Dev -> Master for 2.1.0 release #311

JoseEspinosa · 2023-07-19T13:18:36Z

No description provided.

Dev

nf-core modules update bowtie2/align

…rge_template_v2.7.1

Merge template v2.7.1

…rge-template-v2.7.2

Merge template v2.7.2

This reverts commit 6269ded.

…into devbovreg

Dev

Add read group tag to bowtie2 bams

github-actions · 2023-07-19T13:20:46Z

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

Posted for pipeline commit c580dfc

+| ✅ 155 tests passed       |+
!| ❗   4 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 2.1.0
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
system_exit - System.exit in WorkflowAtacseq.groovy: System.exit(1) [line 18]
system_exit - System.exit in WorkflowAtacseq.groovy: System.exit(1) [line 31]

✅ 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-atacseq_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-atacseq_logo_light.png
files_exist - File found: docs/images/nf-core-atacseq_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: 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/WorkflowAtacseq.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-atacseq_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://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-atacseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-atacseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-atacseq_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/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: 23.04.0, Config: 23.04.0
readme - README Zenodo placeholder was replaced with DOI.
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (228 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: branch.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: linting.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
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 2.9
Run at 2023-07-21 10:19:08

Bump pipeline version to 2.1.0

Get rid of checkIfExists for params paths

maxulysse · 2023-07-20T10:46:53Z

conf/public_aws_ecr.config

you can delete this file

maxulysse · 2023-07-20T10:50:03Z

nextflow.config

+    public_aws_ecr {
+        includeConfig 'conf/public_aws_ecr.config'
+    }


Suggested change

public_aws_ecr {

includeConfig 'conf/public_aws_ecr.config'

}

We can delete that

maxulysse · 2023-07-20T10:50:24Z

nextflow.config

+// Set default registry for Docker and Podman independent of -profile
+// Will not be used unless Docker / Podman are enabled
+// Set to your registry if you have a mirror of containers
+docker.registry = 'quay.io'
+podman.registry = 'quay.io'
+


Suggested change

// Set default registry for Docker and Podman independent of -profile

// Will not be used unless Docker / Podman are enabled

// Set to your registry if you have a mirror of containers

docker.registry = 'quay.io'

podman.registry = 'quay.io'

Duplicate

subworkflows/local/prepare_genome.nf

maxulysse

Minor requests

CHANGELOG.md

Apply review suggestions

JoseEspinosa · 2023-07-20T17:06:24Z

Think all the comments have been addressed in #313

ramprasadn

LGTM! 🚀

Fix multiqc_logo in nextflow_schema

bjlang and others added 30 commits August 29, 2022 15:18

Merge pull request #1 from bjlang/dev

2aa7150

Dev

Merge branch 'dev' into devbovreg

51546c9

update bowtie2/align module

588dabf

bump to 2.1.dev

4af1b88

Update CHANGELOG.md

4cf472f

Update nextflow.config

9687e68

Merge pull request #249 from maxulysse/dev_modules

f584b99

nf-core modules update bowtie2/align

Template update for nf-core/tools version 2.7.1

6f61b09

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

0e2b417

…rge_template_v2.7.1

Merge pull request #251 from JoseEspinosa/merge_template_v2.7.1

a1066fc

Merge template v2.7.1

Template update for nf-core/tools version 2.7.2

de66ade

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

8f4470c

…rge-template-v2.7.2

Update modules to fix lint

0520462

Force gunzip update

e24e74e

Update changelog

21ac2aa

Update modules (remove params.enable_conda)

692ad98

Make prettier happy

6d98c09

Force the update of modules not updated by tools

da85c1b

Make happy prettier again

bd464be

Fix c/p typo

3aef467

Merge pull request #253 from JoseEspinosa/merge-template-v2.7.2

f8af673

Merge template v2.7.2

Pull in changes from nf-core/atacseq v2

0a3c573

This reverts commit 6269ded.

add control to schema_input.json

7127dd6

Fix samplesheet format

53622a6

Merge branch 'devbovreg' of https://github.com/bjlang/nf-core-atacseq …

0f14051

…into devbovreg

Add control_replicate to schema_input.json

53b4b2f

Fix PythonBlack

7da98ec

Still fixing PythonBlack

0570cd8

Update README and CHANGELOG

754dedf

Update usage.md

b89d92c

bjlang and others added 10 commits July 18, 2023 13:22

Merge branch 'dev' of https://github.com/bjlang/nf-core-atacseq into dev

48a6039

Make Prettier happy

1815a68

Merge pull request #308 from bjlang/dev

240f153

Dev

Update bowtie2 args to pass read group fields

6ba7a80

Update changelog

d6e1411

Fix changelog entry

404587b

Replace pattern to make it more clear what is removed

c8b4f7a

Merge pull request #309 from JoseEspinosa/updates

da26ab4

Add read group tag to bowtie2 bams

Bump pipeline version to 2.1.0

0c9e267

Add credits

b3627f6

bjlang and others added 5 commits July 19, 2023 16:25

Merge pull request #310 from JoseEspinosa/dev

a2f7bc0

Bump pipeline version to 2.1.0

Get rid of checkIfExists for params paths

b9efffc

Also remove check for input parameter

fb3f2d0

Use nf-validation for all params validation

c999339

Merge pull request #312 from JoseEspinosa/updates

143f02c

Get rid of checkIfExists for params paths

maxulysse reviewed Jul 20, 2023

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you can delete this file

maxulysse reviewed Jul 20, 2023

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subworkflows/local/prepare_genome.nf Show resolved Hide resolved

maxulysse requested changes Jul 20, 2023

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ramprasadn reviewed Jul 20, 2023

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JoseEspinosa added 2 commits July 20, 2023 17:19

Apply review suggestions

44370aa

Merge pull request #313 from JoseEspinosa/updates

835f97f

Apply review suggestions

ramprasadn approved these changes Jul 20, 2023

View reviewed changes

JoseEspinosa and others added 2 commits July 21, 2023 09:36

Fix multiqc_logo in nextflow_schema

ff83490

Merge pull request #314 from JoseEspinosa/updates

c580dfc

Fix multiqc_logo in nextflow_schema

maxulysse approved these changes Jul 21, 2023

View reviewed changes

JoseEspinosa merged commit d5037cd into master Jul 21, 2023

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Dev -> Master for 2.1.0 release #311

Dev -> Master for 2.1.0 release #311

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nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

Run details

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github-actions bot commented Jul 19, 2023 •

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