Feature/elprep #41

matthdsm · 2022-12-23T08:54:00Z

PR checklist

matthdsm · 2022-12-23T08:55:18Z

This one should work but has a filename collision in ELPREP, we should fix $prefix for the aligner process

github-actions · 2022-12-23T08:55:39Z

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

Posted for pipeline commit 1086fdf

+| ✅ 126 tests passed       |+
#| ❔  18 tests were ignored |#
!| ❗   3 tests had warnings |!

Details

❗ Test warnings:

files_exist - File not found: lib/WorkflowNf-cmgg-preprocessing.groovy
pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
pipeline_name_conventions - Naming does not adhere to nf-core conventions: Contains non alphanumeric characters

❔ 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: assets/nf-core-nf-cmgg-preprocessing_logo_dark.png
files_exist - File is ignored: assets/nf-core-nf-cmgg-preprocessing_logo_light.png
files_exist - File is ignored: conf/test_full.config
files_exist - File is ignored: docs/images/nf-core-nf-cmgg-preprocessing_logo_dark.png
files_exist - File is ignored: docs/images/nf-core-nf-cmgg-preprocessing_logo_light.png
nextflow_config - Config variable ignored: manifest.name
nextflow_config - Config variable ignored: manifest.homePage
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/feature_request.yml
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
files_unchanged - File does not exist: assets/nf-core-nf-cmgg-preprocessing_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-nf-cmgg-preprocessing_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-nf-cmgg-preprocessing_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 or pyproject.toml
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/nf-cmgg-preprocessing/nf-cmgg-preprocessing/.github/workflows/awstest.yml

✅ 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: conf/modules.config
files_exist - File found: conf/test.config
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: 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-nf-cmgg-preprocessing_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.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.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 dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version ends in dev: '1.1.2dev'
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 - 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/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.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 - lib/nfcore_external_java_deps.jar matches the template
files_unchanged - lib/NfcoreSchema.groovy matches the template
files_unchanged - lib/NfcoreTemplate.groovy matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
readme - README Nextflow minimum version in Quick Start section matched config. README: 22.10.0, Config: 22.10.0
template_strings - Did not find any Jinja template strings (166 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
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: linting_comment.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 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.8.dev0
Run at 2023-01-20 06:59:36

Use UGent S3 reference data in iGenomes

subworkflows/local/fastq_to_cram/main.nf

nvnieuwk · 2023-01-19T13:48:56Z

subworkflows/local/fastq_to_cram/main.nf

        ]
    }
-    .groupTuple( by: [0])
+    .groupTuple(by:[0])


No group size here?

dammit! missed that one

size is in the groupKey!

Yep I'm blind!

Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>

nvnieuwk · 2023-01-19T13:51:32Z

Also adding a test for elprep and bamsormadup would be good I think?

matthdsm · 2023-01-19T13:55:49Z

I'm adding unit tests for everything in another branch

nvnieuwk

LGTM then!

matthdsm added 3 commits December 22, 2022 14:41

replace bamsormadup with elprep

aa10d7c

fix config

db06c9c

fix groupKey

1f250ab

matthdsm linked an issue Dec 23, 2022 that may be closed by this pull request

Eval elprep vs bamsormadup #34

Closed

matthdsm added 24 commits January 18, 2023 10:47

update fastp processing

26b6d85

fix concurrentModification error

7f587b1

bump modules

be9d670

update coverage for new mosdepth module

584be24

fix for empty keys in RG

95216bc

Feat/ugent igenomes (#42)

eb9946a

Use UGent S3 reference data in iGenomes

add e-amil config

cba192c

fix issue with coverage subwf

c7acddf

drop fast mode from collectWGSmetrics

67d46ef

bump snap aligner

727d802

update snap config

95a182e

coverage syntax fix

d623dcf

improve logging

0d58358

set default email

2a52a62

fix bamqc

0c58bb7

various fixes for conditionals

eda3093

final fixes for QC

b87c20f

fix snap config

80bbb0c

throw more mem at picard

cfe0380

update mosdepth settings

2b9a6d4

fix mosdepth to 4 cpus

dec0a95

update bclconvert MQC config

5d2575f

bump version to dev

d84660d

fix configs

554223b

Base automatically changed from dev to main January 18, 2023 14:11

matthdsm added 5 commits January 18, 2023 15:34

hotfix for flowcell fastq grouping

ecc453a

drop lane meta value

034afbf

typo

f67d929

fix linting

9e6d469

bump version

07ec358

matthdsm changed the base branch from main to dev January 18, 2023 14:35

matthdsm added 8 commits January 18, 2023 15:36

Merge branch 'dev' into feature/elprep

e6ab947

add "postprocessor" option

9c40b7c

drop groupKey logic

96d2c6c

re-add lane info

080a668

fix fastp split read parsing

befc2ad

fix input fastq sample counting

fede95c

re-add groupkey

7fd9f83

add sormadup import

23068d0

matthdsm requested a review from nvnieuwk January 19, 2023 13:42

matthdsm marked this pull request as ready for review January 19, 2023 13:44

prettier

c5cc82d

nvnieuwk reviewed Jan 19, 2023

View reviewed changes

matthdsm and others added 2 commits January 19, 2023 14:50

update changelog

ae49390

N!ce

53c62b2

Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>

nvnieuwk approved these changes Jan 19, 2023

View reviewed changes

matthdsm added 3 commits January 19, 2023 15:38

prettier

28caa2e

fix read sorting for SE data

76ec89a

set default postprocessor to bamsormadup

1086fdf

matthdsm merged commit c7a0925 into dev Jan 20, 2023

matthdsm deleted the feature/elprep branch January 20, 2023 07:25

matthdsm mentioned this pull request Jan 20, 2023

Grouping doesn't work with flowcell inputs #46

Closed

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Feature/elprep #41

Feature/elprep #41

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matthdsm commented Dec 23, 2022 •

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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matthdsm commented Dec 23, 2022 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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PR checklist

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matthdsm commented Dec 23, 2022

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nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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matthdsm commented Dec 23, 2022 •

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