Code

Release 0.3#92

Code

Merged

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

  Show description for 275c048
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  275c048

• We shouldn't be using this old taxonomy database

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  af953d8

• We also need the taxdb files for the NT database

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  26ad7a6

• File numbers now have three digits

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  79d9bb5

Commits on Jan 10, 2024

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

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  903ebc0

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

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  04ea5e3

• Updated SAMTOOLS_FASTA

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  023a041

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

  Show description for 1d7fe41
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  1d7fe41

Commits on Jan 12, 2024

• Correctly pick up the name of the blast database

  Show description for 7729e20
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  7729e20

• Started the CHANGELOG

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  e0f2486

• Allow FastQ files as input

  Show description for 7046a75
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  7046a75

• Skip the conversion to fasta if the input is fastq

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  e54bc85

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

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  60c2f1d

• Support samplesheets created by nf-core/fetchngs

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  363d796

• Support input read-sets being paired-end

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  74b60dd

• [lint] black

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  a18fe52

• Updated CAT_CAT module that preserves the file extension

  Show description for 7527e7a
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  7527e7a

Commits on Jan 15, 2024

• Report all BUSCOs and in the right order

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  b99101b

Commits on Jan 16, 2024

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

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  9dc30da

Commits on Jan 18, 2024

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

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  48ebdca

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

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  9e19765

• Updated these two modules from upstream

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  a815df0

Commits on Jan 19, 2024

• Updated the CHANGELOG

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  ac42a3a

• Documented the decision tree

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  864d3bc

• Renamed the variables to make the code easier to understand

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  4c27f52

• Not used

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  8dc4f0c

• Fixed the link

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  6789b6f

• Let's make it happen today

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  5e7d53a

• Updated the documentation

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  9a0c6a0

• Explained the purpose of this release

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  1fbde37

• [lint] prettier

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  b8d3ae0

• Revert "Let's make it happen today"

  Show description for 50d2a71
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  50d2a71

Commits on Jan 22, 2024

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

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  5388d77

• Need to make an exception for this file

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  1dbbe9e

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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  1303a69

Commits on Feb 7, 2024

• Allow chosing the output format (png vs svg)

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  8d2ebed

• typo

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  2a3eca7

• Changed the output directory of the images

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  c4c5324

Commits on Feb 9, 2024

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

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  1f4284b

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

  Show description for fcfdb10
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  fcfdb10

• Lower case, please

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  a105dd3

• Pin the version of nf-core

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  ff87d76

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

  Show description for 681362c
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  681362c

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

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  21db9cf

Commits on Feb 10, 2024

• Allow integers (taxon_ids) to be passed

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  aabcfc6