Dev -> Master for v2.0.0 release #293

JoseEspinosa · 2022-08-10T11:07:04Z

No description provided.

Update pipeline template with current tools dev version to fix linting

Finish the update of blacklist bed files

Update modules and small fixes due to update

Make --outdir mandatory

…rging-template-updates-2.3

Merging template updates 2.3

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

Fix missing reports in MultiQC and other publishing discrepancies with DSL1 version

Add missing ending tag

Add tower.yml file with list of pertinent Reports to display in Tower

Add antibody directory to consensus peaks in IGV session

Add back antibody to consensus paths in output description

Update changelog back (antibody again in the results path of consensus peaks)

github-actions · 2022-10-03T15:29:37Z

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

Posted for pipeline commit fd95002

+| ✅ 153 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: '2.0.0'

✅ 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-chipseq_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-chipseq_logo_light.png
files_exist - File found: docs/images/nf-core-chipseq_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/WorkflowChipseq.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-chipseq_logo.png
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .yamllint.yml
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.version
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 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-chipseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-chipseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-chipseq_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: 21.10.3, Config: 21.10.3
readme - README Nextflow minimum version in Quick Start section matched config. README: 21.10.3, Config: 21.10.3
pipeline_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (203 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: ci.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: branch.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
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'.

Run details

nf-core/tools version 2.5.1
Run at 2022-10-03 14:46:07

drpatelh and others added 30 commits March 2, 2022 17:37

Fix merge conflicts

bcd1213

Fix YAMLLint in pipeline

bfc515e

Fix nf-core linting

755cc32

Merge pull request #256 from drpatelh/template_dev

ad0671a

Update pipeline template with current tools dev version to fix linting

Merge branch 'dev' of https://github.com/nf-core/chipseq into updates

717e09d

Reformat chr ids from mm10 to GRCm38

4bb1c93

Reformat v3 blacklist from hg38 to GRCh38

9965100

Keep the manual annotated blacklist files

1b431ae

Update igenomes with the new or reallocated blacklist files

30d0d68

Update changelog

c209480

Add again the logic for using blacklist bed files

7bac1de

Remove v1 bed files from mouse

936d3a8

Update usage with the references to the blacklist files

649d587

Add the blacklist file to filter_bam_bamtools subworkflow

e417d3e

Make markdown lint happy again

7307d98

Merge pull request #257 from JoseEspinosa/blacklist_v2

904a52b

Finish the update of blacklist bed files

Update modules and small fixes due to update

98eaca6

Merge pull request #258 from JoseEspinosa/update_modules

8857b01

Update modules and small fixes due to update

Make --outdir mandatory

e912404

Delete deprecated blacklist files

3cab81d

Make nf-core lint happy

ea0ad89

Merge pull request #259 from JoseEspinosa/outdir_mandatory

d2b06f0

Make --outdir mandatory

Template update for nf-core/tools version 2.3

10573c6

Merge branch 'TEMPLATE' of https://github.com/nf-core/chipseq into me…

7e51da1

…rging-template-updates-2.3

Update changelog

b021695

Fix lint and get rid of some merge tags that were remaining

0f2accb

Fix yamllint

441e917

Merge pull request #262 from JoseEspinosa/merging-template-updates-2.3

a8d1443

Merging template updates 2.3

Template update for nf-core/tools version 2.3.1

dc3a8c0

Template update for nf-core/tools version 2.3.2

d9f7f50

drpatelh and others added 15 commits September 15, 2022 11:47

Add meta.id tag where missing to local modules

6f17b33

Re-factor channel joining for featurecounts

474e226

Remove antibody variable reference in DESeq2 module

3e1857d

Switch deseq2_vst to true by default

d984c09

Add missing header comments to all modules/subworkflows

3ea0140

Fix bug

42feb6f

Fix prettier

9e83c05

Update docs/output.md

e7c5516

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

Merge pull request #304 from drpatelh/updates

84c2299

Fix missing reports in MultiQC and other publishing discrepancies with DSL1 version

Add missing ending tag

a32cef8

Merge pull request #305 from JoseEspinosa/updates

c4c0c3d

Add missing ending tag

Remove redundanct comment

ce0ed8d

Change find command to be more specific

bcc9702

Add tower.yml to render Reports for main files on Tower

255992d

Merge pull request #306 from drpatelh/updates

59d32c8

Add tower.yml file with list of pertinent Reports to display in Tower

mashehu approved these changes Sep 26, 2022

View reviewed changes

drpatelh and others added 12 commits October 2, 2022 00:44

Remove pinning for R packages used in DESeq2 script

3ed06fa

Add antibody directory to consensus peaks in IGV session

09ca349

Update date in CHANGELOG

80fd01c

Update igv_files_to_session.py script

40db9a5

Fix if no consensus peaks are provided

6f8a372

Black

6428b3f

Fix linting

ed10bb9

Merge pull request #308 from drpatelh/updates

7ed79d4

Add antibody directory to consensus peaks in IGV session

Add back antibody to consensus paths in output description

f62ea83

Merge pull request #309 from JoseEspinosa/updates

e39a770

Add back antibody to consensus paths in output description

Update changelog

f96dfd6

Merge pull request #310 from JoseEspinosa/updates

fd95002

Update changelog back (antibody again in the results path of consensus peaks)

JoseEspinosa merged commit 51eba00 into master Oct 3, 2022

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Dev -> Master for v2.0.0 release #293

Dev -> Master for v2.0.0 release #293

JoseEspinosa commented Aug 10, 2022

github-actions bot commented Oct 3, 2022

❗ Test warnings:

✅ Tests passed:

Run details

Dev -> Master for v2.0.0 release #293

Dev -> Master for v2.0.0 release #293

Conversation

JoseEspinosa commented Aug 10, 2022

github-actions bot commented Oct 3, 2022

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

Run details

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