dev => master 2.2.0 #136

edmundmiller · 2024-02-22T18:50:48Z

Didn't get it out in time for the template update 😞

refactor(#107): Clean up Multiqc mix

Borrowed code from rnaseq, had to fix the group pulling for whatever reason Removes old check_samplesheet code as well.

Use fromSamplesheet

To appease nf-core lint

Should fix CI memory requests being too high

Fix CI memory requests

skip-checks: true

Add AWS Megatest

Need it to reproduce https://pubmed.ncbi.nlm.nih.gov/30352805

Add Bowtie 2

What is this, Web Dev?

#134 (comment) Co-authored-by: pinin4fjords <[email protected]>

github-actions · 2024-02-22T18:53:36Z

`nf-core lint` overall result: Failed ❌

Posted for pipeline commit 618e3a7

+| ✅ 158 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   4 tests had warnings |!
-| ❌   9 tests failed       |-

❌ Test failures:

files_exist - File must be removed: lib/Utils.groovy
files_exist - File must be removed: lib/WorkflowMain.groovy
files_exist - File must be removed: lib/NfcoreTemplate.groovy
files_exist - File must be removed: lib/WorkflowNascent.groovy
files_unchanged - .github/CONTRIBUTING.md does not match the template
files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
files_unchanged - .github/workflows/branch.yml does not match the template
files_unchanged - .github/workflows/linting_comment.yml does not match the template
files_unchanged - pyproject.toml does not match the template

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 2.2.0
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 WorkflowNascent.groovy: Optionally add in-text citation tools to this list.
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

❔ Tests ignored:

files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
files_unchanged - File ignored due to lint config: assets/email_template.html

✅ 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: 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-nascent_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-nascent_logo_light.png
files_exist - File found: docs/images/nf-core-nascent_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: 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: 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-nascent_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: lib/nfcore_external_java_deps.jar
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
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.aligner= bwa
nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.max_cpus= 16
nextflow_config - Config default value correct: params.max_memory= 128.GB
nextflow_config - Config default value correct: params.max_time= 240.h
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - .github/.dockstore.yml 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 - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-nascent_logo_light.png matches the template
files_unchanged - docs/images/nf-core-nascent_logo_light.png matches the template
files_unchanged - docs/images/nf-core-nascent_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore 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 (354 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: branch.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: release-announcements.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' contains report_section_order
multiqc_config - 'assets/multiqc_config.yml' contains export_plots
multiqc_config - 'assets/multiqc_config.yml' contains report_comment
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 2.13.1
Run at 2024-03-05 16:21:58

.github/workflows/download_pipeline.yml

README.md

assets/nf-core-nascent_logo_light.png

docs/output.md

main.nf

alyssa-ab

LGTM! (other than maybe the failed linting tests)

Co-authored-by: Matthias Hörtenhuber <[email protected]>

Co-authored-by: mashehu <[email protected]>

edmundmiller and others added 30 commits February 17, 2023 20:28

refactor(#107): Clean up Multiqc mix

0a3359c

Merge pull request #111 from nf-core/cleanup-multiqc

0d3cfdf

refactor(#107): Clean up Multiqc mix

Template update for nf-core/tools version 2.8

9cba10b

Template update for nf-core/tools version 2.9

535b97d

fix: Update ubuntu image to nf-core

1b86d34

feat(nf-validation): Use fromSamplesheet

dbcf8e7

Borrowed code from rnaseq, had to fix the group pulling for whatever reason Removes old check_samplesheet code as well.

