Patch Release 1.5.3 #286

atrigila · 2024-11-05T14:44:19Z

`Changed`

#275 Update samshee module from nf-core.
#276 Template update for nf-core/tools v3.0.2
#284 nf-core modules and subworkflows update. nf-test version update.
#285 Bump to version 1.5.3.

`Fixed`

#277 Improved samplesheet generation to always produce all types of samplesheets, added the ability to explicitly set strandedness, and fixed output paths to correctly reflect the publishDir subdirectory structure.
#281 Update cellranges/mkfastq module to fix missing reports and stats outputs.
#282 Fixed downstream samplesheet paths and publishDir config.

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>

Issue 272

Update cellranges/mkfastq module

Update to nf-test 0.9.2

github-actions · 2024-11-05T14:45:54Z

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

Posted for pipeline commit 9ad27d4

+| ✅ 206 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   6 tests had warnings |!

❗ Test warnings:

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 main.nf: Optionally add in-text citation tools to this list.
pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
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
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
actions_ci - actions_ci

✅ 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-demultiplex_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-demultiplex_logo_light.png
files_exist - File found: docs/images/nf-core-demultiplex_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: conf/igenomes_ignored.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 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: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
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: docs/images/nf-core-demultiplex_logo.png
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/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowDemultiplex.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Found nf-schema plugin
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: validation.help.enabled
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 found: validation.help.beforeText
nextflow_config - Config variable found: validation.help.afterText
nextflow_config - Config variable found: validation.help.command
nextflow_config - Config variable found: validation.summary.beforeText
nextflow_config - Config variable found: validation.summary.afterText
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 variable (correctly) not found: params.max_cpus
nextflow_config - Config variable (correctly) not found: params.max_memory
nextflow_config - Config variable (correctly) not found: params.max_time
nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
nextflow_config - Config variable (correctly) not found: params.validationLenientMode
nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
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 manifest.version does not contain dev for release: 1.5.3
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.trim_fastq= true
nextflow_config - Config default value correct: params.skip_tools= []
nextflow_config - Config default value correct: params.sample_size= 100000
nextflow_config - Config default value correct: params.demultiplexer= bclconvert
nextflow_config - Config default value correct: params.strandedness= auto
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.checkqc_config= []
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.remove_adapter= true
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
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/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 - 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-demultiplex_logo_light.png matches the template
files_unchanged - docs/images/nf-core-demultiplex_logo_light.png matches the template
files_unchanged - docs/images/nf-core-demultiplex_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_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: 24.04.2, Config: 24.04.2
readme - README Zenodo placeholder was replaced with DOI.
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (0 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: linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: template_version_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: ci.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 found and not ignored.
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'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - UNTAR found in conf/modules.config and Nextflow scripts.
modules_config - BCLCONVERT found in conf/modules.config and Nextflow scripts.
modules_config - BCL2FASTQ found in conf/modules.config and Nextflow scripts.
modules_config - BASES2FASTQ found in conf/modules.config and Nextflow scripts.
modules_config - FASTP found in conf/modules.config and Nextflow scripts.
modules_config - FALCO found in conf/modules.config and Nextflow scripts.
modules_config - KRAKEN2 found in conf/modules.config and Nextflow scripts.
modules_config - SEQTK_SAMPLE found in conf/modules.config and Nextflow scripts.
modules_config - MD5SUM found in conf/modules.config and Nextflow scripts.
modules_config - SGDEMUX found in conf/modules.config and Nextflow scripts.
modules_config - FQTK found in conf/modules.config and Nextflow scripts.
modules_config - CELLRANGER_MKFASTQ found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - CHECKQC found in conf/modules.config and Nextflow scripts.
modules_config - SAMSHEE found in conf/modules.config and Nextflow scripts.
modules_config - FASTQ_TO_SAMPLESHEET found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 3.0.2
version_consistency - Version tags are numeric and consistent between container, release tag and config.
included_configs - Pipeline config includes custom configs.

Run details

nf-core/tools version 3.0.2
Run at 2024-11-05 15:12:21

bump version for patch release 1.5.3

apeltzer · 2024-11-06T08:42:17Z

Something weird about the full tests JSON. Not sure where this came from.

atrigila · 2024-11-06T15:09:59Z

If I recall correctly the issue I think arises from the new template. There were some pipelines correcting it in the yml: https://github.com/nf-core/mag/blob/b582aae7d64816e08d6efae7c82ed55ea20ee7b2/.github/workflows/awsfulltest.yml#L18-L25

nf-core-bot and others added 30 commits October 8, 2024 12:30

Template update for nf-core/tools version 3.0.0

5c98797

Template update for nf-core/tools version 3.0.1

96e2f07

tmp

3d9dfa9

Adding samshee

54a98cb

Docs and changelog update

ff60023

Docs

4d305f1

Template update for nf-core/tools version 3.0.2

cca4b18

Merge branch 'dev' into nf-core-template-merge-3.0.2

6c82c05

+ verbose + debug in ci

b313f82

Apply suggestions from code review

9931615

refactor tests

a0d482a

fix doi text

d5df903

fix samplesheet generation

506a744

update pipeline tests and snapshots

6e8068f

Update conf/base.config

856d73b

Update .github/workflows/ci.yml

053fc10

update .nftignore

e47687f

update snapshots

008b4ac

pulled from modules

6e615b9

update snapshots

ba7b97b

PR comments on module

9b33143

add .nftignore and update snpashots

41099aa

update snapshots

97e5096

Apply suggestions from code review

b7fa774

update snapshots

aa30752

Update samshee

1c87181

revert unwanted changes

978e3fe

Update conf/test_full.config

3a42ad4

code polish

a99af46

code polish

e235b22

nschcolnicov and others added 14 commits October 30, 2024 16:05

Fixes in samplesheet generator script and snap updates

c53abee

Update workflows/demultiplex.nf

1df1a08

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>

Merge pull request #282 from nf-core/issue_272

74b1869

Issue 272

update cellranges_mkfastq module

175b85b

update modules

c81f8d3

update to latest nf-test

19b3646

update subworkflows

e1b7035

update changelog

7dcfadb

update snapshot

27aff96

Merge pull request #283 from alanmmobbs93/update/mkfastq

6de9710

Update cellranges/mkfastq module

fix pull number

4da452b

Merge pull request #284 from atrigila/update_nf-test-0.9.2

dc17d88

Update to nf-test 0.9.2

bump versions

5622502

update changelog

f95de98

atrigila linked an issue Nov 5, 2024 that may be closed by this pull request

release v1.5.3 #280

Closed

atrigila requested review from apeltzer, grst and nschcolnicov November 5, 2024 15:10

Merge pull request #285 from atrigila/patch_release

9ad27d4

bump version for patch release 1.5.3

atrigila marked this pull request as ready for review November 5, 2024 16:05

atrigila requested review from nh13, sam-white04, blajoie and a team as code owners November 5, 2024 16:05

nschcolnicov approved these changes Nov 5, 2024

View reviewed changes

apeltzer approved these changes Nov 6, 2024

View reviewed changes

apeltzer merged commit 2e648b5 into master Nov 6, 2024
33 of 34 checks passed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Patch Release 1.5.3 #286

Patch Release 1.5.3 #286

atrigila commented Nov 5, 2024

github-actions bot commented Nov 5, 2024 •

edited

Loading

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

apeltzer commented Nov 6, 2024

atrigila commented Nov 6, 2024

Patch Release 1.5.3 #286

Patch Release 1.5.3 #286

Conversation

atrigila commented Nov 5, 2024

Changed

Fixed

github-actions bot commented Nov 5, 2024 • edited Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

apeltzer commented Nov 6, 2024

atrigila commented Nov 6, 2024

`Changed`

`Fixed`

github-actions bot commented Nov 5, 2024 •

edited

Loading

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