Decoupler #8893
Decoupler #8893
Conversation
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P-value plot files ( |
…into decoupler
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@suzannejin Hi! I've implemented in this PR the requested changes. Please let me know if you have any feedback or if any adjustment are needed , thanks! |
| // This information is used later to determine which method to run for each input | ||
| // Also, reorganize the structure to match them with the modules' input organization | ||
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| ch_input_for_other = ch_input |
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thank you! this is great :)
| input[3] = Channel.of([[], [], [], []]) | ||
| input[3] = Channel.of([ | ||
| ['id':'Condition_genotype_WT_KO', 'variable':'Condition genotype', 'reference':'WT', 'target':'KO', 'blocking':'batch'], | ||
| [], // |
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I don't understand what is this for? Do you necessarily need to provide such a ch_featuresheet with empty stuff?
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is it because of join(ch_featureshseet, by:0)?
If so, have you tried to use remainder:true?
I recall I had to do that for the same reasons in the subworkflow "abundance_differential_filter"
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yes, it's becuase of the join. I'll try that so there is no need to modify the other tests. Thanks for the suggestion!
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Hi @suzannejin, I added remainder: true to the join:
ch_input.join(ch_featuresheet, by: 0, remainder: true)
And updated the multiMap to handle variable tuple sizes since remainder: true creates tuples with different lengths (6 elements when no featuresheet matches, 8 when it does).
Please let me know what you think!
Hi @antoniasaracco, have you tried it with Conda locally? For me, the long decimal issues also happen frequently with Conda. |
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Hello @antoniasaracco, sorry for the delay, and thank you for addressing my comments! |
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Hi @suzannejin , I've implemented the requested changes. Regarding the decoupler test, I also tried with conda locally - tested all profiles (docker, singularity, conda) and couldn't reproduce the inconsistency. The issue seems to be CI-specific. Please let me know if you have any feedback or if any adjustment are needed , thanks! |
| .join(ch_featuresheet, by: 0, remainder: true) | ||
| .multiMap { tuple -> | ||
| def (meta, file, genesets, background, method) = tuple[0..4] | ||
| def features_sheet = tuple.size() > 5 ? tuple[5] : null | ||
| def features_id = tuple.size() > 6 ? tuple[6] : '' | ||
| def features_symbol = tuple.size() > 7 ? tuple[7] : '' |
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| .join(ch_featuresheet, by: 0, remainder: true) | |
| .multiMap { tuple -> | |
| def (meta, file, genesets, background, method) = tuple[0..4] | |
| def features_sheet = tuple.size() > 5 ? tuple[5] : null | |
| def features_id = tuple.size() > 6 ? tuple[6] : '' | |
| def features_symbol = tuple.size() > 7 ? tuple[7] : '' | |
| .join(ch_featuresheet) | |
| .multiMap { meta, file, genesets, background, method, features_sheet, features_id, features_symbol -> |
I think this is over-engineered. Let's just assume the workflow is being called as differentialbundance is calling it- with a predictable feature sheet structure.
| background: | ||
| [ meta_with_method, background ] | ||
| features: | ||
| [ meta_with_method, features_sheet ?: [], features_id, features_symbol] |
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| [ meta_with_method, features_sheet ?: [], features_id, features_symbol] | |
| [ meta_with_method, features_sheet, features_id, features_symbol] |
similarly here
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okay, it looks good to me so far. Let's see what @pinin4fjords says
This reverts commit 4ac8159.
* update snapshot * exchange gtf file for annot tsv file * remove parse_gtf function * exchange gtf file for annot tsv file * update * update * update meta.yml * fix * Include annotation file expected format * Update: reference file * include decoupler to subworkflow * Include decoupler test config * Include decoupler to test file * Update snapshot with decoupler output files * Add decoupler config * Replace gtf annotation file for tsv table for decoupler * Update snapshot to remove pvals plots for decoupler * include decoupler to subworkflow meta.yml * fix syntax error * add decoupler/decoupler tag * fix syntax issue * fix component * Upgrade decoupler output assertion * Improve format validation for annotation tsv file * Include meta for all decoupler inputs * Update decoupler test with new meta input requirement * Fix decoupler input channels * Update decoupler prefix * Update decoupler test with new input channels * Update snapshot * add meta for net and annot inputs * Include method differential to stub results to avoid null names * Add method differential to stub results to avoid null * Include ch_featuresheet into ch_input_for_other * Separate channel for other and channel for decoupler including features to not disturb other profiles tests * update decoupler test * Remove hardcode of gene_id and gene_name columns * update decoupler meta.yml * update decoupler test * Fix: Remove features id and symbol from decoupler meta.yml * Fix: Remove features id and symbol from decoupler input * Fix: Take features id and symbol as external arguments * Fix: Take features id and symbol as external arguments * Fix: Take features id and symbol as external arguments * Fix: remove ch_input_for_decoupler * correct method * Update: update nf-test to work with new input channel * Fix: change method * Fix: update ch_input_for_other channel to include featuresheet only for decoupler * Update snapshot * Fix * Fix: Simplify features form input channel * Update snapshot
PR checklist
Closes #XXX
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda