Fix multiqc in template

[ggabernet]

I've tested creating a template from nf-core/tools dev and running it and the MultiQC execution didn't work, the MultiQC process was just not executed. This should introduce a fix for it.

I'm also puzzled why then the test Create a pipeline and test it worked, as there was also another issue with a variable name

PR checklist

• This comment contains a description of changes (with reason)
• CHANGELOG.md is updated
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated

[codecov]

Codecov Report

Merging #1855 (f8c0cef) into dev (0af65f5) will not change coverage.
The diff coverage is n/a.

❗ Current head f8c0cef differs from pull request most recent head cd5a32b. Consider uploading reports for the commit cd5a32b to get more accurate results

@@           Coverage Diff           @@
##              dev    #1855   +/-   ##
=======================================
  Coverage   64.64%   64.64%           
=======================================
  Files          34       34           
  Lines        4115     4115           
=======================================
  Hits         2660     2660           
  Misses       1455     1455           

Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here.

[ewels]

I'm also puzzled why then the test Create a pipeline and test it worked, as there was also another issue with a variable name

Somewhat ironically, that CI test is now failing 😅

No such variable: text

 -- Check script 'nf-core-testpipeline/./workflows/testpipeline.nf' at line: 94 or see '.nextflow.log' file for more details

[ggabernet]

yes I'm investigating that now

[ewels]

Yeah, looks like the latest tests on dev weren't running MultiQC as you say:

https://github.com/nf-core/tools/actions/runs/3163354597/jobs/5150834572

[54/5031c7] Submitted process > NFCORE_TESTPIPELINE:TESTPIPELINE:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_test_illumina_amplicon.csv)
[bf/f50a25] Submitted process > NFCORE_TESTPIPELINE:TESTPIPELINE:FASTQC (SAMPLE2_PE_T1)
[11/8e0260] Submitted process > NFCORE_TESTPIPELINE:TESTPIPELINE:FASTQC (SAMPLE1_PE_T1)
[52/986799] Submitted process > NFCORE_TESTPIPELINE:TESTPIPELINE:FASTQC (SAMPLE3_SE_T1)
[24/a92aa8] Submitted process > NFCORE_TESTPIPELINE:TESTPIPELINE:FASTQC (SAMPLE3_SE_T2)
[21/3ec66f] Submitted process > NFCORE_TESTPIPELINE:TESTPIPELINE:CUSTOM_DUMPSOFTWAREVERSIONS (1)
-[nf-core/testpipeline] Pipeline completed successfully-

[ggabernet]

yes now the tests pass again but multiqc is not being run

[ggabernet]

Now it works for me 👍

[ewels]

LGTM 👍🏻

Just needs a changelog entry..