v2.2.0 release #203

grst · 2023-03-09T07:39:57Z

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/scrnaseq 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).

Bump to 2.1.1dev

…flows/local/input_check.nf

…nter in samplesheet

…M file read group info

autocanceling previous tests when pushing changes

@ameynert

Found by @ameynert right now 🚨

Fix profile

updated concurrency groups to match nf-core tools

Resolves #150

Fix CI

txp2gene is generated as part of the salmon indexing, but if an index is supplied, the file must be supplied manually

merging the conditional with the assertion on line 30

Update all modules, fix template points

fix txp2gene retrieval bug when salmon_index is supplied

github-actions · 2023-03-09T07:41:35Z

`nf-core lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit 29b0621

+| ✅ 157 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: '2.2.0'

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .editorconfig
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/CONTRIBUTING.md
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/ci.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-scrnaseq_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-scrnaseq_logo_light.png
files_exist - File found: docs/images/nf-core-scrnaseq_logo_dark.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: lib/nfcore_external_java_deps.jar
files_exist - File found: lib/NfcoreSchema.groovy
files_exist - File found: lib/NfcoreTemplate.groovy
files_exist - File found: lib/Utils.groovy
files_exist - File found: lib/WorkflowMain.groovy
files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: conf/igenomes.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: lib/WorkflowScrnaseq.groovy
files_exist - File found: modules.json
files_exist - File found: pyproject.toml
files_exist - File not found check: Singularity
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: docs/images/nf-core-scrnaseq_logo.png
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: .travis.yml
nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: params.show_hidden_params
nextflow_config - Config variable found: params.schema_ignore_params
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/CONTRIBUTING.md matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - .github/workflows/linting.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-scrnaseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-scrnaseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-scrnaseq_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - lib/nfcore_external_java_deps.jar matches the template
files_unchanged - lib/NfcoreSchema.groovy matches the template
files_unchanged - lib/NfcoreTemplate.groovy matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
files_unchanged - pyproject.toml matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 22.10.1, Config: 22.10.1
readme - README Nextflow minimum version in Quick Start section matched config. README: 22.10.1, Config: 22.10.1
pipeline_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (124 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: linting.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - 'assets/multiqc_config.yml' follows the ordering scheme of the minimally required plugins.
multiqc_config - 'assets/multiqc_config.yml' contains a matching 'report_comment'.
multiqc_config - 'assets/multiqc_config.yml' contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.7.2
Run at 2023-03-20 07:50:22

README.md

Fix Seurat container

Update modules

docs/usage.md

nextflow.config

grst · 2023-03-10T07:01:30Z

There are a few minor things to be resolved (see comments), but other than that this looks good to me!

apeltzer

Apart from gregors comments, looks good and we should definitely do a release

fmalmeida

🎉

bump version

update readme

Adding universc to pipeline picture

apeltzer and others added 30 commits October 6, 2022 10:58

Bump to 2.1.1dev

6119a55

Merge pull request #155 from nf-core/bump-dev

f580beb

Bump to 2.1.1dev

Removed function get_samplesheet_paths which is replicated in subwork…

af1ef67

…flows/local/input_check.nf

Samplesheet documentation includes expected cells and sequencing center

6ba39cd

Validation of optional samplesheet columns expected_cells and seq_center

2078e02

Prettier & PythonBlack checks

eafe467

PythonBlack fix

c4acfa7

Clarifying that params.seq_center can be overridden by setting seq_ce…

5fd5ef4

…nter in samplesheet

Allows for sequencing center to be set in samplesheet for STARsolo BA…

407cbb8

…M file read group info

Prettier fix

9e2a19b

Added expected cells to STARsolo via --soloCellFilter

8a13fca

Linting fix

0d58468

Addition of --expect-cells flag using samplesheet input

b9e5d6a

Added optional expected cells parameter to cellranger counts process

260842b

Linting fixes for spaces

1fb7e4e

autocanceling previous tests when pushing changes

0aa9fd9

triggering change to test autocancel

5200121

updated changelog

7313273

Merge pull request #163 from biomage-org/autocancel-old-tests

0d9159f

autocanceling previous tests when pushing changes

Added required/optional to samplesheet columns in usage

3eb297a

Fix CI

8e5629e

Found by @ameynert right now 🚨

Update ci.yml

b8f1dac

Fix profile

[automated] Fix linting with Prettier

66c65e7

updated concurrency groups to match nf-core tools

3a9f0d9

Merge pull request #166 from biomage-org/autocancel-old-tests

d570313

updated concurrency groups to match nf-core tools

Updated simpleaf to version 0.5.3 to allow for expect-cells parameter

7f81988

Merge pull request #164 from nf-core/params_expansion_150

6176637

Resolves #150

Add stub for versions.yml in mtx_to_seurat configuration

dec0d75

Merge pull request #165 from nf-core/fix-broken-ci

2cb7787

Fix CI

Add single-nucleus, RNA velocity option on star.

4b52e7e

azedinez and others added 8 commits March 1, 2023 15:40

require txp2gene file when a salmon_index supplied

da34f07

txp2gene is generated as part of the salmon indexing, but if an index is supplied, the file must be supplied manually

modify assertion error to reflect changes

b0f8c84

tidying up the assertion

1d1a0d8

merging the conditional with the assertion on line 30

fix ci issue

5182197

fix ci syntax issue

73cb4b5

Re-add conda.enabled

f4f7a62

Merge pull request #201 from nf-core/update-and-fix

f8ef18c

Update all modules, fix template points

Merge pull request #202 from azedine-healx/patch-1

a421066

fix txp2gene retrieval bug when salmon_index is supplied

grst requested review from fmalmeida and apeltzer March 9, 2023 07:40

grst added 2 commits March 9, 2023 08:50

Fix Seurat container

ed06233

Update Changelog

2d10e4d

grst commented Mar 9, 2023

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grst added 5 commits March 9, 2023 14:23

Merge pull request #204 from nf-core/fix-193

c67be0b

Fix Seurat container

Update modules

5c0f557

Fix linting

3b914c0

try fix linting

1833fdd

Merge pull request #205 from nf-core/update-modules

2740b41

Update modules

grst commented Mar 10, 2023

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apeltzer approved these changes Mar 10, 2023

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fmalmeida approved these changes Mar 10, 2023

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fmalmeida and others added 6 commits March 10, 2023 08:54

bump version

4df0af6

Merge pull request #206 from nf-core/bump-version

f189432

bump version

Fix README/docs

e0726b8

Merge pull request #207 from grst/update-readme

ddbd469

update readme

Adding universc to pipeline picture

28558c5

Merge pull request #209 from heylf/dev

29b0621

Adding universc to pipeline picture

grst merged commit c6ec217 into master Mar 20, 2023

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v2.2.0 release #203

v2.2.0 release #203

grst commented Mar 9, 2023

github-actions bot commented Mar 9, 2023 •

edited

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❗ Test warnings:

✅ Tests passed:

Run details

grst commented Mar 10, 2023

apeltzer left a comment

fmalmeida left a comment

v2.2.0 release #203

v2.2.0 release #203

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grst commented Mar 9, 2023

PR checklist

github-actions bot commented Mar 9, 2023 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

Run details

grst commented Mar 10, 2023

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github-actions bot commented Mar 9, 2023 •

edited

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`nf-core lint` overall result: Passed ✅ ⚠️