Code

Dev -> Master for 1.1.0 release#86

Code

Merged

edmundmiller merged 80 commits intomasternf-core/demultiplex:masterfrom devnf-core/demultiplex:devCopy head branch name to clipboardJan 23, 2023

+1,498-630

Commits

Commits on Oct 12, 2022

• replace local demultiplex subwf with nf-core one

  matthdsm

  committed
  1179c9a

• drop input_check.nf, fixes #52

  matthdsm

  committed
  e3aad86

• bump bases2fastq module

  matthdsm

  committed
  c49fad5

• WIP, add bases2fastq subworkflow

  matthdsm

  committed
  74dff1b

• control demultiplexer selection with switch

  matthdsm

  committed
  9007f8a

• bugfix

  matthdsm

  committed
  1ebc259

• add docs for bases2fastq fq header

  matthdsm

  committed
  b1329e4

• use b2fq subwf

  matthdsm

  committed
  fee7e64

• bugfix

  matthdsm

  committed
  21576bc

• add @Midnighter's FormattingService to pretty dump some logs

  matthdsm

  committed
  052f68c

• b2fq: fix samplename regex

  matthdsm

  committed
  60d7aaf

Commits on Oct 13, 2022

• kill fastqc, long live falco; fixes #62

  matthdsm

  committed
  1556d35

• fix MQC report, fixes #64

  matthdsm

  committed
  bc5daee

• Update Citations [skip_ci]

  matthdsm

  committed
  d0a0175

• update outputs [skip_ci]

  matthdsm

  committed
  a1cf49e

• add subway map

  nvnieuwk

  committed
  0e21f70

• update changelog [skip_ci]

  matthdsm

  committed
  8080d7d

• update readme [skip_ci]

  matthdsm

  committed
  aff781e

• prettier

  nvnieuwk

  committed
  a50dba9

• Merge pull request #66 from nvnieuwk/subway-map

  Show description for ddefe50
  matthdsm

  authored
  ddefe50

• add subway map

  

  nvnieuwk

  authored and

  matthdsm

  committed
  a44c1a0

• prettier

  

  nvnieuwk

  authored and

  matthdsm

  committed
  7c235c8

• [skip_ci] update changelog

  matthdsm

  committed
  9714133

• Merge pull request #63 from nf-core/feature/nf-core_subworkflows

  Show description for 241ecda
  matthdsm

  authored
  241ecda

Commits on Oct 20, 2022

• fix: Uncomment pipeline-specific instititutional configs

  edmundmiller

  committed
  98ec02f

• chore: Update CHANGELOG

  edmundmiller

  committed
  d05a181

• Merge pull request #67 from nf-core/instititutional-configs

  Show description for 7c1c7ab
  drpatelh

  authored
  7c1c7ab

Commits on Oct 21, 2022

• add wf qc options

  matthdsm

  committed
  03fb0a1

• fix fastq output, update markdowns

  matthdsm

  committed
  a4bc52e

• update schema

  matthdsm

  committed
  8686112

• prettier

  matthdsm

  committed
  25bfda5

• typos

  matthdsm

  committed
  49514e6

• feat(bases2fastq): Apply trimming if trim_fastq

  edmundmiller

  committed
  6bcba1c

Commits on Oct 24, 2022

• change in config to if in workflow

  matthdsm

  committed
  b3c2095

Commits on Nov 4, 2022

• fix wf errors

  matthdsm

  committed
  18164ac

• nfcore linting

  matthdsm

  committed
  a3ae40f

• bump fastp module

  matthdsm

  committed
  4c5c7ba

Commits on Nov 23, 2022

• Merge pull request #70 from nf-core/feat/wf_qc_options

  Show description for e16ca47
  edmundmiller

  authored
  e16ca47

Commits on Nov 24, 2022

• build: Run nf-test init

  edmundmiller

  committed
  7900b05

• test(bclconvert): Add initial test

  edmundmiller

  committed
  8267111

• test(bases2fastq): Add initial test

  edmundmiller

  committed
  9efc4c1

• test(bcl2fastq): Add initial test

  edmundmiller

  committed
  178e315

• chore: Update CHANGELOG

  edmundmiller

  committed
  0c86300

• chore: Make CHANGELOG consistant

  edmundmiller

  committed
  3070bc0

• ci: Yoink pipeline from fetchngs

  edmundmiller

  committed
  87a600a

• docs: Add nf-test badge to README

  edmundmiller

  committed
  4f89ea6

• Merge pull request #73 from nf-core/nf-test

  Show description for 8a5c1e9
  edmundmiller

  authored
  8a5c1e9

Commits on Nov 29, 2022

• bump version number

  

