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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
The text was updated successfully, but these errors were encountered:
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!
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/
Relevant files
nextflow.log file
System information
Windows 11
The text was updated successfully, but these errors were encountered: