Release 2.3.1 PR #344

apeltzer · 2024-04-18T11:36:06Z

PR checklist

Co-authored-by: Maxime U Garcia <[email protected]>

Bump version in dev

Upgrade MQC 1.21

Important! Template update for nf-core/tools v2.13.1

Fix mirtrace cast issue

Fix reported bugs

Fix mirtrace staging bug

adapter auto detection

Fix auto-detection of adapter with fastp

Optional-phred-scores

Co-authored-by: Christopher Mohr <[email protected]>

Fix-mirdeep-out-bump-versions

github-actions · 2024-04-18T11:37:59Z

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

Posted for pipeline commit 31d71fa

+| ✅ 182 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 2.3.1
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!

❔ Tests ignored:

nextflow_config - Config default ignored: params.fastp_known_mirna_adapters

✅ 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-smrnaseq_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-smrnaseq_logo_light.png
files_exist - File found: docs/images/nf-core-smrnaseq_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-smrnaseq_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/Utils.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/WorkflowSmrnaseq.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.protocol= illumina
nextflow_config - Config default value correct: params.umitools_extract_method= string
nextflow_config - Config default value correct: params.umitools_method= dir
nextflow_config - Config default value correct: params.skip_umi_extract_before_dedup= true
nextflow_config - Config default value correct: params.mature= https://mirbase.org/download/mature.fa
nextflow_config - Config default value correct: params.hairpin= https://mirbase.org/download/hairpin.fa
nextflow_config - Config default value correct: params.save_aligned_mirna_quant= true
nextflow_config - Config default value correct: params.three_prime_adapter= AGATCGGAAGAGCACACGTCTGAACTCCAGTCA
nextflow_config - Config default value correct: params.trim_fastq= true
nextflow_config - Config default value correct: params.fastp_min_length= 17
nextflow_config - Config default value correct: params.fastp_max_length= 100
nextflow_config - Config default value correct: params.min_trimmed_reads= 10
nextflow_config - Config default value correct: params.save_merged= true
nextflow_config - Config default value correct: params.phred_offset= 33
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 - 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-smrnaseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-smrnaseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-smrnaseq_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
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 (218 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: awstest.yml
actions_schema_validation - Workflow validation passed: branch.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: release-announcements.yml
actions_schema_validation - Workflow validation passed: 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
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 2024-04-18 12:31:48

grst

LGTM

Bump-modules

christopher-mohr

One comment, my tests are still running but LGTM

CHANGELOG.md

apeltzer and others added 30 commits February 23, 2024 13:40

Bump verison in dev

89ace60

Update nextflow.config

c3d474d

Co-authored-by: Maxime U Garcia <[email protected]>

Merge pull request #320 from nf-core/bump-dev

58dca0d

Bump version in dev

Upgrade MQC 1.21

336bd5b

Template update for nf-core/tools version 2.13.1

1e13a30

Merge pull request #321 from nf-core/upgrade-mqc

1ffb218

Upgrade MQC 1.21

Merge branch 'dev' into nf-core-template-merge-2.13.1

e3ea0d2

Merge pull request #322 from nf-core/nf-core-template-merge-2.13.1

83759fc

Important! Template update for nf-core/tools v2.13.1

change type of reads input

0ead8cd

reinstall bam_sort_stats_samtools

2ad0c27

update CHANGELOG

4ec45d0

update samtools sort module

684a84b

Merge pull request #328 from christopher-mohr/fix_mirtrace_cast

d5910ec

Fix mirtrace cast issue

fix input channel cardinality

fc1c527

fix conda bowtie version

752aeea

add changes to CHANGELOG

f3df2e3

Hopeful fix for mirtrace casting & staging bug

cae7dae

Merge pull request #334 from christopher-mohr/fix_reported_bugs

151d33d

Fix reported bugs

Not working, but pushing for later

4e80ded

perform operation outside module

d39200c

Fix for casting bug

6f4b327

Merge branch 'dev' into fix-mirtrace-staging-bug

5d3b78f

Merge pull request #335 from nf-core/fix-mirtrace-staging-bug

18d4eba

Fix mirtrace staging bug

accept auto-detect as parameter value to activate

3824d68

adapter auto detection

reference correct issue in CHANGELOG

2bfbbd5

Merge pull request #337 from christopher-mohr/fix_adapter_param

38b898a

Fix auto-detection of adapter with fastp

Attempt at fixing the mirtrace part for phred scores

7a34574

Improved wording

1bf28d2

a bit of docs

4eafcac

Add comma from review

ab117d7

apeltzer and others added 11 commits April 17, 2024 09:44

Fixed to match type

75e462b

Fix adding id too

bb96ff1

Fix addition of id

accc707

Fix adapter not specified

50de711

Local adapters, not globals anymore

ee857c5

Fix passing on adapter seq to mirtrace module

aecb218

Merge pull request #342 from nf-core/optional-phred-scores

2741a78

Optional-phred-scores

Fix for mirdeep2

6550f94

Version bump

90d6b16

Update CHANGELOG.md

3a65e94

Co-authored-by: Christopher Mohr <[email protected]>

Merge pull request #343 from nf-core/fix-mirdeep-out-bump-versions

3c1eaf8

Fix-mirdeep-out-bump-versions

apeltzer requested review from christopher-mohr and grst April 18, 2024 11:36

apeltzer marked this pull request as ready for review April 18, 2024 11:36

apeltzer added 2 commits April 18, 2024 11:54

Bump several modules to latest version

09dadb7

Add proper zenodo URI

6039acc

grst approved these changes Apr 18, 2024

View reviewed changes

Merge pull request #345 from nf-core/bump-modules

31d71fa

Bump-modules

christopher-mohr approved these changes Apr 18, 2024

View reviewed changes

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apeltzer merged commit 5901bea into master Apr 18, 2024
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Release 2.3.1 PR #344

Release 2.3.1 PR #344

apeltzer commented Apr 18, 2024

github-actions bot commented Apr 18, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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christopher-mohr left a comment

Release 2.3.1 PR #344

Release 2.3.1 PR #344

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apeltzer commented Apr 18, 2024

PR checklist

github-actions bot commented Apr 18, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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github-actions bot commented Apr 18, 2024 •

edited

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