First official release#17
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…cies tag in get accessions modules; display a warn message when no dataset is found
…vent fetching accessions from GEO; add parameter to control this threshold
Fix some bugs and pass tests with conda and apptainer
remove tests for CI to try and avoid "No space left on disk" error
Increase max shards for nf-test on CI runners
quentinblampey
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quentinblampey
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Hi @OlivierCoen,
This is an amazing work, congrats!
You're probably more experienced with Nextflow than I am, and it looks really great - I just made a few minor comments, it should be easy to update :)
| ch_all_counts = channel.empty() | ||
| ch_all_imputed_counts = channel.empty() | ||
| ch_whole_design = channel.empty() | ||
| ch_whole_design = channel.empty() |
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| ch_whole_design = channel.empty() |
This line was duplicated
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you're right, I'll fix that :)
| ch_whole_gene_id_mapping = channel.empty() | ||
| ch_most_stable_genes_summary = channel.empty() | ||
| ch_all_genes_statistics = channel.empty() | ||
| ch_most_stable_genes_transposed_counts = channel.empty() |
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The three last channels are initialized but never used: ch_most_stable_genes_summary, ch_all_genes_statistics and ch_most_stable_genes_transposed_counts
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Wow good catch! I did some refactoring at some point and forgot to check the initialised channels. Thanks!
| // ----------------------------------------------------------------- | ||
| // AGGREGATION AND FINAL STABILITY SCORE | ||
| // ----------------------------------------------------------------- | ||
| //ch_normfinder_stabilities.join( ch_genorm_stability ).join( ch_section_stats ), |
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| //ch_normfinder_stabilities.join( ch_genorm_stability ).join( ch_section_stats ), |
minor: this commented line can be removed
| .collect( sort: true ) | ||
| .map { files -> [ [ platform: "all" ], files ] } | ||
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| GLOBAL( ch_collected_merged_counts.collect() ) |
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Not sure about this one, but is .collect() not already used above for the same channel? Can this .collect() be removed?
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actually I had put this collect() in order to remove the (1) automatic tag (useful when you know that there will be only one item in the channel). But you're right, this one was a duplicate
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| /* | ||
| ======================================================================================== | ||
| SUBWORKFLOW TO DOWNLOAD EXPRESSIONATLAS ACCESSIONS AND DATASETS |
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The exact same line can be found in many different files, I guess it's not expected? Could you update the comment message?
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absolutely, this should definitely be fixed
Fix minor issues in doc / code style and fix bug in species selection in Expression Atlas get accessions
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This PR is dedicated to officially releasing the pipeline in version 1.0.0.
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).