Add script to run Nextflow configuration regression tests locally

[nwiltsie]

Description

This PR adds a new nfconfigtest script that allows users to run the regression tests locally:

$ ./nfconfigtest --dev --path ~/src/pipeline-recalibrate-BAM/
Looking for tests in pipeline-recalibrate-BAM
#1/2: test/configtest-F16.json
  Failure
  Compare these files and copy any expected changes:
  Original: /Users/nwiltsie/src/pipeline-recalibrate-BAM/test/configtest-F16.json
  Output:   /Users/nwiltsie/src/pipeline-recalibrate-BAM/test/configtest-F16-out.json
#2/2: test/configtest-F32.json
  Success!
1/2 tests passed

The script automatically cleans up any of the -out.json files that do match the expected results, leaving only the files that a user needs to review.

In addition to the script itself, I changed the sed command in the Dockerfile to be a little more robust. The launcher script for Nextflow 24.01.0-edge no longer has double quotes (I'm assuming just to thwart me specifically), so this is just a bit of future-proofing.

$ docker run -it --entrypoint /bin/bash nextflow/nextflow:23.10.0 -c 'grep -o ".\{30\}$" /.nextflow/tmp/launcher/nextflow-one_*/buildkitsandbox/classpath-*' 2>/dev/null
.jar" "nextflow.cli.Launcher"

$ docker run -it --entrypoint /bin/bash nextflow/nextflow:24.01.0-edge -c 'grep -o ".\{30\}$" /.nextflow/tmp/launcher/nextflow-one_*/buildkitsandbox/classpath-*' 2>/dev/null
3.0.jar nextflow.cli.Launcher

Checklist

• This PR does NOT contain Protected Health Information (PHI). A repo may need to be deleted if such data is uploaded.
  Disclosing PHI is a major problem¹ - Even a small leak can be costly².

• This PR does NOT contain germline genetic data³, RNA-Seq, DNA methylation, microbiome or other molecular data⁴.

• This PR does NOT contain other non-plain text files, such as: compressed files, images (e.g. .png, .jpeg), .pdf, .RData, .xlsx, .doc, .ppt, or other output files.

  To automatically exclude such files using a .gitignore file, see here for example.

• I have read the code review guidelines and the code review best practice on GitHub check-list.

• I have set up or verified the main branch protection rule following the github standards before opening this pull request.

• The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].

• I have added the major changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.

Footnotes

1. UCLA Health reaches $7.5m settlement over 2015 breach of 4.5m patient records ↩

2. The average healthcare data breach costs $2.2 million, despite the majority of breaches releasing fewer than 500 records. ↩

3. Genetic information is considered PHI.
   Forensic assays can identify patients with as few as 21 SNPs ↩

4. RNA-Seq, DNA methylation, microbiome, or other molecular data can be used to predict genotypes (PHI) and reveal a patient's identity. ↩

[nwiltsie]

I forgot to add - the script can be downloaded and run independently of this repository (although it won't work properly until f8bf034 is merged, as that changes the exit code).

[yashpatel6]

Looks good! Tested it out and works as expected