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Release candidate 1.11.0 #231

Merged
merged 225 commits into from
Oct 18, 2023
Merged

Release candidate 1.11.0 #231

merged 225 commits into from
Oct 18, 2023

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maxulysse
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PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/fetchngs branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

maxulysse and others added 30 commits August 23, 2023 14:00
@maxulysse
remove public aws ecr profile
dd94d03
@maxulysse
split up config files to be more modular
1c5a396
@maxulysse
Merge pull request #185 from maxulysse/remove_public_aws_ecr
d779e91 
remove public_aws_ecr
@maxulysse
no cascade inclusion of config files
9c5fadb
@maxulysse
use schema_ignore_params to remove warnings
5073409
@maxulysse
fix lint
bc7fd25
@adamrtalbot
Adds emit statement for FASTQs and metadata to SRA workflow
81324d2
@maxulysse @adamrtalbot
Update nextflow.config
82fa500 
Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
@maxulysse
remove if statement
011addc
@maxulysse
Merge pull request #187 from maxulysse/fix_tests
604949b 
Fix tests
@adamrtalbot
Add emit statement to synpase workflow
464397c
@adamrtalbot
Update CHANGELOG.md
97af5cd
@maxulysse
Merge pull request #184 from adamrtalbot/emit_statement_to_SRA_workflow
e7c2e18 
Adds emit statement for FASTQs and metadata to SRA workflow
@maxulysse
Merge pull request #186 from maxulysse/split_configs
addfa36 
split up config files to be more modular
@maxulysse
move out multiqc and versions
c7ab8b8
@maxulysse
enable tests in refactor
372f9e4
@maxulysse
Apply suggestions from code review
5dab8d0
@maxulysse @adamrtalbot
Apply suggestions from code review
aff72b7 
Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
@maxulysse
fix syntax
7f6439c
@maxulysse
Merge pull request #189 from maxulysse/move_things
54e7d7d 
Move out multiQC and versions
@maxulysse
small refactor
6355a33
@maxulysse
staging
ef03d06
@maxulysse
validate input in main.nf
1be5ebc
@maxulysse
use error
698fab1
@maxulysse
Merge pull request #190 from maxulysse/better_syntax
493a544 
tiny refactor
@maxulysse
Merge branch 'refactor' into better_tests
a3b2e8a
@maxulysse
use workflow testing
e83e909
@maxulysse
update snapshot
883a191
@maxulysse
restore versions
da650af
@maxulysse
update workflow
f2d32d2
maxulysse and others added 24 commits October 17, 2023 16:18
@maxulysse
patch custom-dumpsoftwareversions snap
5875c57
@maxulysse
update snaps
4312b74
@adamrtalbot
Replace CUSTOM_DUMPSOFTWAREVERSIONS with collectFile operator
2f47bef
@adamrtalbot
fixup
f941c4d
@adamrtalbot
gitignore
ba19243
@adamrtalbot
Use software versions file that matches MultiQC input
364e6ba
@adamrtalbot
tidy
e6c79c5
@maxulysse
Merge pull request #225 from maxulysse/fix_all
4bd7d3a 
Fix all
@maxulysse
forgot patch
a9d8ae8
@maxulysse
add data
cedd600
@maxulysse
Merge pull request #227 from maxulysse/fix_all_again
fc23783 
fix sratools
@adamrtalbot
Merge branch 'refactor' of github.com:nf-core/fetchngs into collect-s…
643b71d 
…oftware-versions-via-collectfile and remove CUSTOM_DUMPSOFTWAREVERSIONS
@adamrtalbot
Merge pull request #226 from nf-core/collect-software-versions-via-co…
2a02ba7 
…llectfile

Replace CUSTOM_DUMPSOFTWAREVERSIONS with collectFile operator
@maxulysse
tinier tests + patch fasterdump
5884bba
@maxulysse
diff file
b9a8609
@maxulysse
one last test
0d5f1d0
@maxulysse
Merge pull request #228 from maxulysse/refactor
b452bd3 
fix sratools and fewer ids
@maxulysse
Update CHANGELOG.md
b885d52
@maxulysse
Prepare 1.11.0 RC
7948764
@adamrtalbot
qwqUpdate snaps
833ad7e
@adamrtalbot
Merge pull request #230 from maxulysse/dev
f8e9142 
Prepare 1.11.0 RC
@adamrtalbot
Merge remote-tracking branch 'origin/dev' into refactor
e573640
@adamrtalbot @maxulysse
Update .github/workflows/ci.yml
4d13a44 
Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>
@adamrtalbot
Merge pull request #188 from nf-core/refactor
86246fb 
Refactor POC
@github-actions
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github-actions bot commented Oct 18, 2023 •
edited
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 86246fb

+| ✅ 133 tests passed       |+
#| ❔  18 tests were ignored |#
!| ❗   6 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.11.0
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in meta.yml: #Add a description of the subworkflow and list keywords
  • pipeline_todos - TODO string in meta.yml: #Add a list of the modules and/or subworkflows used in the subworkflow
  • pipeline_todos - TODO string in meta.yml: #List all of the channels used as input with a description and their structure
  • pipeline_todos - TODO string in meta.yml: #List all of the channels used as output with a descriptions and their structure

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: assets/multiqc_config.yml
  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/modules.config
  • files_exist - File is ignored: lib/NfcoreTemplate.groovy
  • files_exist - File is ignored: lib/Utils.groovy
  • files_exist - File is ignored: lib/WorkflowFetchngs.groovy
  • files_exist - File is ignored: lib/WorkflowMain.groovy
  • files_exist - File is ignored: lib/nfcore_external_java_deps.jar
  • files_unchanged - File ignored due to lint config: .gitattributes
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File does not exist: lib/nfcore_external_java_deps.jar
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/fetchngs/fetchngs/.github/workflows/awstest.yml
  • multiqc_config - 'assets/multiqc_config.yml' not found

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-18 10:04:55

edmundmiller
edmundmiller approved these changes Oct 18, 2023
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In the name of progress.

@maxulysse maxulysse merged commit 04ee503 into master Oct 18, 2023
50 checks passed
This pull request was closed.
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Reviewers

@edmundmiller edmundmiller edmundmiller approved these changes

@sateeshperi sateeshperi sateeshperi approved these changes

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@maxulysse maxulysse

@adamrtalbot adamrtalbot

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5 participants
@maxulysse @edmundmiller @sateeshperi @adamrtalbot @drpatelh