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Longread only functionality#718

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muabnezor wants to merge 27 commits intonf-core:devnf-core/mag:devfrom muabnezor:longread_onlymuabnezor/mag:longread_onlyCopy head branch name to clipboard

+5,199-191

Commits

Commits on Nov 25, 2024

• Add longread only test config

  muabnezor

  committed
  5ffb327

• Change samplesheet validation schema to allow for longread-only samplesheets

  muabnezor

  committed
  695da2b

• Check if both short, and long reads are given

  muabnezor

  committed
  f67b6b3

• fix validation schema for samplesheet

  muabnezor

  committed
  bb78aab

Commits on Nov 26, 2024

• Merge remote-tracking branch 'upstream/dev' into longread_only

  muabnezor

  committed
  992b01e

• Add separate wubworkflow for longread host removal

  muabnezor

  committed
  bfd404c

• Add longread meta-assemblers metaflye and metamdbg

  muabnezor

  committed
  387284d

• Add longread assemble config

  muabnezor

  committed
  6948316

Commits on Nov 27, 2024

• Prepare binning for longread assemblies

  muabnezor

  committed
  762f12b

Commits on Nov 28, 2024

• Fix config and how long reads are prepared for binning

  muabnezor

  committed
  c7a5cdf

• change jgi_summarize_bam_contig_depths --percentidentity default from 97 to 90 when dealing with longreads

  muabnezor

  committed
  18ae00d

• Fix longread binning preparation from all combination of assemblies, and reads

  muabnezor

  committed
  8a22939

Commits on Nov 29, 2024

• format

  muabnezor

  committed
  038a87b

• Fix longread hostremoval, and fix --longread_percentidentiy parameter in config

  muabnezor

  committed
  3ff8de2

• Add test_longread to profiles, and ci testing

  muabnezor

  committed
  e277290

• Fix validation schema, and fix assembly channels for longread and shortread assemblers, when assembly input is given

  muabnezor

  committed
  75a36f2

• Change logic in samplesheet validation, ch_raw_short_reads should be empty if no files are given

  muabnezor

  committed
  67d44d0

• fix custom samtools view module

  muabnezor

  committed
  ca4d101

Commits on Dec 5, 2024

• Merge branch 'dev' into longread_only

  muabnezor

  authored
  cfd43e7

Commits on Dec 6, 2024

• Make sure filtlong works without short reads. the join operator should also return remainder in case the ch_short_reads channel is empty. Change config for FILTLONG to only use '--trim' option if s…

  Show description for 6765ab1
  muabnezor

  committed
  6765ab1

• Make sure FILTLONG is not run when there are no long reads

  muabnezor

  committed
  e73975c

Commits on Dec 11, 2024

• Fix grouping logic for channels in longreads_binning_preparation subworkflow

  muabnezor

  committed
  686fafe

Commits on Dec 12, 2024

• make assembly into subworkflow

  muabnezor

  committed
  a0279fe

• Fix long read assembly input

  muabnezor

  committed
  28f72af

• Update docs

  muabnezor

  committed
  1c4b364

• Update citations for tools

  muabnezor

  committed
  34067db

Commits on Dec 13, 2024

• Fix versions channel in subworkflows

  muabnezor

  committed
  26a0fe7