Dev -> Master for v2.3 release #273
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Correctly call MULTIQC_TSV_FROM_LIST
Small fixes to remove dummy files and params calls in nf-core/modules
Remove duplicate variants in ARTIC ONT pipeline
Add long format table to ONT output
Bump version to 2.3
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saramonzon
approved these changes
Feb 3, 2022
Fixes to ivar_variants_to_vcf.py script
Pre-release bug fixes
JoseEspinosa
approved these changes
Feb 4, 2022
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| withName: 'MULTIQC_TSV_FAIL_READS' { |
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I guess here is not a problem since the MULTIQC not aliased process does indeed set the same path, but maybe it would be better to alias it to MULTIQC_MAIN to avoid any issue?
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You will love this one 👀 , there is a new version of all these modules after this PR has been merged nf-core/modules#1261
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Bah, it can wait for the next release now that we have tested everything. Didn't even see that it was merged! Thought we were still discussing it 👀
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@drpatelh found this warnings when running |
heuermh
reviewed
Feb 4, 2022
| A [`nextclade dataset`](https://docs.nextstrain.org/projects/nextclade/en/latest/user/datasets.html#nextclade-datasets) feature was introduced in [Nextclade CLI v1.3.0](https://github.com/nextstrain/nextclade/releases/tag/1.3.0) that fetches input genome files such as reference sequences and trees from a central dataset repository. We have uploaded Nextclade dataset [v2022-01-18](https://github.com/nextstrain/nextclade_data/releases/tag/2022-01-24--21-27-29--UTC) to [nf-core/test-datasets](https://github.com/nf-core/test-datasets/blob/viralrecon/genome/MN908947.3/nextclade_sars-cov-2_MN908947_2022-01-18T12_00_00Z.tar.gz?raw=true), and for reproducibility, this will be used by default if you specify `--genome 'MN908947.3'` when running the pipeline. However, there are a number of ways you can use a more recent version of the dataset: | ||
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| * Supply your own by setting: `--nextclade_dataset <PATH_TO_DATASET>` | ||
| * Let the pipeline create and use the latest version by setting: `--nextclade_dataset false --nextclade_dataset_tag false` |
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I'd suggest not including this as an option, as it allows for non-reproducibility
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We have had a number of users that just want to use the latest version and this allows them to do that 🤷🏽
heuermh
reviewed
Feb 4, 2022
| input_file.eachLine { line -> | ||
| def val = line.split(sep)[col] | ||
| if (uniqify) { | ||
| if (!vals.contains(val)) { |
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This would make my algorithms teacher upset, better to use a Set in this case. Will suggest this change elsewhere
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This will have to wait until the next release now! Minor change :)
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Yep, no problem. There are more low hanging fruit than this for improving performance 😉
Use ft,sb filters for Fisher's exact test and strand bias
No way around this I'm afraid. It's because we initialise |
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Thanks guys! |
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