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Dev -> Master for 1.0.0 release #61

Merged
merged 224 commits into from
Oct 6, 2022
Merged

Dev -> Master for 1.0.0 release #61

merged 224 commits into from
Oct 6, 2022

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edmundmiller
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@edmundmiller edmundmiller commented Oct 6, 2022 •
edited
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Ignore the failing dockercloud CI

thanhleviet and others added 30 commits March 6, 2020 09:51
@thanhleviet
Add dockerfile for bcl2fastq and cellranger
eff94c5
@csawye01
modified: conf/cellranger.conf
3728b7e 
	modified:   .gitignore
@csawye01
new file: docs/example_samplesheet.csv
c0215bc
@thanhleviet
update environment.yml
0063941
@csawye01
modified: environment.yml
d11eb95
@csawye01
modified: environment.yml
2ccfc39
@drpatelh
Merge branch 'dev' into master
049a3d8
@drpatelh
Merge pull request #5 from thanhleviet/master
4d9e7de 
Add dockerfile for bcl2fastq and cellranger
@thanhleviet
update Dockerfile for cellranger
104279e
@TomKellyGenetics
Update docker file for cellranger
baab7f3 
cellranger requires a specific implementation of tSNE
@drpatelh
Update requirements.txt
b4efb7f
@drpatelh
Merge pull request #7 from thanhleviet/master
49f8fff 
update Dockerfile for cellranger
@drpatelh
Merge pull request #8 from TomKellyGenetics/patch-1
6537457 
Update docker file for cellranger
@drpatelh
Template update for nf-core/tools version 1.9
fd5bdd9
@drpatelh
Update template to tools 1.9
85833be
@drpatelh
Merge pull request #9 from drpatelh/TEMPLATE
b6ae2a3 
Template update for nf-core/tools version 1.9
@drpatelh
Update custom container paths
a425fd4
@drpatelh
Add bioconda badge
84ee96a
@drpatelh
Get Docker image directly from Tom Kelly
d16ce50
@drpatelh
Merge pull request #10 from drpatelh/dev
19a4a8c 
Template changes for tools 1.9
@drpatelh
All params to snake_case
78d701f
@drpatelh
All params to snake_case
e1f0ff5
@drpatelh
Change samplesheet to input
5f848c2
@drpatelh
Adjust spacing
aede7de
@drpatelh
Fix markdownlint
c536b0d
@drpatelh
Fix markdownlint
d6a5fc6
@drpatelh
Add skip_kraken2 param
aadb90e
@drpatelh
Add skip_kraken2 param
8b2202f
@drpatelh
Merge pull request #11 from drpatelh/dev
b6d3153 
Fix markdownlint
@nf-core-bot
Template update for nf-core/tools version 1.10.1
6db1ad3
matthdsm and others added 21 commits October 5, 2022 09:00
@matthdsm
fix import in subwf
2da4c70
@matthdsm
fix linting
354ce38
@matthdsm
update modules for linting
0955abf
@matthdsm
Merge pull request #55 from nf-core/nf-core-template-merge-2.6
fcce50d 
Important! Template update for nf-core/tools v2.6
@edmundmiller
fix(bases2fastq): Add output dir back to bases2fastq
e64c89b
@edmundmiller
Merge pull request #54 from nf-core/bases2fastq-output
f022eb5 
Add output dir back to bases2fastq
@edmundmiller
chore: Bump demupsoftwareversions
a295d33
@edmundmiller
test(b2fq): Update to remove lane
411700d
@edmundmiller
docs: Clean up usage
9d39fc6
@edmundmiller
docs: Clean up output and remove cellranger
a88d7f1
@edmundmiller
docs(output): Borrow FastQC from rnaseq
ff92f3d
@edmundmiller
docs(output): Add details to files
ca3d007
@edmundmiller
docs(output): Borrow fastp from viralrecon
090a29f
@edmundmiller
docs(output): Add outputs for md5sum
0b4b337
@edmundmiller
docs(output): Update output directory
2e7ea30
@edmundmiller
docs: Update README for 1.0.0
39f0bc1
@edmundmiller
chore: Add citations
4369895
@edmundmiller
chore: nf-core bump-version 1.0.0
b97fa4a
@matthdsm @edmundmiller
Fix github hande
f92df1e
@edmundmiller
style: Move bases2fastq samplesheet to assets
7346a05
@edmundmiller
Merge pull request #58 from nf-core/release-prep
b6c4f50 
Release prep
@edmundmiller edmundmiller added this to the v1.0.0 milestone Oct 6, 2022
@edmundmiller edmundmiller self-assigned this Oct 6, 2022
@edmundmiller edmundmiller changed the title Dev -> Master for 3.8.1 release Dev -> Master for 1.0.0 release Oct 6, 2022
@edmundmiller edmundmiller requested review from drpatelh, matthdsm and a team October 6, 2022 13:54
@edmundmiller edmundmiller merged commit b0a004e into master Oct 6, 2022
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github-actions bot commented Oct 6, 2022 •
edited
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b6c4f50

+| ✅ 156 tests passed       |+
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '1.0.0'
  • pipeline_todos - TODO string in README.md: Add full-sized test dataset and amend the paragraph below if applicable
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

✅ Tests passed:

Run details

  • nf-core/tools version 2.6
  • Run at 2022-10-06 13:51:04

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@matthdsm matthdsm matthdsm approved these changes

@drpatelh drpatelh Awaiting requested review from drpatelh

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@edmundmiller edmundmiller

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@edmundmiller @matthdsm @thanhleviet @csawye01 @drpatelh @TomKellyGenetics @nf-core-bot @KevinMenden @cmgg-be