Release 3.4.2 #1484

maxulysse · 2024-04-25T09:34:00Z

PR checklist

3.5.0dev - back to dev

feat(nf-prov): pin nf-prov to 1.2.2

Improve cloud testing matrix strategy

github-actions · 2024-04-25T09:36:06Z

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

Posted for pipeline commit 552d049

+| ✅ 180 tests passed       |+
#| ❔  14 tests were ignored |#
!| ❗   4 tests had warnings |!

Details

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 3.4.2
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:

files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: conf/modules.config
files_exist - File is ignored: lib/WorkflowMain.groovy
files_exist - File is ignored: lib/NfcoreTemplate.groovy
files_exist - File is ignored: lib/WorkflowSarek.groovy
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
actions_ci - actions_ci
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sarek/sarek/.github/workflows/awstest.yml
template_strings - template_strings

✅ 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-sarek_logo_light.png
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-sarek_logo_light.png
files_exist - File found: docs/images/nf-core-sarek_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: 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-sarek_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/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.step= mapping
nextflow_config - Config default value correct: params.split_fastq= 50000000
nextflow_config - Config default value correct: params.nucleotides_per_second= 200000
nextflow_config - Config default value correct: params.clip_r1= 0
nextflow_config - Config default value correct: params.clip_r2= 0
nextflow_config - Config default value correct: params.three_prime_clip_r1= 0
nextflow_config - Config default value correct: params.three_prime_clip_r2= 0
nextflow_config - Config default value correct: params.trim_nextseq= 0
nextflow_config - Config default value correct: params.group_by_umi_strategy= Adjacency
nextflow_config - Config default value correct: params.aligner= bwa-mem
nextflow_config - Config default value correct: params.ascat_min_base_qual= 20
nextflow_config - Config default value correct: params.ascat_min_counts= 10
nextflow_config - Config default value correct: params.ascat_min_map_qual= 35
nextflow_config - Config default value correct: params.cf_coeff= 0.05
nextflow_config - Config default value correct: params.cf_contamination= 0
nextflow_config - Config default value correct: params.cf_minqual= 0
nextflow_config - Config default value correct: params.cf_mincov= 0
nextflow_config - Config default value correct: params.cf_ploidy= 2
nextflow_config - Config default value correct: params.sentieon_haplotyper_emit_mode= variant
nextflow_config - Config default value correct: params.sentieon_dnascope_emit_mode= variant
nextflow_config - Config default value correct: params.sentieon_dnascope_pcr_indel_model= CONSERVATIVE
nextflow_config - Config default value correct: params.dbnsfp_fields= rs_dbSNP,HGVSc_VEP,HGVSp_VEP,1000Gp3_EAS_AF,1000Gp3_AMR_AF,LRT_score,GERP++_RS,gnomAD_exomes_AF
nextflow_config - Config default value correct: params.vep_custom_args= --everything --filter_common --per_gene --total_length --offline --format vcf
nextflow_config - Config default value correct: params.vep_version= 111.0-0
nextflow_config - Config default value correct: params.vep_out_format= vcf
nextflow_config - Config default value correct: params.genome= GATK.GRCh38
nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
nextflow_config - Config default value correct: params.vep_cache= s3://annotation-cache/vep_cache/
nextflow_config - Config default value correct: params.snpeff_cache= s3://annotation-cache/snpeff_cache/
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.test_data_base= https://raw.githubusercontent.com/nf-core/test-datasets/sarek3
nextflow_config - Config default value correct: params.seq_platform= ILLUMINA
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/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 - docs/README.md matches the template
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
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: ncbench.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: cloudtest.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: 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 2024-05-07 10:15:57

Add new citation

Fixing call to GATK4_HAPLOTYPECALLER

…for these tests

feat(release): prepare release 3.4.2

fix(tests): remove md5sum for all mosdepth tests + update dependency for these tests

fix: remove string none option from params.ascat_genome

nextflow.config

tests/config/pytesttags.yml

tests/test_aligner_bwamem.yml

asp8200 · 2024-05-06T09:39:29Z

tests/test_annotation_cache.yml


 - name: Fail to locate VEP cache
-  command: nextflow run main.nf -profile test_cache,annotation --vep_cache s3://annotation-cache/vep_cache/ --vep_cache_version 1 --tools vep --input false --build_only_index --outdir results
+  command: nextflow run main.nf -profile test,annotation --vep_cache s3://annotation-cache/vep_cache/ --vep_cache_version 1 --tools vep --input false --build_only_index --outdir results


So sometimes the argument following --input is interpreted as a path and at other times as a boolean? I don't find that so nice, but I guess it doesn't matter.

I'd say input is always interpreted as a path, but using false is a way to just unset the value and override the default value in the test profile.
I agree with you, not ideal

SPPearce

Looks good to me.

