Update: pangolin modules#12211
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ammaraziz wants to merge 5 commits into
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LouisLeNezet
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Jul 2, 2026
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Just some simplification on the version expression, but good to go otherwise.
| @@ -63,7 +63,6 @@ nextflow_process { | |||
| { assert path(process.out.report[0][1]).readLines().first().contains("taxon,lineage,conflict,ambiguity_score,scorpio_call,scorpio_support,scorpio_conflict,scorpio_notes,version,pangolin_version,scorpio_version,constellation_version,is_designated,qc_status,qc_notes,note") }, | |||
| { assert snapshot( | |||
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Could you instead use sanitizeOutput(process.out, unstableKeys:["report"]) ?
This way this will also snapshot the versions.
| output: | ||
| tuple val(meta), path('*.csv'), emit: report | ||
| path "versions.yml" , emit: versions | ||
| tuple val("${task.process}"), val('pangolin'), eval("pangolin -v | sed -n 's/pangolin \\([0-9.]*\\).*/\\1/p'"), emit: versions_pangolin, topic: versions |
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This could be simplified as
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| tuple val("${task.process}"), val('pangolin'), eval("pangolin -v | sed -n 's/pangolin \\([0-9.]*\\).*/\\1/p'"), emit: versions_pangolin, topic: versions | |
| tuple val("${task.process}"), val('pangolin'), eval("pangolin -v | sed 's/pangolin //'"), emit: versions_pangolin, topic: versions |
| pattern: "*.{csv}" | ||
| ontologies: | ||
| - edam: http://edamontology.org/format_3752 # CSV | ||
| - edam: http://edamontology.org/format_3752 |
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Suggested change
| - edam: http://edamontology.org/format_3752 | |
| - edam: http://edamontology.org/format_3752 #CSV |
| @@ -25,7 +25,6 @@ nextflow_process { | |||
| { assert process.success }, | |||
| { assert snapshot( | |||
| path("${prefix}") , emit: db | ||
| path "versions.yml" , emit: versions | ||
| path("${prefix}") , emit: db | ||
| tuple val("${task.process}"), val('pangolin-dataset'), eval("pangolin -pv | sed -n 's/pangolin-data \\([0-9.]*\\).*/\\1/p'"), emit: versions_pangolin_dataset, topic: versions |
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Same here
Suggested change
| tuple val("${task.process}"), val('pangolin-dataset'), eval("pangolin -pv | sed -n 's/pangolin-data \\([0-9.]*\\).*/\\1/p'"), emit: versions_pangolin_dataset, topic: versions | |
| tuple val("${task.process}"), val('pangolin-dataset'), eval("pangolin -pv | sed 's/pangolin-data //'"), emit: versions_pangolin_dataset, topic: versions |
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|
@ammaraziz , do you want to get this finished off? |
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Hi guys,
Retrying this pull request, last one had a silly issue on my end.
Migrated to using topics channels for both modules
Modified the test files as they were testing for
version.ymlUpdate dependencies:
pangolinversion updated to 4.4pangolin-dataversion updated to 1.39snakemake-minimalversion updated to 9.21.1 - I chose a version that looked stable, fixed bugs but didnt introduce too many new features just to be sure.Thanks!