This fixes an issue introduced in #302. The aim was to imitate the depricated userEmulation . However, process.containerOptions is also used when specifying singularity profile and this obviously results in issues.
PR checklist
[x] This comment contains a description of changes (with reason).
[ ] If you've fixed a bug or added code that should be tested, add tests!
[ ] If you've added a new tool - have you followed the pipeline conventions in the contribution docs
[ ] If necessary, also make a PR on the nf-core/mhcquant branch on the nf-core/test-datasets repository.
[ ] Make sure your code lints (nf-core lint).
[x] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
[ ] Usage Documentation in docs/usage.md is updated.
[ ] Output Documentation in docs/output.md is updated.
[ ] CHANGELOG.md is updated.
[ ] README.md is updated (including new tool citations and authors/contributors).
This fixes an issue introduced in #302. The aim was to imitate the depricated
userEmulation. However,process.containerOptionsis also used when specifying singularity profile and this obviously results in issues.PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).