CHANGELOG.md

README.md

Adding an important comtributor

add another contributor

Adding Simon and Ken

Update CITATIONS.md with fgbio

fix(TYPO): index_alignement should be index_alignment

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

adamrtalbot and others added 19 commits January 17, 2024 11:30

Rename cloudtest back to awstest

c081571

Change logic of cloud tests workflow

79fd632

fixup

7c81a4a

Add repo protection back in

5b2cad0

[automated] Fix linting with Prettier

e2778aa

Change logic of if statement in cloud tests

0420159

Trying contains statement

3347823

Add comments|

2aff87c

CHANGELOG

a328f6d

feat(dev): bump to 3.5.0dev and restart dev on dev branch

3fd14c2

Merge pull request #1477 from maxulysse/dev

991476c

3.5.0dev - back to dev

feat(nf-prov): pin nf-prov to 1.2.2

7843389

feat(CHANGELOG): update CHANGELOG

f2e082c

Merge branch 'dev' into improve_cloud_tests_matrix

176b50d

Update .devcontainer/devcontainer.json

f338898

Rename awstest to cloudtest

1275645

Merge pull request #1482 from maxulysse/nf-prov

55e6839

feat(nf-prov): pin nf-prov to 1.2.2

Merge pull request #1378 from nf-core/improve_cloud_tests_matrix

752494f

Improve cloud testing matrix strategy

Merge branch 'master' into dev

3acdf93

FriederikeHanssen and others added 10 commits April 25, 2024 12:47

add new citation

335c8ac

Update CHANGELOG.md

dd0809e

Merge pull request #1485 from FriederikeHanssen/paper

502b6de

Add new citation

Updating sentieon modules to 202308.02

c189b6a

Updating changelog

5598939

Using monespace font for tools names in dependency table

944033a

More monospace font

0aff681

Making sure certain channels are value channels

020b33a

Updating changelog

eaa1373

Merge pull request #1488 from asp8200/fixing_test_full_germline

3fd2743

Fixing call to GATK4_HAPLOTYPECALLER

maxulysse and others added 7 commits May 3, 2024 18:29

fix(tests): remove md5sum for all mosdepth tests + update dependency …

e7ae4f8

…for these tests

Merge pull request #1498 from maxulysse/prepare_3.4.2

f153203

feat(release): prepare release 3.4.2

Apply suggestions from code review

5f2dc64

Merge pull request #1499 from maxulysse/mosdepth_md5sum

017d1ee

fix(tests): remove md5sum for all mosdepth tests + update dependency for these tests

fix: remove string none option from params.ascat_genome

5e549bf

Update nextflow.config

8ff6b3d

Merge pull request #1501 from kenibrewer/fix/ascate-genome-params

0777103

fix: remove string none option from params.ascat_genome

asp8200 reviewed May 6, 2024

View reviewed changes

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asp8200 reviewed May 6, 2024

View reviewed changes

tests/config/pytesttags.yml Show resolved Hide resolved

asp8200 reviewed May 6, 2024

View reviewed changes

tests/test_aligner_bwamem.yml Show resolved Hide resolved

asp8200 reviewed May 6, 2024

View reviewed changes

asp8200 approved these changes May 6, 2024

View reviewed changes

nh13 added 2 commits May 6, 2024 17:29

Update CITATIONS.md with fgbio

da72de0

fix(TYPO): index_alignement should be index_alignment

4bbc7c2

SPPearce approved these changes May 7, 2024

View reviewed changes

CHANGELOG.md Outdated Show resolved Hide resolved

README.md Outdated Show resolved Hide resolved

maxulysse and others added 13 commits May 7, 2024 10:43

Update README.md

5773d74

Adding an important comtributor

Update CHANGELOG.md

d1f5820

Update README.md

66d6e9c

add another contributor

Merge pull request #1509 from nf-core/maxulysse-patch-1

795a56b

Adding Simon and Ken

Update CHANGELOG.md

a2c3904

Merge branch 'dev' into nh13-patch-1

0a449fe

Update CHANGELOG.md

6eb8943

Merge branch 'dev' into nh13-index-alignment-typo

551cf08

Update README.md

8e87fcb

Merge pull request #1505 from nf-core/nh13-patch-1

9ec46ca

Update CITATIONS.md with fgbio

Merge branch 'dev' into nh13-index-alignment-typo

21e216e

Merge pull request #1506 from nf-core/nh13-index-alignment-typo

448a4d9

fix(TYPO): index_alignement should be index_alignment

Apply suggestions from code review

552d049

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

asp8200 approved these changes May 7, 2024

View reviewed changes

maxulysse merged commit b5b766d into master May 7, 2024

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Release 3.4.2 #1484

Release 3.4.2 #1484

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maxulysse commented Apr 25, 2024

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github-actions bot commented Apr 25, 2024 •

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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Release 3.4.2 #1484

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maxulysse commented Apr 25, 2024

PR checklist

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nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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asp8200 May 6, 2024

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github-actions bot commented Apr 25, 2024 •

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