chore: Update snapshot because of remove input_check

243b4dd

Merge pull request #117 from nf-core/fromSamplesheet

024d7b7

Use fromSamplesheet

Template update for nf-core/tools version 2.10

9712163

chore: Update CHANGELOG

feddaff

Template update for nf-core/tools version 2.11

15b8ff3

Template update for nf-core/tools version 2.11.1

ec24cfb

style: Run prettier

0c37e30

chore: Update some tenses in changelog

802a1d3

chore: Update changelog

4040146

build: nf-core subworkflows update

5764e54

refactor: nf-core subworkflows install fastq_align_bwa

4fbaa24

build: nf-core modules update multiqc gffread

6841c45

To appease nf-core lint

Merge pull request #128 from nf-core/template-cleanup

a492c55

Template update for nf-core/tools version 2.12

1494fff

style: Run nf-core lint --fix files_unchanged

c55e541

chore: Update changelog with 2.12

f95831f

test: build config from fetchngs

88a7852

Should fix CI memory requests being too high

test: Hard code params into config

dfc0450

chore: Bump snapshots

92299f3

Merge pull request #131 from nf-core/ci-memory

717a487

Fix CI memory requests

test(#66): Add AWS Mega Test

93ddcbd

skip-checks: true

Merge pull request #130 from nf-core/full_test

fbf44d4

Add AWS Megatest

test(#119): Add a test for gzipped references

2b32a6b

build: nf-core modules update gunzip

2a182d8

edmundmiller and others added 15 commits February 15, 2024 12:42

build: nf-core modules install bowtie2/build

609f1ac

feat: Add bowtie2 alignment

e79b86d

Need it to reproduce https://pubmed.ncbi.nlm.nih.gov/30352805

fix: Remove stray println meta

55e4498

feat: Add Bowtie2 output to MultiQC

3b96a35

chore: Add Bowtie 2 docs

4757367

Merge pull request #132 from nf-core/bowtie2

839cc85

Add Bowtie 2

chore: Remove samplesheet check process declaration

2c751f5

test: Restructure tests to have test files next to nextflow scripts

c2ff65b

What is this, Web Dev?

chore: Update CHANGELOG for release

05e4601

chore: nf-core modules update

60225d6

refactor(TI): Update PINTS args passing and use 'disable-small' in tests

44a7168

style: Fix nf-core lint errors

b720c18

test(grohmm): Remove snapshots

c5c8d7e

#134 (comment) Co-authored-by: pinin4fjords <[email protected]>

chore: Bump version to 2.2.0

7c66cbc

Merge pull request #134 from nf-core/release-prep

b0d5bc1

edmundmiller self-assigned this Feb 22, 2024

edmundmiller marked this pull request as draft February 26, 2024 18:25

edmundmiller force-pushed the dev branch from 7840300 to 79e56ee Compare February 29, 2024 18:45

edmundmiller marked this pull request as ready for review February 29, 2024 19:27

mashehu approved these changes Mar 1, 2024

View reviewed changes

edmundmiller added this to the 2.2.0 milestone Mar 1, 2024

edmundmiller requested a review from alyssa-ab March 1, 2024 16:11

alyssa-ab approved these changes Mar 3, 2024

View reviewed changes

edmundmiller force-pushed the dev branch from 79e56ee to 0d2e8c1 Compare March 4, 2024 20:32

edmundmiller and others added 3 commits March 5, 2024 10:18

chore: Fix release date

062aa8a

Apply suggestions from code review

e024be4

Co-authored-by: Matthias Hörtenhuber <[email protected]>

chore: Regenerate nf-core logo light

618e3a7

Co-authored-by: mashehu <[email protected]>

edmundmiller force-pushed the dev branch from 9bc50ae to 618e3a7 Compare March 5, 2024 16:19

edmundmiller merged commit 02bbefb into master Mar 5, 2024
5 of 9 checks passed

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dev => master 2.2.0 #136

dev => master 2.2.0 #136

edmundmiller commented Feb 22, 2024 •

edited

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github-actions bot commented Feb 22, 2024 •

edited

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❌ Test failures:

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

alyssa-ab left a comment

dev => master 2.2.0 #136

dev => master 2.2.0 #136

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edmundmiller commented Feb 22, 2024 • edited Loading

github-actions bot commented Feb 22, 2024 • edited Loading

nf-core lint overall result: Failed ❌

❌ Test failures:

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

alyssa-ab left a comment

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edmundmiller commented Feb 22, 2024 •

edited

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github-actions bot commented Feb 22, 2024 •

edited

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`nf-core lint` overall result: Failed ❌