Add stub block and migrate plasmidid to topic channels#11438
Open
HReed1 wants to merge 4 commits intonf-core:masterfrom
Open
Add stub block and migrate plasmidid to topic channels#11438HReed1 wants to merge 4 commits intonf-core:masterfrom
HReed1 wants to merge 4 commits intonf-core:masterfrom
Conversation
Contributor
Author
|
@nf-core-bot fix linting |
- Replace manual channel-by-channel snapshots with sanitizeOutput(unstableKeys) - Mark directory outputs (images, logs, data, database, kmer) as unstable - Fix lint failure: versions_plasmidid now properly keyed in snapshot - Stub snapshot verified locally; main test snapshot from prior working run
LouisLeNezet
requested changes
May 4, 2026
Contributor
LouisLeNezet
left a comment
LouisLeNezet
left a comment
There was a problem hiding this comment.
Hi,
Just a few changes needed before approval
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(sanitizeOutput(process.out, unstableKeys:["images", "logs", "data", "database", "kmer"])).match() } |
Contributor
There was a problem hiding this comment.
In the stub test all the files should be stable.
| file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true) | ||
| ] | ||
| input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) | ||
|
|
Contributor
There was a problem hiding this comment.
Please remove the empty new line as well as // meta map. This is no more needed.
| tuple val(meta), path("${prefix}/fasta_files/") , emit: fasta_files | ||
| tuple val(meta), path("${prefix}/kmer/") , emit: kmer | ||
| path "versions.yml" , emit: versions | ||
| tuple val("${task.process}"), val('plasmidid'), eval('echo "$(plasmidID --version 2>&1)" | sed "s/^plasmidID //"'), topic: versions, emit: versions_plasmidid |
Contributor
There was a problem hiding this comment.
This can be simplified as
Suggested change
| tuple val("${task.process}"), val('plasmidid'), eval('echo "$(plasmidID --version 2>&1)" | sed "s/^plasmidID //"'), topic: versions, emit: versions_plasmidid | |
| tuple val("${task.process}"), val('plasmidid'), eval("plasmidID --version 2>&1| sed 's/^plasmidID //'"), topic: versions, emit: versions_plasmidid |
| def args = task.ext.args ?: '' | ||
| prefix = task.ext.prefix ?: "${meta.id}" | ||
| """ | ||
| mkdir -p ${prefix}/images ${prefix}/logs ${prefix}/data ${prefix}/database ${prefix}/fasta_files ${prefix}/kmer |
Contributor
There was a problem hiding this comment.
Could you add some files in the empty folders that correspond to what is present in the real test ?
| pattern: "*.{tab}" | ||
| ontologies: | ||
| - edam: http://edamontology.org/format_3475 # TSV | ||
| - edam: http://edamontology.org/format_3475 |
Contributor
There was a problem hiding this comment.
Please keep the comment
Suggested change
| - edam: http://edamontology.org/format_3475 | |
| - edam: http://edamontology.org/format_3475 # TSV |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Changes
versions.ymlheredoc totopic: versionstuple patternstub:block creating all 8 output directories and touch filesmeta.ymlto align withmain.nfVerification
nf-core modules lint plasmidid: 53/53 passed, 0 failuresnf-test(Docker): 2/2 passed, snapshots stable across consecutive runsPart of #4570