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Release 0.3#92

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muffato merged 45 commits intomainsanger-tol/blobtoolkit:mainfrom devsanger-tol/blobtoolkit:devCopy head branch name to clipboardFeb 12, 2024

+1,005-168

Commits

Commits on Jan 9, 2024

• Fixed the conditional flowing

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• We shouldn't be using this old taxonomy database

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• We also need the taxdb files for the NT database

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• File numbers now have three digits

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Commits on Jan 10, 2024

• bugfix: removed extra brackets that were only needed in Snakemake rules

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• bugfix: the headers are separated with regular whitespace, not tabs

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• Updated SAMTOOLS_FASTA

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• We want *all* the reads in the output file

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Commits on Jan 12, 2024

• Correctly pick up the name of the blast database

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• Started the CHANGELOG

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• Allow FastQ files as input

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• Skip the conversion to fasta if the input is fastq

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• Like in the genome-note pipeline having a duplicated profile entry causes some problems

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• Support samplesheets created by nf-core/fetchngs

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• Support input read-sets being paired-end

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• [lint] black

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• Updated CAT_CAT module that preserves the file extension

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Commits on Jan 15, 2024

• Report all BUSCOs and in the right order

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Commits on Jan 16, 2024

• Removed "--update-plot" as it is not used by default in the Snakemake version

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Commits on Jan 18, 2024

• Bumped up the number of retries to better accommodate larger genomes

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• Bumped up the version of blobtoolkit because of a bug in windowsstat

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• Updated these two modules from upstream

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Commits on Jan 19, 2024

• Updated the CHANGELOG

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• Documented the decision tree

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• Renamed the variables to make the code easier to understand

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• Not used

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• Fixed the link

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• Let's make it happen today

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• Updated the documentation

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• Explained the purpose of this release

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• [lint] prettier

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• Revert "Let's make it happen today"

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Commits on Jan 22, 2024

• Pin the version of prettier to match the nf-core dependency we have

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• Need to make an exception for this file

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Commits on Jan 25, 2024

• bugfix: if only 1 BUSCO is provided (only lineage with a match), the object is a path, not a list

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Commits on Feb 7, 2024

• Allow chosing the output format (png vs svg)

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• typo

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• Changed the output directory of the images

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Commits on Feb 9, 2024

• Because only one format can be chosen, they have to be marked as optional

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• Moved the blobdir a level below, as per our convention

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• Lower case, please

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• Pin the version of nf-core

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• Merge pull request #88 from sanger-tol/fixes_for_prod

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• Bumped the version number up. A release is coming !

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Commits on Feb 10, 2024

• Allow integers (taxon_ids) to be passed

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