removed unused line to fix compilation error

[alxndrdiaz]

PR checklist

• [ ] 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/blobtoolkit branch on the nf-core/test-datasets repository.
• [ ] Make sure your code lints (nf-core lint).
• [ ] 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).

[alxndrdiaz]

If the unused line is not removed there is the following compilation error:

nextflow run main.nf -profile test,singularity

Module compilation error
- file : /nfs/users/nfs_a/ar34/blobtoolkit/./workflows/blobtoolkit.nf
- cause: Unexpected input: 'def' @ line 10, column 1.
   def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
   ^

When the line is removed the error disappears:

executor >  local (6)
[29/5acc0c] process > NFCORE_BLOBTOOLKIT:BLOBTOOLKIT:INPUT_CHECK:INPUT_TOL (1)                       [100%] 1 of 1 ✔
[12/3c9813] process > NFCORE_BLOBTOOLKIT:BLOBTOOLKIT:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv) [100%] 1 of 1 ✔
[f2/16cd28] process > NFCORE_BLOBTOOLKIT:BLOBTOOLKIT:SAMTOOLS_VIEW (mMelMel3_T2)                     [100%] 4 of 4 ✔
........
-[nf-core/blobtoolkit] Pipeline completed successfully-
WARN: There's no process matching config selector: CUSTOM_DUMPSOFTWAREVERSIONS
WARN: There's no process matching config selector: FASTQC
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: ... -- Use env variable NXF_SINGULARITY_CACHEDIR to specify a different location

[muffato]

Hi. The problem actually comes from this commit: https://github.com/sanger-tol/blobtoolkit/commit/378a56f805478bf9b906075551a95cffbfe480cb . You can see that the line was sort-of moved.

Rather than removing it, can you move it back to where it was, i.e. right after CONFIG FILES ?

[alxndrdiaz]

Hi. The problem actually comes from this commit: 378a56f . You can see that the line was sort-of moved.

Rather than removing it, can you move it back to where it was, i.e. right after CONFIG FILES ?

Done. Used:

git checkout 378a56f -- workflows/blobtoolkit.nf

Then made the requested change and pushed the changes with git push.