Sfitz nftest assertions

[sorelfitzgibbon]

Description

Add assertions to nftest: compares actual to expected output

Testing Results

output: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/unreleased/sfitz-nftest-assertions

nftest run a_mini-all-tools-std-input

original run:

output/hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/unreleased/sfitz-nftest-assertions/a_mini-all-tools-std-input-1
log: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/unreleased/sfitz-nftest-assertions/log-nftest-20230926T152143Z.log

post main merge:

output/hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/unreleased/sfitz-nftest-assertions/a_mini-all-tools-std-input
log: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/unreleased/sfitz-nftest-assertions/log-nftest-20230928T021502Z.log
slurm log: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/unreleased/sfitz-nftest-assertions/slurm-69085.out

nftest run a_mini-somaticsniper

log: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/unreleased/sfitz-nftest-assertions/log-nftest-20230925T223258Z.log

nftest run a_mini-strelka2

log: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/unreleased/sfitz-nftest-assertions/log-nftest-20230925T223430Z.log

nftest run a_mini-mutect2

log: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/unreleased/sfitz-nftest-assertions/log-nftest-20230925T223856Z.log

nftest run a_mini-muse

log: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/unreleased/sfitz-nftest-assertions/log-nftest-20230925T224243Z.log

nftest run a_mini-mutect2-multiple-samples

log: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/unreleased/sfitz-nftest-assertions/log-nftest-20230925T224332Z.log

nftest run a_mini-mutect2-tumor-only

log: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/unreleased/sfitz-nftest-assertions/log-nftest-20230925T224851Z.log

Checklist

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

• I have reviewed the Nextflow pipeline standards.

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

• I have added my name to the contributors listings in the manifest block in the nextflow.config as part of this pull request; I am listed already, or do not wish to be listed. (This acknowledgement is optional.)

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

• I have updated the version number in the metadata.yaml and manifest block of the nextflow.config file following semver, or the version number has already been updated. (Leave it unchecked if you are unsure about new version number and discuss it with the infrastructure team in this PR.)

• I have tested the pipeline on at least one A-mini sample.

[sorelfitzgibbon]

@yashpatel6 main has been merged and branch retested. Ready to go methinks.

[yashpatel6]

Looks good! Anything else to add @maotian06 ?

[tyamaguchi-ucla]

@yashpatel6 Not related to this PR but do we want to consider adding a CODEOWNERS to this pipeline?

[yashpatel6]

@yashpatel6 Not related to this PR but do we want to consider adding a CODEOWNERS to this pipeline?

We definitely should, I've opened an issue to add this

Quoting for arguments

[yashpatel6]

Quoting to account for spaces

[yashpatel6]

@maotian06 Anything else to add?

[tyamaguchi-ucla]

Quoting to account for spaces

Just wondering if this is something we can catch by GitHub action (linter) or not that straightforward? @yashpatel6
https://www.shellcheck.net/wiki/SC2086

[yashpatel6]

Quoting to account for spaces

Just wondering if this is something we can catch by GitHub action (linter) or not that straightforward? @yashpatel6 https://www.shellcheck.net/wiki/SC2086

If the shellcheck linter was added to our cicd linter, it would get caught like any other linter errors with other languages; I opened an issue for adding shell script linting to cicd

[maotian06]

Looks good to me!!!