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MultiQC #163

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chasemc opened this issue May 21, 2021 · 4 comments
Closed

MultiQC #163

chasemc opened this issue May 21, 2021 · 4 comments
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enhancement New feature or request nextflow Nextflow related issues/code

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@chasemc
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chasemc commented May 21, 2021

Some of the as-yet-unused nf-core template is some MultiQC stuff. We can either go ahead and incorporate it or remove these files.

https://multiqc.info/
@chasemc chasemc added the enhancement New feature or request label May 21, 2021
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chasemc commented May 21, 2021

https://github.com/KwanLab/Autometa/pull/157/files#r637044735

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chasemc commented May 21, 2021

ping @jason-c-kwan @WiscEvan @Sidduppal

@chasemc chasemc mentioned this issue May 21, 2021
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@evanroyrees evanroyrees added the nextflow Nextflow related issues/code label May 24, 2021
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🔥 I vote for removing the multiQC/fastQC stuff, as Autometa was implemented for binning, not assembly/QC

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Yeah, I think we should remove fastQC/multiQC.

evanroyrees added a commit that referenced this issue Jan 28, 2022
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🔥🍏 Fixes #163
65539e5
evanroyrees added a commit that referenced this issue Jan 30, 2022
@evanroyrees
🐛 🎨 🍏 Fix kingdom-handling and mounting NCBI databases into docker co…
1c0229d 
…ntainer (#229)

* 🎨🍏 Add optional output and logic to handle archaea input
* 🎨🔥🍏 Remove unnecessary subworkflow for binning summary and binning.
* 🎨🍏 Add working version of using either bacteria or archaea based on params.kingdom
* 🎨🐛🍏 Add meta.cov_from_assembly = spades for mock data spades coverage channel
* 🎨🍏🔥 Remove redundant code in autometa.nf channels and unused params line in binning_summary.nf
* 🎨🍏 fixes #187 KMER sub-workflow
* 🎨✅ Fix test for unclustered_recruitment.py
* 🎨🐛🍏🐍 Re-write unclustered recruitment features table to output-features and main to output-main
* 🎨🐍🐛 Incorrect cluster col usage in get_metabin_stats for binnin/summary.py
* 🎨🍏 Rename bin_contigs.nf to binning.nf
* 🎨🍏 Update tags for kmers, binning and recruitment
* 🎨🐍 Update kmers main behavior so kmer pipeline may be run at multiple different stages
* 🎨🍏 Update modules.config for new local kmer and binning processes
* 🔥🍏 Fixes #163
* 🎨🐛🐍 Fix main logic for handling missing files for kmers
* 🔥🐛 Remove added args in main logic of kmers.py
* 🔥✅ Remove unnecessary import
* 💚🔥🐛 Remove duplicat norm_df fixture in test_kmers.py
* 🔥 Remove unused import in test_recursive_dbscan.py
* ✅🎨🐍🍏 Add behavior to raise/handle 204 exit code for autometa-binning/binning.nf
* ✅ Add test for raising a TableFormatError
* 🍏 Add errorStrategy to binning.nf to ignore the 204 error
* 🐍🎨 Add sys.exit(204) exit code when raising a BinninError or TableFormatError for recursive_dbscan.py
* 🎨🍏🐍 Replace 0 exit code with 204 and add handling 204 exitcode in RECRUIT
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@chasemc @evanroyrees @Sidduppal