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Commits on Mar 10, 2023

• Glimpse2 concordance (#3007)

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  LouisLeNezet

  and

  matthdsm

  authored
  7a6733b

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Commits on Mar 9, 2023

• Cellranger update (#3013)

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  apeltzer

  and

  grst

  authored
  abe9c71

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• add args to cellranger mkref (#3012)

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  grst

  authored
  63d27c4

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• update vcf extract relate somalier to guidelines (#2995)

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  nvnieuwk

  authored
  78ae86a

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• update bam stats samtools to guidelines (#2987)

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  nvnieuwk

  and

  matthdsm

  authored
  b4b7f89

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• update somatic tumor normal vc subwf to guidelines (#2993)

  nvnieuwk

  authored
  81861a8

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• Bump version of umi-tools to 1.14 (#2971)

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  3 peopleauthored
  6d9c7e4

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• New module GLIMPSE2_ligate (#2999)

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  LouisLeNezet

  and

  matthdsm

  authored
  2bf8ac9

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• update bam markduplicates subwf to guidelines (#2986)

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  nvnieuwk

  authored
  6f1697c

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• Bbmap bbnorm (#2969)

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  4 peopleauthored
  10b8f5e

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• update crumble (#3005)

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  priyanka-surana

  authored
  70358ed

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Commits on Mar 8, 2023

• FASTP - Remove --stdout to not bloat log files (#3000)

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  apeltzer

  authored
  20a5086

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• Update amplify/predict (#2998)

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  jasmezz

  and

  Midnighter

  authored
  5293fc5

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• Update module smoothxg: adjust the output path so that only the final graph is emitted in the channel (#2997)

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  Simon Heumos

  authored
  8ef527c

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• add module bcftools/split (#2996)

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  matthdsm

  authored
  2eabfa8

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• update vcf_annotate_snpeff to guidelines (#2985)

  nvnieuwk

  authored
  fb0333d

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• Plink indep (#2992)

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  atrigila

  authored
  6c2a440

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• New module Glimpse2 phase (#2977)

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  3 peopleauthored
  00587f2

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• add module goleft/indexsplit (#2989)

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  matthdsm

  and

  nvnieuwk

  authored
  a689351

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• Glimpse phase input management (#2964)

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  LouisLeNezet

  authored
  6e09054

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Commits on Mar 7, 2023

• New module: kallisto/quant (#2844)

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  anoronh4

  and

  ramprasadn

  authored
  fa9226d

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• New module: Plink bcf (#2981)

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  atrigila

  authored
  f58d2ef

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• Glimpse2 chunk (#2927)

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  3 peopleauthored
  37cc453

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• Transdecoder input gzip fasta file (#2814)

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  4 peopleauthored
  ca9b98f

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• Fix meta.ymls based on json schema (#2917)

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  3 peopleauthored
  0f8a77f

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• Sambamba markdup (#2838)

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  3 peopleauthored
  74deab5

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• module: gget (#2777)

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  3 peopleauthored
  7ba476b

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• Merge queue ci update (#2976)

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  jfy133

  and

  matthdsm

  authored
  8da4256

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• Add on section for allowing merge_groups (#2975)

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  jfy133

  and

  matthdsm

  authored
  3e7da87

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• add schema to validate meta.ymls (#2913)

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  mashehu

  authored
  56a5276

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• Update gtdbtk to v2.1.1 (#2339)

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  3 peopleauthored
  57d1d24

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• New module: sam2lca (#2358)

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  3 peopleauthored
  a7385cb

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• add module for midas/run (#2696)

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  rpetit3

  and

  matthdsm

  authored
  6e5f7d6

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• bioconda error fixed (#2974)

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  mapo9

  authored
  5bdba15

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• bam_variant_calling_freebayes (#2217)

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  3 peopleauthored
  7064fcb

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