Code

Release 2.9.0#725

Code

Merged

d4straub merged 127 commits intomasternf-core/ampliseq:masterfrom devnf-core/ampliseq:devCopy head branch name to clipboardApr 3, 2024

+7,370-3,046

Commits

Commits on Jan 16, 2024

• bump-version 2.9.0dev

  d4straub

  committed
  e89a674

Commits on Jan 17, 2024

• Merge pull request #692 from d4straub/bump-version-2.9.0dev

  Show description for 2da3147
  d4straub

  authored
  2da3147

Commits on Jan 29, 2024

• Template update for nf-core/tools version 2.12

  nf-core-bot

  committed
  0d8dce4

Commits on Feb 1, 2024

• template update 2.12

  d4straub

  committed
  1d3c72d

• fix indent and trailing whitespace

  d4straub

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  d19bdac

• fix software versions in nf.test.snap

  d4straub

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  e0f0e76

• fix prettier

  d4straub

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  ae32e2c

• fix linting: ignore params.report_*

  d4straub

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  fe61543

• fix prettier

  d4straub

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  039ca64

• update subworkflow fasta_newick_epang_gappa

  d4straub

  committed
  93a5869

• Merge pull request #697 from d4straub/merging-template-updates-2.12

  Show description for bc1a10e
  d4straub

  authored
  bc1a10e

Commits on Feb 2, 2024

• fix README badges

  d4straub

  committed
  bbd5518

Commits on Feb 5, 2024

• update CHANGELOG

  d4straub

  committed
  37bf03f

• fix typo

  d4straub

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  effb048

• add --save_intermediates

  d4straub

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  376c2de

• fix unused line

  d4straub

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  5fa1d1d

• move primers to meta map

  d4straub

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  117e426

Commits on Feb 6, 2024

• Merge pull request #699 from d4straub/fix-readme-and-nextflow_schema

  Show description for 2aa390c
  d4straub

  authored
  2aa390c

• apply harshil alignment

  d4straub

  committed
  739ccbd

• Merge pull request #700 from d4straub/export-more-qza

  Show description for 2a23b1b
  d4straub

  authored
  2a23b1b

• Merge branch 'dev' of https://github.com/nf-core/ampliseq into add-multiple-regions-analysis

  d4straub

  committed
  c26cbac

• process regions with --input_mutiregion

  d4straub

  committed
  3f16376

Commits on Feb 7, 2024

• fix when no primers are given

  d4straub

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  45fefd4

• produce per-region ASV tables and fasta

  d4straub

  committed
  715ae05

Commits on Feb 8, 2024

• adjust container and input

  d4straub

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  0f04676

Commits on Feb 9, 2024

• add SIDLE workflow from d4straub/pipesidle

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  aa1ff5a

• add sidle reference taxonomy entries & custom input

  d4straub

  committed
  afbb18f

• fix prettier

  d4straub

  committed
  a8bc971

Commits on Feb 22, 2024

• plugin sidle output to downstream analysis

  d4straub

  committed
  0185e0c

Commits on Feb 23, 2024

• --sidle_ref_taxonomy greengenes works

  d4straub

  committed
  5b4d4d0

Commits on Mar 8, 2024

• Add multiregion test

  d4straub

  committed
  fdb8d68

• update documentation and changelog

  d4straub

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  74de9fb

• Fix prettier

  d4straub

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  2b72e2a

• update README

  d4straub

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  1617780

• add smaller test database

  d4straub

  committed
  f68b18a

• make sidle_ref_taxonomy entry tree_qza optional

  d4straub

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  c26a2c2

• Fix prettier

  d4straub

  committed
  6b7a5a4

Commits on Mar 11, 2024

• update multiregion nf.test

  d4straub

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  2370c40

• update multiregion.nf.test.snap

  d4straub

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  35b0ddc

• correct multiregion.nf.test

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  5bdb033

• fix sidle silva ref db

  d4straub

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  cd30e46

• adjust settings based on ref db

  d4straub

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  cef0875

Commits on Mar 13, 2024

• silva ref db works

  d4straub

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  d6a6939

• cleanup

  d4straub

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  221a554

• check incompatible params with sidle

  d4straub

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  dd3698e

• fix overzealous check

  d4straub

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  8c711a7

Commits on Mar 18, 2024

• removed phytoref

  

