j2salmingo commented 6 months ago

Description

Updates BWA-MEM2 and HISAT2 Docker images to use the image built using SAMTools 1.17. Updates the Picard image to use version 3.1.1.

Closes #258

Testing Results

a_mini_n2-spark
- sample: a_mini_n2
- input csv: /hot/software/pipeline/pipeline-align-DNA/Nextflow/development/input/csv/a_mini_n2.csv
- config: ./test/a_mini_n2-spark.config
- output: /hot/software/pipeline/pipeline-align-DNA/Nextflow/development/unreleased/jsalmingo-update-docker-images/a_mini_n2-picard/align-DNA-10.0.0/a_mini_n2-spark/
a_mini_n2-picard
- sample: a_mini_n2
- input csv: /hot/software/pipeline/pipeline-align-DNA/Nextflow/development/input/csv/a_mini_n2.csv
- config: ./test/a_mini_n2-picard.config
- output: /hot/software/pipeline/pipeline-align-DNA/Nextflow/development/unreleased/jsalmingo-update-docker-images/a_mini_n2-picard/align-DNA-10.0.0/a_mini_n2-picard
a_mini_n2-picard_yaml
- sample: a_mini_n2
- input csv: ./test/a_mini_n2-picard_yaml.yaml
- config: ./test/a_mini_n2-picard_yaml.config
- output: /hot/software/pipeline/pipeline-align-DNA/Nextflow/development/unreleased/jsalmingo-update-docker-images/a_mini_n2-picard/align-DNA-10.0.0/a_mini_n2-picard_yaml

Checklist

[X] I have read the code review guidelines and the code review best practice on GitHub check-list.
[X] I have reviewed the Nextflow pipeline standards.
[X] 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].
[X] I have set up the branch protection rule following the github standards before opening this pull request, or the branch protection rule has already been set up.
[X] I have added my name to the contributors listings in the manifest block in the nextflow.config as part of this pull request, am listed already, or do not wish to be listed. (This acknowledgement is optional.)
[X] 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.
[X] 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.)
[X] I have tested the pipeline on at least one A-mini sample with aligner setting to BWA-MEM2, HISAT2, and both. The paths to the test config files and output directories were attached in the Testing Results section.

j2salmingo commented 6 months ago

/fix-tests

nwiltsie commented 6 months ago

(Sorry, this isn't working yet, frustratingly!)

nwiltsie commented 6 months ago

Gahhhh, more permissions issues. The tests are indeed passing but the old review can't be dismissed. I promise I tested all of this, these are new failures!

github-actions[bot] commented 5 months ago

Bleep bloop, I am a robot.

Alas, some of the Nextflow configuration tests failed!

test/configtest-F16.json

@ ["params","bwa_and_samtools_version"]
+ "2.2.1_samtools-1.17"
@ ["params","hisat2_and_samtools_version"]
+ "2.2.1_samtools-1.17"
@ ["params","picardtools_version"]
+ "3.1.1"

If the above changes are surprising, stop and determine what happened.

If the above changes are expected, there are two ways to fix this:

Automatically: Post a comment starting with "/fix-tests" (without the quotes) and I will update the tests for you (you must review my work afterwards).
Manually: Follow these steps on Confluence.

j2salmingo commented 5 months ago