All pull requests

Pull requests

• Add an option in PR template to no AI contribution

  #8480·lldelisle opened Oct 2, 2026Contributor·1 of 9 tasks·

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• Remove usage of sam_fa_indexes

  #8479·lldelisle opened Oct 2, 2026Contributor·5 of 7 tasks·

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  1

• Bedtools stop using __dbkeys__ to use fasta_indexes data table

  skip-version-check
  #8478·lldelisle opened Oct 2, 2026Contributor·5 of 7 tasks·

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  4

• busco DM: do not use space in value and path

  #8477·bernt-matthias opened Oct 1, 2026Contributor·3 of 8 tasks·

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• add pretext-to-asm

  #8476·rlibouba opened Oct 1, 2026Contributor·

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• Update IMPC query tool

  #8473·AndreaFurlani opened Sep 30, 2026Contributor·5 of 8 tasks·

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  3

• MultiQC: detect errors by exit code, not by "error:" in output

  #8472·afgane opened Sep 30, 2026Contributor·6 of 8 tasks·

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  2

• Add Mashtree wrapper

  ready-for-review
  #8467·CWestergaard opened Sep 28, 2026Contributor·5 of 7 tasks·

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  7

• Updating tools/cramino from version 1.3.0 to 2.0.0

  #8459·gxydevbot opened Sep 28, 2026Collaborator·

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• add chronaeon

  ready-for-review
  #8455·d-callan opened Sep 24, 2026Contributor·6 of 8 tasks·

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  41

• Add Perseus wrapper

  #8452·matnguyen opened Sep 22, 2026·4 of 8 tasks·

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  12

• Fix Panaroo bug

  ready-for-review
  #8451·SaimMomin12 opened Sep 22, 2026Contributor·4 of 8 tasks·

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  1

  4

• Trimmomatic: stop the JVM applying _JAVA_OPTIONS twice

  #8437·afgane opened Sep 18, 2026Contributor·6 of 8 tasks·

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• Update bcftools

  #8435·mertydn opened Sep 18, 2026Contributor·4 of 8 tasks·

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• Updating tools/ensembl_vep from version @DB_VERSION@.2 to 116.2

  #8430·gxydevbot opened Sep 18, 2026Collaborator·

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  1

• Make the homer peaks option produce the peak file it advertises

  #8424·guerler opened Sep 15, 2026Collaborator·

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• Declare the query_impc g_out parameter at the scope the macro expands it

  #8423·guerler opened Sep 14, 2026Collaborator·

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• Test fixes assertions

  skip-version-check
  #8419·guerler opened Sep 13, 2026Collaborator·5 of 8 tasks·

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  4

• Assert the sickle log records and qualify its format_source references

  #8418·guerler opened Sep 13, 2026Collaborator·5 of 8 tasks·

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• Test fixes stacks2

  #8417·guerler opened Sep 13, 2026Collaborator·5 of 8 tasks·

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• Add --name parameter to sourmash_sketch

  #8414·d-callan opened Sep 11, 2026Contributor·5 of 8 tasks·

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  4

• Update picrust2 to 2.6.3

  ready-for-review
  #8404·SaimMomin12 opened Sep 7, 2026Contributor·4 of 8 tasks·

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  1

• Updating tools/semibin from version 2.1.0 to 2.5.0

  #8401·gxydevbot opened Sep 7, 2026Collaborator·

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  2

• Update disco to 1.3.0

  #8395·SaimMomin12 opened Sep 7, 2026Contributor·3 of 8 tasks·

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• multiqc: add fastq_screen, mosdepth, fgbio, and umitools plugins

  #8381·bgruening opened Sep 1, 2026Member·

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  1