Release 0.3.0 #325

fellen31 · 2024-08-14T12:30:02Z

PR checklist

* bump dev version * Update CHANGELOG.md

* add nf-test * add ci * update CI * add config * add nextflow config * remove old comments * Update CHANGELOG * add stub * review comments and test for no intervals * formatting * Update subworkflows/local/short_variant_calling/tests/nextflow.config * Update conf/modules/short_variant_calling.config * use max resources instead of hardcoding

* rework presets * Update CHANGELOG * Update CHANGELOG.md * Turn off ONT repeat calling by default. * update docs * Update docs/usage.md Co-authored-by: Anders Jemt <[email protected]> --------- Co-authored-by: Anders Jemt <[email protected]>

* Add modeltype parameter * Just allow ONT_R104 and PACBIO

* Don't allow running HiPhase with ONT data * Update workflows/nallo.nf Co-authored-by: Anders Jemt <[email protected]> --------- Co-authored-by: Anders Jemt <[email protected]>

* add ont tests * Update CHANGELOG.md * fix hp tag * remove tags * Don't run hiphase * Keep parallel_snv 1

* Remove --extra_gvcfs * update snap * Update CHANGELOG.md

* rework presets * Update CHANGELOG * Update CHANGELOG.md * Turn off ONT repeat calling by default. * update docs * allow ont data with hificnv

* add nf-test for pipeline * update test * Update CHANGELOG.md * Delete tests/nextflow_schema.json * update test

* reorganise processes * remove multisample * update snap * update snap * fix more stuff * Update conf/modules/short_variant_calling.config Co-authored-by: Anders Jemt <[email protected]> * Move versions under process * update snap --------- Co-authored-by: Anders Jemt <[email protected]>

* reorganise processes * update snap * update snap * fix more stuff * Update conf/modules/short_variant_calling.config Co-authored-by: Anders Jemt <[email protected]> * update snap * test snv annotation * test snv annotation --------- Co-authored-by: Anders Jemt <[email protected]>

* add stranger * Update CHANGELOG.md * Update CHANGELOG.md * add citation

* light refactoring of snv calling process names * add groupKey

* change ont preset and snapshot bam reads md5 * Run mosdepth in fast mode (#250) * change ont preset and snapshot bam reads md5 * fix merge snap

* annotate multisample * add main

#252) * fix duplicate snvs * use scatter genome instead * Update subworkflows/local/scatter_genome/main.nf Co-authored-by: Ramprasad Neethiraj <[email protected]> --------- Co-authored-by: Ramprasad Neethiraj <[email protected]>

* wip * no clinical set before filtervep is working * Reviewer comments

* parallel snv-annotation * review comments

…mple (#277)

* Improve non-autosomal calling in DeepVariant * Update nextflow_schema.json Co-authored-by: Anders Jemt <[email protected]> * conditional haploid contigs * Update conf/modules/short_variant_calling.config Co-authored-by: Anders Jemt <[email protected]> --------- Co-authored-by: Anders Jemt <[email protected]>

github-actions · 2024-08-14T12:32:09Z

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

Posted for pipeline commit 14849a8

+| ✅ 167 tests passed       |+
#| ❔  20 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 0.3.0

❔ Tests ignored:

files_exist - File is ignored: CODE_OF_CONDUCT.md
files_exist - File is ignored: assets/nf-core-nallo_logo_light.png
files_exist - File is ignored: docs/README.md
files_exist - File is ignored: docs/images/nf-core-nallo_logo_light.png
files_exist - File is ignored: docs/images/nf-core-nallo_logo_dark.png
files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: conf/modules.config
nextflow_config - Config variable ignored: manifest.name
nextflow_config - Config variable ignored: manifest.homePage
files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
files_unchanged - File ignored due to lint config: assets/nf-core-nallo_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-nallo_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-nallo_logo_dark.png
files_unchanged - File ignored due to lint config: docs/README.md
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
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: 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/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: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/output.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-nallo_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/WorkflowNallo.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.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
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 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.skip_aligned_read_qc= false
nextflow_config - Config default value correct: params.skip_raw_read_qc= false
nextflow_config - Config default value correct: params.skip_short_variant_calling= false
nextflow_config - Config default value correct: params.skip_assembly_wf= false
nextflow_config - Config default value correct: params.skip_mapping_wf= false
nextflow_config - Config default value correct: params.skip_methylation_wf= false
nextflow_config - Config default value correct: params.skip_repeat_calling= false
nextflow_config - Config default value correct: params.skip_repeat_annotation= false
nextflow_config - Config default value correct: params.skip_phasing_wf= false
nextflow_config - Config default value correct: params.skip_snv_annotation= false
nextflow_config - Config default value correct: params.skip_cnv_calling= false
nextflow_config - Config default value correct: params.skip_call_paralogs= false
nextflow_config - Config default value correct: params.skip_rank_variants= false
nextflow_config - Config default value correct: params.igenomes_ignore= true
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
nextflow_config - Config default value correct: params.preset= revio
nextflow_config - Config default value correct: params.variant_caller= deepvariant
nextflow_config - Config default value correct: params.phaser= whatshap
nextflow_config - Config default value correct: params.hifiasm_mode= hifi-only
nextflow_config - Config default value correct: params.parallel_alignments= 1
nextflow_config - Config default value correct: params.parallel_snv= 13
nextflow_config - Config default value correct: params.vep_cache_version= 110
nextflow_config - Config default value correct: params.deepvariant_model_type= PACBIO
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.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
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
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_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (505 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: fix-linting.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: ci_master.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 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 '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 - HIFIASM 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 2024-08-29 09:19:16

* Split vep plugins into vep cache and vep plugins * review comments * Keep SpliceAI in tests

* citations * dynamic method description * citations * Add back MultiQC * Add back fastqc

