sentieon-bwamem #994

asp8200 · 2023-04-13T07:39:17Z

The new CI-tests for sentieon/bwamem are now passing.

Let me know what you think.

TO-DO: Update the changelog.

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).

…N_BWAMEM_MEM2_DRAGMAP_SENTIEON

github-actions · 2023-04-13T07:56:24Z

`nf-core lint` overall result: Passed ✅

Posted for pipeline commit cfab8d8

+| ✅ 151 tests passed       |+
#| ❔   9 tests were ignored |#

❔ 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/NfcoreSchema.groovy
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.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 manifest.version ends in dev: '3.2dev'
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 - .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: 22.10.1, Config: 22.10.1
readme - README Nextflow minimum version in Quick Start section matched config. README: 22.10.1, Config: 22.10.1
pipeline_todos - No TODO strings found
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: linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: awsfulltest_germline.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: pytest-workflow.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.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 2.7.2
Run at 2023-04-13 14:07:47

subworkflows/local/prepare_genome/main.nf

tests/config/tags.yml

maxulysse · 2023-04-13T09:15:08Z

workflows/sarek.nf

@@ -335,10 +335,13 @@ workflow SAREK {
    bwa                    = params.bwa                     ? Channel.fromPath(params.bwa).collect()       : PREPARE_GENOME.out.bwa
    bwamem2                = params.bwamem2                 ? Channel.fromPath(params.bwamem2).collect()   : PREPARE_GENOME.out.bwamem2
    dragmap                = params.dragmap                 ? Channel.fromPath(params.dragmap).collect()   : PREPARE_GENOME.out.hashtable
+    sentieon               = params.sentieon                ? Channel.fromPath(params.sentieon).collect()  : PREPARE_GENOME.out.sentieon


we should use params.bwa for that, the way I see it params.sentieon should only be a flag to allow usage of aligner sentieon-bwamem and the extra sentieon tools

Not sure I understand why we need params.sentieon.

basically select that you want to use bwa but the sentieon implementaion

but for that I would specify --aligner sentieon-bwamem

workflows/sarek.nf

.github/workflows/pytest-workflow.yml

conf/modules/prepare_genome.config

workflows/sarek.nf

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

…waindex stuff

maxulysse · 2023-04-13T14:48:20Z

I created a new sentieon branch from dev so that we can merge all sentieon related stuff all at once in dev once we're happy.

maxulysse · 2023-04-13T14:48:56Z

I'm thinking we might need to have do a release before we actually finish sentieon, so just to be on the safe side

asp8200 added 6 commits April 12, 2023 10:46

WIP: Adding the aligner sentieon-bwamem to new subworkflow FASTQ_ALIG…

5bd487b

…N_BWAMEM_MEM2_DRAGMAP_SENTIEON

Minor adjustments for sentieon bwamem

a564940

Setting up CI-test of sentieon-bwamem

49ad6a3

Adding package cryptography to python env

245fcc2

Blackened

621d9dc

Moving license_message.py

037030b

asp8200 requested a review from maxulysse as a code owner April 13, 2023 07:39

maxulysse mentioned this pull request Apr 13, 2023

DRAFT: Adding sentieon-bwamem #991

Closed

9 tasks

maxulysse reviewed Apr 13, 2023

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maxulysse reviewed Apr 13, 2023

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maxulysse reviewed Apr 13, 2023

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asp8200 added 2 commits April 13, 2023 12:57

WIP: Trying to avoid using sentieon-bwaindex

409f9ec

Move sentieon/bwamem to aligner-section

745fa22

maxulysse reviewed Apr 13, 2023

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asp8200 and others added 4 commits April 13, 2023 14:51

Update conf/modules/prepare_genome.config

8bd20b3

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

Update workflows/sarek.nf

2b823ce

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

Update .github/workflows/pytest-workflow.yml

3fd474d

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

Fixing CI-test for sentieon/bwamem and getting rid of more sentieon/b…

cfab8d8

…waindex stuff

asp8200 changed the title ~~DRAFT: sentieon-bwamem~~ sentieon-bwamem Apr 13, 2023

asp8200 requested review from maxulysse and FriederikeHanssen April 13, 2023 14:27

maxulysse changed the base branch from dev to sentieon April 13, 2023 14:47

maxulysse approved these changes Apr 13, 2023

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maxulysse merged commit 543ef58 into sentieon Apr 13, 2023

maxulysse deleted the add_sentieon_bwamem branch April 13, 2023 15:18

edmundmiller added the sentieon label Dec 9, 2024

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sentieon-bwamem #994

sentieon-bwamem #994

asp8200 commented Apr 13, 2023 •

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github-actions bot commented Apr 13, 2023 •

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❔ Tests ignored:

✅ Tests passed:

Run details

maxulysse Apr 13, 2023

FriederikeHanssen Apr 13, 2023

asp8200 Apr 13, 2023

FriederikeHanssen Apr 13, 2023

asp8200 Apr 13, 2023

maxulysse commented Apr 13, 2023

maxulysse commented Apr 13, 2023

sentieon-bwamem #994

sentieon-bwamem #994

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asp8200 commented Apr 13, 2023 • edited Loading

PR checklist

github-actions bot commented Apr 13, 2023 • edited Loading

nf-core lint overall result: Passed ✅

❔ Tests ignored:

✅ Tests passed:

Run details

maxulysse Apr 13, 2023

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FriederikeHanssen Apr 13, 2023

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maxulysse commented Apr 13, 2023

maxulysse commented Apr 13, 2023

asp8200 commented Apr 13, 2023 •

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github-actions bot commented Apr 13, 2023 •

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`nf-core lint` overall result: Passed ✅