DSL2: Qualimap #998

jbv2 · 2023-06-09T09:39:10Z

Closes #997

PR checklist

github-actions · 2023-06-09T10:08:00Z

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

Posted for pipeline commit b032ef7

+| ✅ 156 tests passed       |+
!| ❗  18 tests had warnings |!

❗ Test warnings:

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: Include a figure that guides the user through the major workflow steps. Many nf-core
pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline
pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
pipeline_todos - TODO string in base.config: Check the defaults for all processes
pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
pipeline_todos - TODO string in test_humanbam.config: Specify the paths to your test data on nf-core/test-datasets
pipeline_todos - TODO string in test_humanbam.config: Give any required params for the test so that command line flags are not needed
pipeline_todos - TODO string in test.config: Specify the paths to your test data on nf-core/test-datasets
pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
schema_description - No description provided in schema for parameter: skip_damage_calculation

✅ 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-eager_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-eager_logo_light.png
files_exist - File found: docs/images/nf-core-eager_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/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/WorkflowEager.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-eager_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.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 manifest.version ends in dev: 3.0.0dev
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 - assets/nf-core-eager_logo_light.png matches the template
files_unchanged - docs/images/nf-core-eager_logo_light.png matches the template
files_unchanged - docs/images/nf-core-eager_logo_dark.png 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/NfcoreTemplate.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: 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 (185 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: ci.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: awsfulltest.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: awstest.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 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 2.9
Run at 2023-07-14 09:16:53

scarlhoff

Looks good already, just needs some more channel manipulation to integrate module into the workflow and minor other changes. Please also check that the test profiles actually execute the qualimap module :)

conf/modules.config

docs/output.md

CITATIONS.md

nextflow_schema.json

workflows/eager.nf

Co-authored-by: Selina Carlhoff <[email protected]>

scarlhoff

Some minor things, mainly add meta to snp capture bed and tag&ext.prefix in the modules.config

docs/output.md

nextflow_schema.json

workflows/eager.nf

conf/modules.config

Co-authored-by: Selina Carlhoff <[email protected]>

Waiting for CI test Co-authored-by: Selina Carlhoff <[email protected]>

conf/modules.config

nextflow_schema.json

workflows/eager.nf

conf/modules.config

docs/output.md

nextflow_schema.json

workflows/eager.nf

TCLamnidis · 2023-06-30T12:46:39Z

workflows/eager.nf

+            }
+            .combine(
+                by: 0,
+                snpcapture_bed_input


See my previous comment. Since ch_snpcapture_bed lacks a meta, all this will likely create an empty channel and hence won't run the module. Once the meta is added, things should go through the module.

Make sense. I think now meta is there

The module still doesn't seem to execute in the tests.

docs/output.md

Co-authored-by: Thiseas C. Lamnidis <[email protected]>

jfy133 · 2023-07-14T10:01:43Z

Closing in favouer of #1011

jbv2 and others added 5 commits June 2, 2023 13:15

Adding first version of qualimap (not functional yet)

2811ea3

adding snpcapture as channel

b4da458

changing mqc output

56f9ae6

Merge branch 'dev' into qualimap

5e5d357

minor changes, waiting for docker

fe23a31

TCLamnidis requested a review from scarlhoff June 9, 2023 13:13

scarlhoff requested changes Jun 12, 2023

View reviewed changes

TCLamnidis linked an issue Jun 16, 2023 that may be closed by this pull request

DSL2: Add qualimap module #997

Closed

TCLamnidis changed the title ~~Qualimap~~ DSL2: Qualimap Jun 16, 2023

TCLamnidis added the DSL2 label Jun 16, 2023

jbv2 and others added 2 commits June 23, 2023 10:19

Apply suggestions from code review

10c6d2d

Co-authored-by: Selina Carlhoff <[email protected]>

Apply suggestions from code review

0014cd0

Co-authored-by: Selina Carlhoff <[email protected]>

jbv2 requested a review from scarlhoff June 23, 2023 09:04

scarlhoff requested changes Jun 23, 2023

View reviewed changes

jbv2 and others added 2 commits June 30, 2023 10:12

Apply suggestions from code review

f4797ed

Co-authored-by: Selina Carlhoff <[email protected]>

prettier

f00573b

jbv2 requested a review from a team June 30, 2023 08:58

Apply suggestions from code review

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Waiting for CI test Co-authored-by: Selina Carlhoff <[email protected]>

jbv2 commented Jun 30, 2023

View reviewed changes

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nextflow_schema.json Outdated Show resolved Hide resolved

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jbv2 added 4 commits June 30, 2023 11:13

Apply suggestions from code review

31f473f

minor changes after merging reviews

8e053c4

removing duplicated code lines

c4c1daa

removing duplicated code lines

89776d8

TCLamnidis requested changes Jun 30, 2023

View reviewed changes

jbv2 and others added 5 commits July 6, 2023 16:32

Apply suggestions from code review

4ddc639

Co-authored-by: Thiseas C. Lamnidis <[email protected]>

Apply suggestions from code review

937e96a

Merge branch 'qualimap' of https://github.com/jbv2/eager into qualimap

5bcc7ff

Apply suggestions from code review

c5bacf3

Co-authored-by: Thiseas C. Lamnidis <[email protected]>

Adding warning

a45be9d

jbv2 and others added 10 commits July 6, 2023 16:50

Merge branch 'qualimap'

f033a4c

Adding map to snpcapture

6db6d45

adding map to snpcapture

57a9e49

prettier

727b98f

Merge branch 'dev' into qualimap

2d7f9b9

Update nextflow_schema.json

6f3344f

Co-authored-by: Thiseas C. Lamnidis <[email protected]>

removing duplicate lines

51f4853

Merge branch 'qualimap' of https://github.com/jbv2/eager into qualimap

fcfa34f

Merge branch 'dev' into qualimap

c84d68f

readd qualimap

b032ef7

jfy133 marked this pull request as draft July 14, 2023 09:17

jfy133 closed this Jul 14, 2023

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DSL2: Qualimap #998

DSL2: Qualimap #998

jbv2 commented Jun 9, 2023 •

edited by TCLamnidis

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github-actions bot commented Jun 9, 2023 •

edited

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❗ Test warnings:

✅ Tests passed:

Run details

scarlhoff left a comment •

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scarlhoff left a comment

TCLamnidis Jun 30, 2023

jbv2 Jul 6, 2023

TCLamnidis Jul 7, 2023

jfy133 commented Jul 14, 2023

DSL2: Qualimap #998

DSL2: Qualimap #998

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jbv2 commented Jun 9, 2023 • edited by TCLamnidis Loading

PR checklist

github-actions bot commented Jun 9, 2023 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

Run details

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TCLamnidis Jun 30, 2023

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jfy133 commented Jul 14, 2023

jbv2 commented Jun 9, 2023 •

edited by TCLamnidis

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edited

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

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