  matthdsm

  authored and

  edmundmiller

  committed
  d05f2af

• update dump tags

  

  matthdsm

  authored and

  edmundmiller

  committed
  11c52ab

• overhaul input parsing

  

  matthdsm

  authored and

  edmundmiller

  committed
  31b2089

• test: Run nf-test generate function

  edmundmiller

  committed
  85e43fa

• test: Comment out future tests

  edmundmiller

  committed
  b78dc8a

• style: Fix comment indent

  edmundmiller

  committed
  59114d4

• test: Function fails for extract_csv

  edmundmiller

  committed
  a68e0b5

Commits on Nov 30, 2022

• Merge pull request #75 from nf-core/feat/update_input_parsing

  Show description for 9d323f4
  matthdsm

  authored
  9d323f4

Commits on Dec 5, 2022

• chore: Highlight test files

  edmundmiller

  committed
  759bd92

Commits on Dec 6, 2022

• Merge pull request #76 from nf-core/highlist-test-files

  Show description for 6f55436
  edmundmiller

  authored
  6f55436

Commits on Dec 8, 2022

• Template update for nf-core/tools version 2.7.1

  nf-core-bot

  committed
  d6ce995

Commits on Dec 19, 2022

• Template update for nf-core/tools version 2.7.2

  nf-core-bot

  committed
  01189ac

Commits on Jan 18, 2023

• fixed if statements for skip_tools

  glichtenstein

  committed
  c7956ff

• fix(#82): Use correct fastp output

  edmundmiller

  committed
  75aba89

Commits on Jan 19, 2023

• test: Update tests

  Show description for 445b8de
  edmundmiller

  committed
  445b8de

• test(#82): Add test to skip trimming

  edmundmiller

  committed
  73a7ac2

• test(#82): Add test for skipping fastp

  edmundmiller

  committed
  aa6e3fa

• test(#82): Add test to skip both fastp and fastqc

  edmundmiller

  committed
  767493c

• test(#82): Test only skipping fastqc

  edmundmiller

  committed
  9ca8e4b

• chore: Update CHANGELOG

  edmundmiller

  committed
  fc1482a

• Merge pull request #83 from glichtenstein/bug/fixed-if-statements-for-skip-tools

  Show description for ee55bc3
  edmundmiller

  committed
  ee55bc3

Commits on Jan 20, 2023

• Merge branch 'dev' into nf-core-template-merge-2.7.2

  edmundmiller

  committed
  fd26331

• chore: Add new nextflow version to CHANGELOG

  edmundmiller

  committed
  313b407

• chore: Bump modules

  Show description for cf39b96
  edmundmiller

  committed
  cf39b96

• chore: Update CHANGELOG

  edmundmiller

  committed
  092c0b0

• Merge pull request #78 from nf-core/nf-core-template-merge-2.7.2

  Show description for fffc464
  edmundmiller

  authored
  fffc464

• chore: Add DOI

  edmundmiller

  committed
  8812f1e

• style: Turn contributors into a list

  edmundmiller

  committed
  6a65269

• docs: Update link to samplesheet

  Show description for 90dcf8d
  edmundmiller

  committed
  90dcf8d

Commits on Jan 23, 2023

• fix: Shortern doi

  Show description for 26120fc
  edmundmiller

  committed
  26120fc

• chore: Add attributions to CHANGELOG

  Show description for 5f0cc88
  edmundmiller

  committed
  5f0cc88

• test: Remove commented out code

  edmundmiller

  committed
  4f7bd03

• chore: Bump version

  edmundmiller

  committed
  bb45880