When I specify the parameters --ignore_r1 or --ignore_3prime_r1, it triggers an error during the methylation extraction process of bismark. The issue comes from the non expansion of the variables in the modules.config file. It is solved by replacing simple quotes by double quotes in the modules.config file. I am opening a PR in parallel of this bug report with the fix https://github.com/nf-core/methylseq/pull/359
Command used and terminal output
nextflow run nf-core/methylseq -r 2.5.0 -profile test,apptainer --outdir test --ignore_r1 5
Command error:
.command.sh: line 3: ${params.ignore_r1}: bad substitution
Description of the bug
When I specify the parameters
--ignore_r1or--ignore_3prime_r1, it triggers an error during the methylation extraction process of bismark. The issue comes from the non expansion of the variables in the modules.config file. It is solved by replacing simple quotes by double quotes in the modules.config file. I am opening a PR in parallel of this bug report with the fix https://github.com/nf-core/methylseq/pull/359Command used and terminal output
Relevant files
No response
System information