3.2 release #229

yuukiiwa · 2023-03-13T05:35:16Z

Have made PRs for these tools to nf-core/modules, but they got conda problems:
clair3: nf-core/modules#3058
pepper_margin_deepvariant: nf-core/modules#3060
nanopolish_index_eventalign: nf-core/modules#917

bambu version

release 3.1 pull request

update

github-actions · 2023-03-13T05:35:39Z

Python linting (`black`) is failing

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To fix this CI test, please run:

Install black: pip install black
Fix formatting errors in your pipeline: black .

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github-actions · 2023-03-13T05:37:40Z

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

Posted for pipeline commit 5247122

+| ✅ 157 tests passed       |+
!| ❗   5 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 3.1.0
pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

✅ 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-nanoseq_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-nanoseq_logo_light.png
files_exist - File found: docs/images/nf-core-nanoseq_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/WorkflowNanoseq.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-nanoseq_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-nanoseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-nanoseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-nanoseq_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: 22.10.1, Config: 22.10.1
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 (180 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: 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 2.10
Run at 2023-10-09 14:48:26

…h existing nf-core modules

Update 3_1 dev meta

tmp: aws access denied

christopher-hakkaart · 2023-10-12T08:47:51Z

modules/local/clair3.nf

+    conda 'bioconda::clair3=0.1.10'
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/clair3:0.1.10--hdfd78af_0' :
+        'biocontainers/clair3:0.1.10--hdfd78af_0' }"


This might be an older version of the tool there. I'll check this and see if there is a newer version available.

christopher-hakkaart · 2023-10-12T08:48:28Z

modules/local/m6anet_dataprep.nf

christopher-hakkaart

LMTM!

christopher-hakkaart and others added 8 commits February 24, 2023 22:12

Simplify samplesheet, input check, and qcat

49345a1

remove tools and add back in slowly

342429b

Fix vc branch, sv calling

a4ff7dc

Adding graphmap

5e2fcc7

Merge pull request #220 from nf-core/update_3_1

565a139

bambu version

Merge pull request #222 from nf-core/dev

6e563e5

release 3.1 pull request

Update align_graphmap2.nf

368f1ef

Merge pull request #228 from nf-core/master

d71927b

update

yuukiiwa and others added 11 commits March 13, 2023 13:40

make sure that python black is still passing

f78633d

Update check_samplesheet.py

f5d238a

python blacked

962aa51

convert local modules with existing nf-core/modules

6c6d67b

refactoring

45d21a5

replace medaka with clair3

5f5dcd1

done refactoring: one fasta & gtf per run; replaced local modules wit…

4f8a9f5

…h existing nf-core modules

PRETTY

d094261

fix

38507c5

fix

9eabb15

fix

e3ac9c4

yuukiiwa marked this pull request as ready for review March 21, 2023 04:27

christopher-hakkaart and others added 6 commits March 21, 2023 14:53

Remove mapping and add in more meta information

17fd627

tidy lines

3d05290

fix check_samplesheet

ada62a9

Merge pull request #232 from nf-core/update_3_1_dev_meta

69f9f5a

Update 3_1 dev meta

convert sniffles and cutesv to nf-core/modules

b127e3a

PRETTY

403b456

christopher-hakkaart self-assigned this Mar 28, 2023

Template update for nf-core/tools version 2.8

371ce6d

yuukiiwa and others added 25 commits May 23, 2023 15:35

igenome

855ce8b

clean up

398ab24

tmp: aws access denied

9ae4d1a

tmp: aws access denied

95ac0ec

tmp: aws access denied

7fcdb46

tmp: aws access denied

2fa1fc5

tmp: aws access denied

6cb98e2

tmp: aws access denied

d86f3d2

tmp: aws access denied

9358a7c

tmp: aws access denied

8ba80ba

tmp: aws access denied

5322c90

tmp: aws access denied

210d774

tmp: aws access denied

4a75758

tmp: aws access denied

357ec04

tmp: aws access denied

ecdf027

Merge pull request #246 from nf-core/update_3_1_igenome

4af13f4

tmp: aws access denied

Update test.config

47c7d85

test

5ae8db5

nf-core modules update (All modules)

65990ab

fix samtools stats path

791f9dd

update

e994f27

fix graphmap

3aa5ed6

linting fix

3812706

fix

bf4cd0a

PRETTY!

5247122

christopher-hakkaart reviewed Oct 12, 2023

View reviewed changes

modules/local/m6anet_dataprep.nf

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Awesome!

christopher-hakkaart approved these changes Oct 16, 2023

View reviewed changes

christopher-hakkaart merged commit 2020960 into dev Oct 16, 2023
14 checks passed

yuukiiwa deleted the update_3_1_dev branch October 16, 2023 11:53

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3.2 release #229

3.2 release #229

yuukiiwa commented Mar 13, 2023 •

edited

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github-actions bot commented Mar 13, 2023

github-actions bot commented Mar 13, 2023 •

edited

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❗ Test warnings:

✅ Tests passed:

Run details

christopher-hakkaart Oct 12, 2023

christopher-hakkaart Oct 12, 2023

christopher-hakkaart left a comment

3.2 release #229

3.2 release #229

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yuukiiwa commented Mar 13, 2023 • edited Loading

github-actions bot commented Mar 13, 2023

Python linting (black) is failing

github-actions bot commented Mar 13, 2023 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

Run details

christopher-hakkaart Oct 12, 2023

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yuukiiwa commented Mar 13, 2023 •

edited

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Python linting (`black`) is failing

github-actions bot commented Mar 13, 2023 •

edited

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