Release 3.4.3 #1595

maxulysse · 2024-07-16T07:47:14Z

PR checklist

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

…-template-update-2.13.2dev

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

feat(version): bump pipeline to 3.5.0dev

…st-template-update-2.13.2dev

FEAT: prepare RC 3.4.3

CHANGELOG.md

github-actions · 2024-07-16T08:20:15Z

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

Posted for pipeline commit fc7b47e

+| ✅ 199 tests passed       |+
#| ❔  12 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 3.4.3
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_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
actions_ci - actions_ci
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sarek/sarek/.github/workflows/awstest.yml
template_strings - template_strings
modules_config - modules_config

✅ 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 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-sarek_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/WorkflowSarek.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 - 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
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/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: release-announcements.yml
actions_schema_validation - Workflow validation passed: cloudtest.yml
actions_schema_validation - Workflow validation passed: ncbench.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: branch.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.
base_config - UNZIP found in conf/base.config and Nextflow scripts.
base_config - FASTQC found in conf/base.config and Nextflow scripts.
base_config - FASTP found in conf/base.config and Nextflow scripts.
base_config - BWAMEM1_MEM found in conf/base.config and Nextflow scripts.
base_config - CNVKIT_BATCH found in conf/base.config and Nextflow scripts.
base_config - GATK4_MARKDUPLICATES found in conf/base.config and Nextflow scripts.
base_config - GATK4_APPLYBQSR found in conf/base.config and Nextflow scripts.
base_config - MOSDEPTH found in conf/base.config and Nextflow scripts.
base_config - STRELKA found in conf/base.config and Nextflow scripts.
base_config - SAMTOOLS_CONVERT found in conf/base.config and Nextflow scripts.
base_config - GATK4_MERGEVCFS found in conf/base.config and Nextflow scripts.
base_config - MULTIQC found in conf/base.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: 2.14.1

Run details

nf-core/tools version 2.14.1
Run at 2024-08-05 14:01:03

maxulysse · 2024-07-16T09:14:03Z

Expected snapshots in HaplotypeCaller are dropped in #1596 , as we will be updating all that with nf-test, I'd rather kill the old functionalities than keeping them alive.

Same for Deepvariant with #1597

FIX: drop snapshot from Haplotypecaller tests

FIX: drop snapshot from Deepvariant tests

asp8200 · 2024-07-23T07:42:56Z

I see the usage.md has been updated. I had a quick look here https://nf-co.re/sarek/dev/docs/usage and it seems to render fine.

subworkflows/local/annotation_cache_initialisation/main.nf

asp8200 · 2024-07-23T08:03:20Z

Looks good. Not too many changes. A small release - the way I like it 😁. (I didn't look at the changes to the CNVKIT subworkflow, so hopefully somebody else will take a critical look at that.)

FriederikeHanssen · 2024-07-29T13:45:43Z

Triggered the full size tests

subworkflows/local/bam_variant_calling_cnvkit/main.nf

FriederikeHanssen

Tentatively approvig. Waiting for the full size tests to pass

subworkflows/local/bam_variant_calling_cnvkit/main.nf

workflows/sarek/main.nf

FriederikeHanssen · 2024-07-30T07:41:48Z

@nf-core-bot fix linting

Remove empty outdirs

FriederikeHanssen · 2024-08-07T09:53:11Z

tested the download locally with the latest tools release. @mashehu gave me permission to release with the failing test: https://nfcore.slack.com/archives/CE5LG7WMB/p1722964196047559?thread_ts=1722873465.605869&cid=CE5LG7WMB

