Reference checksum validation

[yashpatel6]

Description

Adding basic validation for reference checksums, with failed checks resulting in a warning but not failure of test cases

Pipeline Run Results

Testing log: /hot/software/package/tool-NFTest/Python/development/unreleased/yashpatel-reference-checksums/log-nftest-20240113T020243Z.log

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'm not 100% clear on the use case here. It seems like the nftest.yml file you used had these changes made...

diff --git a/nftest.yml b/nftest.yml
index 30d31e4..2691d1d 100644
--- a/nftest.yml
+++ b/nftest.yml
@@ -10,10 +10,19 @@ cases:
     message: Testing proper separation between even and odd
     nf_script: ./main.nf
     nf_config: ./test/test_1000_divisor13.config
+    reference_files:
+      - reference_parameter_name: a_reference_param
+        reference_parameter_path: /hot/user/yashpatel/new.txt
+        reference_checksum: 2153bae19fd93c9110fd0067d5bde2f3
+        reference_checksum_type: 'md5'
+      - reference_parameter_name: another_reference_param
+        reference_parameter_path: /hot/user/yashpatel/new.txt
+        reference_checksum: 2153bae19fd93c9110fd0067d5bde2f4
+        reference_checksum_type: 'md5'

... and I can see that a_reference_param and another_reference_param were added to the nextflow command...

2024-01-13 02:02:43,731 - NFTest - INFO - NXF_WORK='/scratch/$SLURM_JOB_ID/./pipeline-demo-pipeline-test/work' nextflow run ./main.nf -c /hot/user/yashpatel/pipeline-demo-pipeline/pipeline-demo-pipeline/test/global.config -c ./test/test_1000_divisor13.config --a_reference_param /hot/user/yashpatel/new.txt --another_reference_param /hot/user/yashpatel/new.txt --output_dir /hot/user/yashpatel/pipeline-demo-pipeline/pipeline-demo-pipeline/out/Even-and-odd-output

... and a warning was issued that one of the checksums failed to match...

2024-01-13 02:02:43,730 - NFTest - WARNING - Checksum for reference file: another_reference_param=/hot/user/yashpatel/new.txt - `2153bae19fd93c9110fd0067d5bde2f3` does not match expected checksum of `2153bae19fd93c9110fd0067d5bde2f4`

Can you elaborate a little on what you're intending to use this for? My best guess would be to ensure that referenced but untracked files (like large BAMs) used as test inputs do not change.

[yashpatel6]

The primary use-case here is for reference files in pipelines, for example reference genomes or GATK bundles that get used in pipelines. For perfect reproducibility, the same reference files need to be used but currently, there's no check for the actual input reference files so I've added a check here with the tests at least. If the check does fail, the tests will continue but with the warning as a guiding point in case tests fail or as a note to keep in mind