* Split vep plugins into vep cache and vep plugins * Fix file requirements

Update usage

peterpru

Looks great to me 👍

docs/README.md

docs/output.md

Co-authored-by: Peter Pruisscher <[email protected]>

fellen31 and others added 30 commits June 27, 2024 13:11

Bump dev version to 0.3.0dev (#229)

ffbbb28

* bump dev version * Update CHANGELOG.md

Rework --preset parameter (#232)

39fc829

* rework presets * Update CHANGELOG * Update CHANGELOG.md * Turn off ONT repeat calling by default. * update docs * Update docs/usage.md Co-authored-by: Anders Jemt <[email protected]> --------- Co-authored-by: Anders Jemt <[email protected]>

Add deepvariant_model_type parameter (#234)

18d1eb0

* Add modeltype parameter * Just allow ONT_R104 and PACBIO

Don't allow running HiPhase with ONT data (#235)

53bb361

* Don't allow running HiPhase with ONT data * Update workflows/nallo.nf Co-authored-by: Anders Jemt <[email protected]> --------- Co-authored-by: Anders Jemt <[email protected]>

Add ONT tests (#231)

0ea8efd

* add ont tests * Update CHANGELOG.md * fix hp tag * remove tags * Don't run hiphase * Keep parallel_snv 1

Remove --extra_gvcfs (#238)

a053494

* Remove --extra_gvcfs * update snap * Update CHANGELOG.md

Allow ONT with HiFiCNV (#233)

d9873c6

* rework presets * Update CHANGELOG * Update CHANGELOG.md * Turn off ONT repeat calling by default. * update docs * allow ont data with hificnv

Remove CONVERT_ONT_READNAMES (#237)

ca3ea3a

Add nf-test for pipeline (#239)

d359bb6

* add nf-test for pipeline * update test * Update CHANGELOG.md * Delete tests/nextflow_schema.json * update test

Annotate repeat expansions with Stranger (#245)

0735185

* add stranger * Update CHANGELOG.md * Update CHANGELOG.md * add citation

Light refactoring of snv calling process names (#246)

8bc567d

* light refactoring of snv calling process names * add groupKey

Run mosdepth in fast mode (#250)

d8faba6

updagte vep annotation (#244)

3c761de

Change ONT minimap2 preset and snapshot BAM reads (#247)

97df846

* change ont preset and snapshot bam reads md5 * Run mosdepth in fast mode (#250) * change ont preset and snapshot bam reads md5 * fix merge snap

Annotate multisample SNV VCF (#251)

04bea11

* annotate multisample * add main

fix stranger (#256)

8de16ec

faster test (#258)

9764f32

remove todos (#257)

f580e97

Add rank_variants (#255)

55c55c5

* wip * no clinical set before filtervep is working * Reviewer comments

Run snv-annotation in parallel (#261)

0fabd11

* parallel snv-annotation * review comments

update deepvariant and htslib (#260)

b7ade8e

Fix modkit warning (#267)

4b6099d

Add BCFTools stats for SNVs (#269)

7a6cb47

Only output unphased aligments when phasing is off (#268)

a00684a

Allow CNV calling to start as soon as SNV calling as done for that sa…

901d7cb

…mple (#277)

Add skip for QC aligned reads (#271)

2b430d7

fellen31 and others added 4 commits August 13, 2024 20:27

Use project name in echtvar encode (#312)

ed66340

Fix typo (#315)

c7dc538

Remove samtools reset from fastq (#319)

f319465

Split vep_cache into vep_cache and vep_plugin_files (#314)

341b8b5

* Split vep plugins into vep cache and vep plugins * review comments * Keep SpliceAI in tests

fellen31 closed this Aug 15, 2024

fellen31 and others added 8 commits August 15, 2024 15:49

Update citations (#320)

4548dc2

* citations * dynamic method description * citations * Add back MultiQC * Add back fastqc

Use meta.id in BUILD_INTERVALS input (#321)

e64470f

Fix file requirements (#317)

cc6d26a

* Split vep plugins into vep cache and vep plugins * Fix file requirements

Fix parallel alignments in CI tests (#323)

1f15553

Fix file requirements

e76879d

ignore .prettierignore

7a855b1

update parameters

107869f

try again with linting

b14b7ad

fellen31 reopened this Aug 15, 2024

Merge pull request #318 from fellen31/update-usage

83f346c

Update usage

jemten marked this pull request as ready for review August 19, 2024 14:36

jemten requested a review from a team as a code owner August 19, 2024 14:36

peterpru previously approved these changes Aug 26, 2024

View reviewed changes

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docs/output.md Outdated Show resolved Hide resolved

Update docs/README.md

a6e4fee

Co-authored-by: Peter Pruisscher <[email protected]>

fellen31 dismissed peterpru’s stale review via a6e4fee August 27, 2024 06:37

fellen31 added 2 commits August 27, 2024 08:40

Update output.md

8ed32d7

version bump and fix missing stranger in readme (#330)

6d2c31f

peterpru previously approved these changes Aug 27, 2024

View reviewed changes

Use updated sex in genmod PED-file (#332)

10d7081

fellen31 dismissed peterpru’s stale review via 10d7081 August 28, 2024 12:53

Add sample name to TRGT output (#333)

14849a8

peterpru approved these changes Aug 29, 2024

View reviewed changes

fellen31 merged commit 1453238 into master Aug 30, 2024
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Release 0.3.0 #325

Release 0.3.0 #325

fellen31 commented Aug 14, 2024

github-actions bot commented Aug 14, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

peterpru left a comment

Release 0.3.0 #325

Release 0.3.0 #325

Conversation

fellen31 commented Aug 14, 2024

PR checklist

github-actions bot commented Aug 14, 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 Aug 14, 2024 •

edited

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