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Dev -> Master for v2.2 release#221

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Merged

drpatelh merged 49 commits intomasternf-core/viralrecon:masterfrom devnf-core/viralrecon:devCopy head branch name to clipboardJul 29, 2021

+1,390-804

Commits

Commits on Jun 15, 2021

• Bump version to 2.2dev

  drpatelh

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• Merge pull request #207 from drpatelh/updates

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  JoseEspinosa

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Commits on Jun 18, 2021

• Add wget command to download fastq_dir_to_samplesheet.py

  drpatelh

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• Print warning if dashes or spaces found in sample name

  drpatelh

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• Fix Black lint

  drpatelh

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• Fix bugs in fastq_dir_to_samplesheet.py

  drpatelh

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• Update script

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• Minor update

  drpatelh

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• Merge pull request #211 from drpatelh/updates

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  JoseEspinosa

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Commits on Jun 28, 2021

• Fix bug in getting software version for PycoQC process

  drpatelh

  committed
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• Initialise empty channel for PycoQC

  drpatelh

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• Upddate CHANGELOG

  drpatelh

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• Merge pull request #213 from drpatelh/updates

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  drpatelh

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Commits on Jul 13, 2021

• Template update for nf-core/tools version 2.0

  KevinMenden

  committed
  b1b9fb9

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• Template update for nf-core/tools version 2.0.1

  nf-core-bot

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  20119b5

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• Fix merge conflicts

  drpatelh

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Commits on Jul 14, 2021

• Update modules and add modules.json

  drpatelh

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• Update kraken2 module

  drpatelh

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• Update .nf-core.yml

  drpatelh

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• Update CHANGELOG

  drpatelh

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  37ba137

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• Make linters happy

  drpatelh

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• Ignore final newlines for JSON files

  drpatelh

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• Sort modules.json

  drpatelh

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• Remove remnant files from sync

  drpatelh

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• Change software to modules everywhere

  drpatelh

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• Fix channel issue from updating bedtools genomecov

  drpatelh

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  9854eaa

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• Remove redundant text introduced by sync

  drpatelh

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• Bump MultiQC version

  drpatelh

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Commits on Jul 15, 2021

• Merge pull request #217 from drpatelh/updates

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  drpatelh

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• Amend docs to use medaka model string by default

  drpatelh

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• Merge pull request #219 from drpatelh/updates

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  drpatelh

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Commits on Jul 20, 2021

• Bump Pangolin to 3.1.7

  drpatelh

  committed
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• Small template fixes

  drpatelh

  committed
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• Replace Pangolin MultiQC custom content with official module

  drpatelh

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• Bump version to v2.2

  drpatelh

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Commits on Jul 21, 2021

• Merge pull request #220 from drpatelh/updates

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  drpatelh

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• Fix file pattern regex in JSON schema

  drpatelh

  committed
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• Replace commas with semi-colon in summary metrics

  drpatelh

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Commits on Jul 22, 2021

• Convert variable to string

  drpatelh

  committed
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• Merge pull request #224 from drpatelh/updates

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  JoseEspinosa

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Commits on Jul 27, 2021

• Template update for nf-core/tools version 2.1

  nf-core-bot

  committed
  c25b4d1

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• Fix merge conflicts

  drpatelh

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Commits on Jul 28, 2021

• Fix bug removing summary reports

  drpatelh

  committed
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• Change ARTIC Guppyplex defaults when using --primer_set_version 1200

  drpatelh

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• Update CHANGELOG

  drpatelh

  committed
  14bf3a0

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• Fix #226

  drpatelh

  committed
  66ff1c2

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• Re-install updated Nextclade module

  drpatelh

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• Update date in CHANGELOG

  drpatelh

  committed
  a9c51b7

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• Merge pull request #230 from drpatelh/updates

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