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Call consensus for pathogen screening#31

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LilyAnderssonLee wants to merge 19 commits intodevgenomic-medicine-sweden/meta-val:devfrom consensusgenomic-medicine-sweden/meta-val:consensusCopy head branch name to clipboard

+1,521-54

Commits

Commits on Oct 24, 2024

• Prepare bam file to each individual taxid

  LilyAnderssonLee

  committed
  3ae2e29

Commits on Nov 18, 2024

• Add medaka, samtools to call consensus

  LilyAnderssonLee

  committed
  a8a0481

Commits on Nov 22, 2024

• add docs to consensus step

  LilyAnderssonLee

  committed
  4fb5fb7

Commits on Nov 25, 2024

• update subworkflow taxid_bam_fasta

  LilyAnderssonLee

  committed
  4c84e3e

Commits on Nov 26, 2024

• correct reference file name

  LilyAnderssonLee

  committed
  c07dee9

• delete GUNZIP

  LilyAnderssonLee

  committed
  4298cc4

Commits on Dec 4, 2024

• update the docs

  LilyAnderssonLee

  committed
  83b0c21

• update configs

  LilyAnderssonLee

  committed
  9ca2e85

• update configs

  LilyAnderssonLee

  committed
  0b7e91e

• Update schema

  LilyAnderssonLee

  committed
  cc603b4

• update schema

  LilyAnderssonLee

  committed
  ddb5a08

• Update output.md

  LilyAnderssonLee

  authored
  81d909a

• Update output.md

  LilyAnderssonLee

  authored
  bb67183

• compress the consensus sequences

  LilyAnderssonLee

  committed
  e793455

• update modules.config

  LilyAnderssonLee

  committed
  299c602

Commits on Dec 6, 2024

• update ch_reference in metaval.nf

  LilyAnderssonLee

  committed
  03b5e79

Commits on Dec 10, 2024

• Update nextflow_schema.json

  Show description for b04c2d0
  

  LilyAnderssonLee

  and

  sofstam

  authored
  b04c2d0

• update the modules.config and taxid_bam_fasta.nf

  LilyAnderssonLee

  committed
  46fa20c

• update modules.config

  LilyAnderssonLee

  committed
  5e2c1e5