Code

Fixes for production, March 2024#95

Code

Merged

muffato merged 36 commits intomainsanger-tol/blobtoolkit:mainfrom prod_fixsanger-tol/blobtoolkit:prod_fixCopy head branch name to clipboardApr 17, 2024

+1,959-474

Commits

Commits on Feb 9, 2024

• Upgraded the BTK container version to enable better reporting of a wrong accession being used

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  196427a

• Updated the minimap2/align module

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  b65e399

Commits on Feb 26, 2024

• Same format for the trace files as the readmapping and genomenote pipelines

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  0f509b4

Commits on Mar 15, 2024

• bugfix: put the summary.json in the blobdir so that it is published too

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  0e3a4a0

Commits on Mar 22, 2024

• Upgraded the BTK container version to handle None in CSV files

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  fc7c576

• Make minimap2 support large genomes

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  f04b749

• Pull the genome size as a meta field to allow usage in every process

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  40fbde5

• Don't modify the blobdir in place

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  46d231d

• Compress the blobdir

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  bb428b2

• Updated the changelog

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  9ee35c0

• Updated the documentation

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  2c1bd1f

• Version bump

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  d7fa228

• Updated the resource requirements of fasta_windows

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  b53b497

• Updated the resource requirements of BUSCO

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  f99b542

• Updated the resource requirements of WINDOWSTATS_INPUT

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  72a639b

• Updated the resource requirements of BLOBTOOLKIT_WINDOWSTATS

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  54862de

• Added missing FastQ extensions

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  424d7e0

• Also support FastA files

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  f8c3cd0

• Updated the input JSON

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  8f7e029

• Updated the CHANGELOG

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  75bbc21

• Only BAM and CRAM are accepted for aligned reads

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  7dd24b3

• There is no patch for cat/cat

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  a71b759

• Updated all nf-core modules

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  857d094

• No need to compress the file if we need to decompress it right after

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  ff43207

• Count the number of reads in each input file

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  b967b51

• Optimised settings for minimap2, taken from the read-mapping pipeline

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  bf82511

Commits on Mar 26, 2024

• Updated these versions too

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  fd86c4e

• Slightly increased the runtime

  Show description for c8253f5
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  c8253f5

Commits on Mar 28, 2024

• Missing space

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  eecf569

Commits on Apr 2, 2024

• bugfix: meta needs to have the lineage information so that the join can pair all outputs from the same genome

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  cf1dc98

• bugfix: these files can be missing if no gene is found

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  328e905

• Actually need more resources for BUSCO

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  e273433

Commits on Apr 3, 2024

• Tidy up the busco directory before publication

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  4c723c7

Commits on Apr 8, 2024

• Better explanation

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  f4e236f

Commits on Apr 9, 2024

• Updated the BUSCO resources

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  7417c5b

Commits on Apr 17, 2024

• Updated the README

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  8af7fa8