  Danilo Di Leo

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  256fc6b

• CHANGELOG

  

  Danilo Di Leo

  committed
  9f25806

• updated changelog

  

  Danilo Di Leo

  committed
  5b5cd78

• re-arrange param documentation and rename --input_multiregion to --multiregion

  d4straub

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  77e03b1

• removed phytoref from schema.json

  

  Danilo Di Leo

  committed
  3f4a64e

• prevent execution with conda

  d4straub

  committed
  8575090

• Update CHANGELOG.md

  danilodileo

  authored
  daa9dce

• Merge pull request #710 from danilodileo/remove-phytoref

  Show description for e366469
  d4straub

  authored
  e366469

• updated code for collecting data from gtdb

  

  Danilo Di Leo

  committed
  85791f9

• updated comment

  

  Danilo Di Leo

  committed
  48d02b8

• updated CHANGELOG

  

  Danilo Di Leo

  committed
  0f4346c

• remove empty lines

  d4straub

  committed
  dc5e8a3

• Merge pull request #702 from d4straub/add-multiple-regions-analysis

  Show description for 6e727a4
  d4straub

  authored
  6e727a4

• Merge pull request #711 from danilodileo/fix-gtdb-bacteria-info-only

  Show description for 922b391
  d4straub

  authored
  922b391

• add subworkflows and include functions

  d4straub

  committed
  65e4209

• move all custom functions from lib to utils

  d4straub

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  d9c7b59

• remove lib and references to it

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  f0bc0b5

• Template update for nf-core/tools version 2.13.1

  d4straub

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  33ccad2

Commits on Mar 19, 2024

• merge template update 2.13.1

  d4straub

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  c508a18

• fix linting

  d4straub

  committed
  95918b2

• fix summary report

  d4straub

  committed
  db4ec6b

• remove redundant sample sheet parsing

  d4straub

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  656c56c

• update CHANGELOG and README

  d4straub

  committed
  9912514

• keep software_versions.yml

  d4straub

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  8e2da36

• remove software versions string from nf-test

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  3207215

• use smaller unite db for test profiles

  d4straub

  committed
  54e28be

• use sintax instead of dada to satisfy memory limit

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  2756612

• disable addsh and correct expected files

  d4straub

  committed
  d0e02f1

• further adapt expected files by tests

  d4straub

  committed
  aba8c0b

Commits on Mar 20, 2024

• Apply suggestions from code review

  Show description for 7f3e4b6
  

  d4straub

  and

  mashehu

  authored
  7f3e4b6

• Merge pull request #713 from d4straub/update-template-2.13.1

  Show description for d05e42e
  d4straub

  authored
  d05e42e

• fix vsearch cluster filtering

  d4straub

  committed
  7466813

• Update CHANGELOG.md

  Show description for 583deca
  

  d4straub

  and

  erikrikarddaniel

  authored
  583deca

Commits on Mar 25, 2024

• Merge pull request #715 from d4straub/fix-vsearch-cluster

  Show description for f4ac5f6
  d4straub

  authored
  f4ac5f6

• Fix file sorting with radix method

  d4straub

  committed
  eecf6cc

• Merge pull request #717 from d4straub/fix-file-sorting-wit-radix

  Show description for 152331d
  d4straub

  authored
  152331d

• Require a minimum sequence length of 50bp after ITSx

  d4straub

  committed
  f15c9dd

Commits on Mar 26, 2024

• Merge pull request #718 from d4straub/fix-itsx-short-sequences

  Show description for c828ef4
  d4straub

  authored
  c828ef4

• export all versions

