1.1.1 - LATÜRNICH #186

subwaystation · 2024-03-14T10:22:42Z

PR checklist

This is a small PR which just fixes some bugs.

bump pipeline version to 1.2.0dev - LATÜRNICH

Bug

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

fix wfmash v0.12.6 parameters and other bugs

bump bcftools to 1.19

prepare 1.1.1 release

github-actions · 2024-03-14T10:24:12Z

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

Posted for pipeline commit 5daf69e

+| ✅ 187 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

files_exist - File not found: conf/igenomes.config
nextflow_config - Config manifest.version should end in dev: 1.1.1
readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
pipeline_todos - TODO string in README.md: Add full-sized test dataset and amend the paragraph below if applicable
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_unchanged - File ignored due to lint config: assets/nf-core-pangenome_logo_light.png

✅ 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-pangenome_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-pangenome_logo_light.png
files_exist - File found: docs/images/nf-core-pangenome_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: .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-pangenome_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/WorkflowPangenome.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.wfmash_map_pct_id= 90.0
nextflow_config - Config default value correct: params.wfmash_segment_length= 5000
nextflow_config - Config default value correct: params.wfmash_mash_kmer= 19
nextflow_config - Config default value correct: params.wfmash_mash_kmer_thres= 0.001
nextflow_config - Config default value correct: params.wfmash_sparse_map= 1.0
nextflow_config - Config default value correct: params.wfmash_chunks= 1
nextflow_config - Config default value correct: params.wfmash_hg_filter_ani_diff= 30
nextflow_config - Config default value correct: params.wfmash_n_mappings= 1
nextflow_config - Config default value correct: params.seqwish_min_match_length= 23
nextflow_config - Config default value correct: params.seqwish_transclose_batch= 10000000
nextflow_config - Config default value correct: params.seqwish_sparse_factor= 0.0
nextflow_config - Config default value correct: params.smoothxg_max_path_jump= 0
nextflow_config - Config default value correct: params.smoothxg_max_edge_jump= 0
nextflow_config - Config default value correct: params.smoothxg_poa_length= 700,900,1100
nextflow_config - Config default value correct: params.smoothxg_block_ratio_min= 0
nextflow_config - Config default value correct: params.smoothxg_pad_max_depth= 100
nextflow_config - Config default value correct: params.smoothxg_poa_padding= 0.001
nextflow_config - Config default value correct: params.smoothxg_poa_params= 1,19,39,3,81,1
nextflow_config - Config default value correct: params.smoothxg_consensus_prefix= Consensus_
nextflow_config - Config default value correct: params.smoothxg_poa_cpus= 0
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.validationLenientMode= true
nextflow_config - Config default value correct: params.schema_ignore_params= igenomes_base
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 - docs/images/nf-core-pangenome_logo_light.png matches the template
files_unchanged - docs/images/nf-core-pangenome_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
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (175 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/plain'
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: fix-linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: linting.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 2024-03-14 11:12:40

.github/workflows/download_pipeline.yml

.github/workflows/linting.yml

CHANGELOG.md

README.md

nextflow_schema.json

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

subwaystation · 2024-03-14T11:14:48Z

@mashehu The linter was only unhappy with .github/workflows/linting.yml. I think I added all your suggestions, thanks!

heuermh

Tests ok for me on Docker!

.github/PULL_REQUEST_TEMPLATE.md

subwaystation · 2024-03-15T07:24:25Z

Thanks for the approval @heuermh !

heuermh · 2024-03-15T12:29:50Z

Thank you, @subwaystation, nice work!

subwaystation and others added 18 commits February 28, 2024 14:47

bump pipeline version to 1.2.0dev - LATÜRNICH

7b0d784

Merge pull request #181 from subwaystation/prepare_120

54af90f

bump pipeline version to 1.2.0dev - LATÜRNICH

Template update for nf-core/tools version 2.13.1

cf1a29b

fix wfmash v0.12.6 parameters

a68f506

give smoothxg more threads in hla.config

355329f

revert vg version back to 1.40 and update vg deconstruct code

b9ffbeb

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

853c2f3

merge template update 2.13.1

244a445

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

0f69e5d

Update nextflow.config

fae571a

Bug

Update nextflow.config

9250435

Merge pull request #182 from nf-core/nf-core-template-merge-2.13.1

2c3e231

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

Merge branch 'dev' into wfmash_0.12.6_parameters

5adbc20

Merge pull request #183 from nf-core/wfmash_0.12.6_parameters

7ebd370

fix wfmash v0.12.6 parameters and other bugs

bump bcftools to 1.19

d8f2aa7

Merge pull request #184 from nf-core/bcftools_1.19

f6f86fd

bump bcftools to 1.19

prepare 1.1.1 release

19ecf00

Merge pull request #185 from subwaystation/dev

c42285b

prepare 1.1.1 release

reflect vcf_spec changes also in the schema

fe7d639

subwaystation requested review from mashehu and heuermh March 14, 2024 10:29

subwaystation mentioned this pull request Mar 14, 2024

How to use Bgzip #167

Closed

mashehu requested changes Mar 14, 2024

View reviewed changes

subwaystation and others added 6 commits March 14, 2024 12:00

Update CHANGELOG.md

0ee3458

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

Update nextflow_schema.json

b2cb539

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

remove warning as suggested by review

b9434e3

Update nextflow_schema.json

c19f69a

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

Update .github/workflows/linting.yml

3071e95

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

revert liniting.yml review suggestion

57aa173

Update .github/workflows/download_pipeline.yml

5daf69e

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

subwaystation requested a review from mashehu March 14, 2024 12:09

mashehu approved these changes Mar 14, 2024

View reviewed changes

heuermh approved these changes Mar 14, 2024

View reviewed changes

.github/PULL_REQUEST_TEMPLATE.md Show resolved Hide resolved

subwaystation merged commit 7fb3047 into master Mar 15, 2024
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1.1.1 - LATÜRNICH #186

1.1.1 - LATÜRNICH #186

subwaystation commented Mar 14, 2024 •

edited

github-actions bot commented Mar 14, 2024 •

edited

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

subwaystation commented Mar 14, 2024

heuermh left a comment

subwaystation commented Mar 15, 2024

heuermh commented Mar 15, 2024

1.1.1 - LATÜRNICH #186

1.1.1 - LATÜRNICH #186

Conversation

subwaystation commented Mar 14, 2024 • edited

PR checklist

github-actions bot commented Mar 14, 2024 • edited

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

subwaystation commented Mar 14, 2024

heuermh left a comment

Choose a reason for hiding this comment

subwaystation commented Mar 15, 2024

heuermh commented Mar 15, 2024

subwaystation commented Mar 14, 2024 •

edited

github-actions bot commented Mar 14, 2024 •

edited

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