Allow patterns in file paths

[yashpatel6]

Description

Closes #49

Adding support for patterns in file paths

Tests

Tested with pipeline-demo-pipeline

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. ↩

[zhuchcn]

Looks good. So users can specify the expected file as /path/to/dir/*.bam?

[sorelfitzgibbon]

I think it's more to avoid having to keep updating the pipeline version number in the assertions. I will try to test this with call-sSNV later today.

[yashpatel6]

Right, to basically make the file specification more generalize-able without having to update tests with every pipeline version update or minor tool update, etc

[sorelfitzgibbon]

Just tested this branch in pipeline-call-sSNV. Wild card paths worked.
uclahs-cds/pipeline-call-sSNV#248

[zhuchcn]

Looks good to me, too!

Sorry I thought this was a new PR..

[yashpatel6]

@aholmes anything else to add here?

[aholmes]

@aholmes anything else to add here?

Nope, looks good!