is no surprise. You need to additionally specify another profile that will take care of all the dependencies: docker, singularity or conda (not recommended, though).

[drpatelh]

Hi @andrebolerbarros ! Did @MatthiasZepper suggestions work for you? I will close this issue because it seems to be an issue getting the pipeline to run and you will be better served getting real-time help from the community for these sorts of things by joining the nf-core Slack Workspace and asking your questions in the #rnaseq channel. Thanks!