lescai and others added 30 commits April 26, 2024 14:42

added new modules for cnvkit

8957d93

updated cnvkit calling subwf

f8c531d

updated variant calling germline all for cnvkit

06a74d0

updated cnvkit_reference on germline call in sarek main

46d0867

check for missing something

33ffaf2

check for missing something

65ee900

check for missing something

359aca6

updated config file for cnvkit

51adb8c

fixed exported vcf name

89737aa

changed config selector to remove cnvkit alias

a04d896

Update conf/modules/cnvkit.config

f67b7f1

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

updated docs and changelog

0353e91

Merge branch 'dev' into cnvkit_update

5aec56c

Template update for nf-core/tools version 2.13.2.dev0

5af2e5d

Merge branch 'TEMPLATE' of https://github.com/nf-core/sarek into test…

07e0368

…-template-update-2.13.2dev

prettified changelog

08a28b3

Update CHANGELOG.md

ac3580f

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

Merge branch 'dev' into cnvkit_update

eb20856

feat(version): bump pipeline to 3.5.0dev

77398d3

Merge pull request #1513 from maxulysse/3.5.0dev

8555f27

feat(version): bump pipeline to 3.5.0dev

Template update for nf-core/tools version 2.13.2.dev0

2c09df9

Template update for nf-core/tools version 2.13.2.dev0

0ff1ae8

Template update for nf-core/tools version 2.14.0

a6008e6

Merge branch 'TEMPLATE' of https://github.com/mirpedrol/sarek into te…

58ef79d

…st-template-update-2.13.2dev

Merge branch 'dev' into test-template-update-2.13.2dev

5aa9a25

Template update for nf-core/tools version 2.13.2.dev0

84900cb

Template update for nf-core/tools version 2.14.0

8bb7d5b

fix linting + update CHANGELOG

3b6e7cd

Apply suggestions from code review

5c6547e

Apply suggestions from code review

1920e05

maxulysse added 2 commits July 15, 2024 15:54

prepare RC 3.4.3

6a77b9a

Merge pull request #1593 from maxulysse/prepare_3.4.3

81b8a15

FEAT: prepare RC 3.4.3

maxulysse requested a review from FriederikeHanssen as a code owner July 16, 2024 07:47

maxulysse mentioned this pull request Jul 16, 2024

Release 3.4.3 #1594

Closed

maxulysse commented Jul 16, 2024

View reviewed changes

CHANGELOG.md Show resolved Hide resolved

Update CHANGELOG.md

1e87aca

FIX: drop snapshot from Haplotypecaller tests

c9d7639

maxulysse added 3 commits July 16, 2024 12:18

Merge pull request #1596 from maxulysse/fix_old_pytests

0667702

FIX: drop snapshot from Haplotypecaller tests

FIX: drop snapshot from Deepvariant tests

fa9961d

Merge pull request #1597 from maxulysse/fix_old_pytests_ii

9f11b67

FIX: drop snapshot from Deepvariant tests

asp8200 reviewed Jul 23, 2024

View reviewed changes

subworkflows/local/annotation_cache_initialisation/main.nf Show resolved Hide resolved

FriederikeHanssen reviewed Jul 29, 2024

View reviewed changes

subworkflows/local/bam_variant_calling_cnvkit/main.nf Show resolved Hide resolved

FriederikeHanssen approved these changes Jul 29, 2024

View reviewed changes

subworkflows/local/bam_variant_calling_cnvkit/main.nf Outdated Show resolved Hide resolved

workflows/sarek/main.nf Outdated Show resolved Hide resolved

workflows/sarek/main.nf Show resolved Hide resolved

FriederikeHanssen added 2 commits July 30, 2024 09:34

Update workflows/sarek/main.nf

425fb91

Update subworkflows/local/bam_variant_calling_cnvkit/main.nf

b7d79bf

FriederikeHanssen and others added 3 commits August 5, 2024 12:27

remove empty output directories

56828b9

Update CHANGELOG.md

96b4a87

fix linting

e48d9bd

kenibrewer approved these changes Aug 5, 2024

View reviewed changes

Merge pull request #1612 from FriederikeHanssen/empty_outdirs

fc7b47e

Remove empty outdirs

FriederikeHanssen requested a review from kenibrewer August 5, 2024 15:24

asp8200 approved these changes Aug 7, 2024

View reviewed changes

FriederikeHanssen merged commit e92242e into master Aug 7, 2024
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Release 3.4.3 #1595

Release 3.4.3 #1595

maxulysse commented Jul 16, 2024

github-actions bot commented Jul 16, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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maxulysse commented Jul 16, 2024 •

edited

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asp8200 commented Jul 23, 2024

asp8200 commented Jul 23, 2024 •

edited

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FriederikeHanssen commented Jul 29, 2024

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FriederikeHanssen commented Jul 30, 2024

FriederikeHanssen commented Aug 7, 2024

Release 3.4.3 #1595

Release 3.4.3 #1595

Conversation

maxulysse commented Jul 16, 2024

PR checklist

github-actions bot commented Jul 16, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

maxulysse commented Jul 16, 2024 • edited Loading

asp8200 commented Jul 23, 2024

asp8200 commented Jul 23, 2024 • edited Loading

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FriederikeHanssen commented Jul 30, 2024

FriederikeHanssen commented Aug 7, 2024

github-actions bot commented Jul 16, 2024 •

edited

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

maxulysse commented Jul 16, 2024 •

edited

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asp8200 commented Jul 23, 2024 •

edited

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