Update modules #822

FriederikeHanssen · 2022-11-09T22:50:44Z

TODO:

new dragmap version causes Segmentation fault
Run Mutect2 manual tests

PR checklist

This comment contains a description of changes (with reason).
If you've fixed a bug or added code that should be tested, add tests!
If you've added a new tool - have you followed the pipeline conventions in the contribution docs- [ ] If necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repository.
Make sure your code lints (nf-core lint).
Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
Usage Documentation in docs/usage.md is updated.
Output Documentation in docs/output.md is updated.
CHANGELOG.md is updated.
README.md is updated (including new tool citations and authors/contributors).

github-actions · 2022-11-09T22:59:57Z

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

Posted for pipeline commit 9da7e76

+| ✅ 151 tests passed       |+
#| ❔   8 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
schema_description - No description provided in schema for parameter: cnvkit_reference

❔ Tests ignored:

files_exist - File is ignored: conf/modules.config
files_exist - File is ignored: conf/test.config
files_exist - File is ignored: conf/test_full.config
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: lib/NfcoreTemplate.groovy
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: 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: 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: lib/nfcore_external_java_deps.jar
files_exist - File found: lib/NfcoreSchema.groovy
files_exist - File found: lib/NfcoreTemplate.groovy
files_exist - File found: lib/Utils.groovy
files_exist - File found: lib/WorkflowMain.groovy
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: lib/WorkflowSarek.groovy
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: .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: .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.show_hidden_params
nextflow_config - Config variable found: params.schema_ignore_params
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.version
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 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 manifest.version ends in dev: '3.1dev'
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
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/README.md matches the template
files_unchanged - lib/nfcore_external_java_deps.jar matches the template
files_unchanged - lib/NfcoreSchema.groovy 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: 21.10.3, Config: 21.10.3
readme - README Nextflow minimum version in Quick Start section matched config. README: 21.10.3, Config: 21.10.3
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
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: pytest-workflow.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: awsfulltest_germline.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: awstest.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' 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 2.6
Run at 2022-11-13 22:27:20

maxulysse · 2022-11-10T10:54:05Z

Can you add such a section with the newly updated tools:
https://github.com/nf-core/sarek/blob/dev/CHANGELOG.md#dependencies

workflows/sarek.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

FriederikeHanssen · 2022-11-10T15:51:05Z

Run nf-core/setup-nextflow@v1
Error: Could not retrieve Nextflow release matching 21.10.3.
API rate limit exceeded for installation ID 1565271.
Error: Could not parse the download URL
Cannot read properties of undefined (reading 'filter')
Error: versionSpec parameter is required
Warning: Nextflow appears to have installed correctly, but an error was thrown while running it.

that time of the week again

CHANGELOG.md

modules/local/sambamba.nf

maxulysse

Looking good

FriederikeHanssen · 2022-11-11T14:52:07Z

not sure whats up with all the test failures picked some random ones to run locally and they worked fine.

FriederikeHanssen · 2022-11-13T17:05:31Z

ok think I found all to update, only one missing is svdb (some issues with getting the tests to pass with the new version) and VEP potentially

tests/csv/3.0/tumor_mutational_burden.csv

FriederikeHanssen · 2022-11-13T21:55:38Z

Ran mutect2 manual tests as well, look fine

modules/nf-core/dragmap/align/dragmap-align.diff

update easy modules

9b391b5

FriederikeHanssen added 4 commits November 10, 2022 00:16

update mappers

77db1e7

update mappers

0a09464

Merge remote-tracking branch 'origin/modules_update' into modules_update

c509474

update markduplicates

d73d32e

FriederikeHanssen added 6 commits November 10, 2022 12:16

fix dragmap index

f50d9d4

update tiddit

66ae278

update changelog

8c88760

correct versions

92fc3d4

merge upstream/dev

4014ded

Update fastp

008ba1f

maxulysse reviewed Nov 10, 2022

View reviewed changes

workflows/sarek.nf Outdated Show resolved Hide resolved

FriederikeHanssen and others added 2 commits November 10, 2022 16:48

UPdate samtools view

2f03e4a

Update workflows/sarek.nf

2fedc52

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

maxulysse reviewed Nov 10, 2022

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CHANGELOG.md Outdated Show resolved Hide resolved

maxulysse reviewed Nov 10, 2022

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CHANGELOG.md Outdated Show resolved Hide resolved

FriederikeHanssen added 7 commits November 10, 2022 16:59

update samtools/collatefastq

a33a2c2

comment empty input channels

e1347a9

update deepvariant

b27f0df

Update bcftools

deb4ed4

Update freebayes

382b1f7

merge upstream/dev

7f3e8b0

update CHANGELOG

e03d837

maxulysse reviewed Nov 11, 2022

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maxulysse reviewed Nov 11, 2022

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FriederikeHanssen added 2 commits November 11, 2022 12:43

fix channel input

e7b76e3

remove accidental sambamba addition

6f0b61a

FriederikeHanssen added 2 commits November 11, 2022 14:59

update dragmap

5de1bfb

uuuuugh more meta2 map issues

1d8065b

FriederikeHanssen added 2 commits November 12, 2022 00:46

formatting

c9967ab

update samtools

4495e34

some checksums

835c11b

maxulysse reviewed Nov 13, 2022

View reviewed changes

tests/csv/3.0/tumor_mutational_burden.csv Outdated Show resolved Hide resolved

FriederikeHanssen added 4 commits November 13, 2022 20:46

remove tmb test files

0f8cb71

dragen test always using docker

01843c0

dragmap update causes segementation fault

750bc31

new dragmpa version has segmentation dump faults

bd2884b

FriederikeHanssen added 3 commits November 13, 2022 23:25

dragmap version was never reported

9da7e76

md5sums

f7b05dd

update changelog

edc29d3

maxulysse reviewed Nov 14, 2022

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FriederikeHanssen marked this pull request as ready for review November 14, 2022 19:17

maxulysse approved these changes Nov 14, 2022

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maxulysse merged commit 757ccaf into nf-core:dev Nov 14, 2022

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Update modules #822

Update modules #822

FriederikeHanssen commented Nov 9, 2022 •

edited

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github-actions bot commented Nov 9, 2022 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

maxulysse commented Nov 10, 2022

FriederikeHanssen commented Nov 10, 2022

maxulysse left a comment

FriederikeHanssen commented Nov 11, 2022

FriederikeHanssen commented Nov 13, 2022

FriederikeHanssen commented Nov 13, 2022

Update modules #822

Update modules #822

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FriederikeHanssen commented Nov 9, 2022 • edited Loading

PR checklist

github-actions bot commented Nov 9, 2022 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

maxulysse commented Nov 10, 2022

FriederikeHanssen commented Nov 10, 2022

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FriederikeHanssen commented Nov 11, 2022

FriederikeHanssen commented Nov 13, 2022

FriederikeHanssen commented Nov 13, 2022

FriederikeHanssen commented Nov 9, 2022 •

edited

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