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
@ ["process","afterScript"]
+ {"1":"","2":"","3":"","closure":""}
@ ["process","ext"]
+ {"capture_logs":true,"commonAfterScript":{"1":"","2":"","3":"","closure":""},"log_dir":{"1":"ext","2":"ext","3":"ext","closure":"ext"}}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
nwiltsie
Description
Closes #321
Testing Results
NFTest
input: sample_id: a_mini_n2_spark input_csv: /hot/software/pipeline/pipeline-align-DNA/Nextflow/development/input/csv/a_mini_n2.csv reference_fasta_bwa: /hot/ref/tool-specific-input/BWA-MEM2-2.2.1/GRCh38-BI-20160721/index/genome.fa reference_fasta_index_files_bwa: /hot/ref/tool-specific-input/BWA-MEM2-2.2.1/GRCh38-BI-20160721/index/genome.fa. reference_fasta_hisat2: /hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta reference_fasta_index_files_hisat2: /hot/ref/tool-specific-input/HISAT2-2.2.1/GRCh38-BI-20160721/index/Homo_sapiens_assembly38..ht2
output: work_dir: /scratch/185380 output_dir: /hot/software/pipeline/pipeline-align-DNA/Nextflow/development/unreleased/jsalmingo-use-methods-setup-process-afterscript/a_mini_n2-spark output_dir_base_bwa: /hot/software/pipeline/pipeline-align-DNA/Nextflow/development/unreleased/jsalmingo-use-methods-setup-process-afterscript/a_mini_n2-spark/align-DNA-10.1.0/a_mini_n2_spark output_dir_base_hisat2: /hot/software/pipeline/pipeline-align-DNA/Nextflow/development/unreleased/jsalmingo-use-methods-setup-process-afterscript/a_mini_n2-spark/align-DNA-10.1.0/a_mini_n2_spark log_output_dir_bwa: /hot/software/pipeline/pipeline-align-DNA/Nextflow/development/unreleased/jsalmingo-use-methods-setup-process-afterscript/a_mini_n2-spark/align-DNA-10.1.0/a_mini_n2_spark/log-align-DNA-10.1.0-20240625T211311Z/ log_output_dir_hisat2: /hot/software/pipeline/pipeline-align-DNA/Nextflow/development/unreleased/jsalmingo-use-methods-setup-process-afterscript/a_mini_n2-spark/align-DNA-10.1.0/a_mini_n2_spark/log-align-DNA-10.1.0-20240625T211311Z/
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
manifestblock in thenextflow.configas 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.mdunder the next release version or unreleased, and updated the date.[X] I have updated the version number in the
metadata.yamlandmanifestblock of thenextflow.configfile 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.