  d4straub

  committed
  34458bc

• update CHANGELOG

  d4straub

  committed
  63a0707

• update nf-core modules

  d4straub

  committed
  7932b84

• update phyloseq

  d4straub

  committed
  8c0200c

• update DADA2

  d4straub

  committed
  dc4067f

• update CHANGELOG

  d4straub

  committed
  bc02894

• fix groovyjarjarantlr4.v4.runtime.LexerNoViableAltException

  d4straub

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  2e29f65

• update CHANGELOG

  d4straub

  committed
  7ceb8ab

• fix prettier

  d4straub

  committed
  7a27dc4

• update nf.test.snap md5sums

  d4straub

  committed
  c7af669

• Update summarize_barrnap.py

  Show description for 42a7556
  vaulot

  authored
  42a7556

• update another .snap

  d4straub

  committed
  0cb077e

• Merge pull request #721 from d4straub/fix-groovyjarjarantlr4.v4.runtime.LexerNoViableAltException

  Show description for a9a6d82
  d4straub

  authored
  a9a6d82

• Update summarize_barrnap.py

  Show description for 76bbddd
  vaulot

  authored
  76bbddd

• Update CHANGELOG.md

  vaulot

  authored
  dd7272e

• Merge branch 'dev' into dev

  d4straub

  authored
  3a3532d

• fix versions in format taxonomy scripts

  d4straub

  committed
  0baff8a

• Merge branch 'dev' of https://github.com/nf-core/ampliseq into export-all-versions

  d4straub

  committed
  0297f1a

• Merge pull request #722 from vaulot/dev

  Show description for 0926dc2
  d4straub

  authored
  0926dc2

• Merge pull request #719 from d4straub/export-all-versions

  Show description for 0c24ff3
  d4straub

  authored
  0c24ff3

• Merge branch 'dev' of https://github.com/nf-core/ampliseq into update-modules

  d4straub

  committed
  717aa49

• Merge pull request #720 from d4straub/update-modules

  Show description for 43378b5
  d4straub

  authored
  43378b5

Commits on Mar 27, 2024

• update params docs

  d4straub

  committed
  a7609e0

• re-do workflow figure

  d4straub

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  9c7f78c

• update CHENGALOG

  d4straub

  committed
  e575b85

• improve figure

  d4straub

  committed
  b3af0be

• adjust figure

  d4straub

  committed
  6f0b65a

• Merge pull request #723 from d4straub/update-param-docu-2.9.0

  Show description for db4cc0a
  d4straub

  authored
  db4cc0a

• bump version to 2.9.0

  d4straub

  committed
  3b0ea74

• fix typo

  d4straub

  committed
  d6cf941

Commits on Mar 28, 2024

• Merge pull request #724 from d4straub/bump-version-2.9.0

  Show description for 08db42e
  d4straub

  authored
  08db42e

• fix Download Pipeline Workflow

  d4straub

  committed
  8a0f5f2

• Apply suggestions from code review

  Show description for 1c5ea7c
  

  d4straub

  and

  mirpedrol

  authored
  1c5ea7c

• Merge pull request #726 from d4straub/fix-Download-Pipeline-Workflow

  Show description for 3f2f466
  d4straub

  authored
  3f2f466

Commits on Apr 2, 2024

• Apply suggestions from code review

  Show description for a060f2f
  

  d4straub

  and

  mashehu

  authored
  a060f2f

• Update nextflow.config

  Show description for 53cb658
  

  d4straub

  and

  mashehu

  authored
  53cb658

• Fix linting in release-announcements.yml

  d4straub

  authored
  4a11f03

• add pattern to sidle_ref_tree_custom

  d4straub

  committed
  92b3984

• update CHANGELOG

  d4straub

  committed
  c9def1d

• fix pattern

  d4straub

  committed
  066df3d

• Merge pull request #728 from d4straub/update-nextflowschema

  Show description for b68e479
  d4straub

  authored
  b68e479

• retrieve sidle container from quay.io/nf-core

  d4straub

  committed
  b42e8f0

• Merge pull request #729 from d4straub/pipesidle-container

  Show description for 4707d38
  d4straub

  authored
  4707d38