Organize into subworkflows by alyssa-ab · Pull Request #59 · nf-core/viralintegration

alyssa-ab · 2023-03-28T20:44:07Z

Closes #58

github-actions · 2023-03-28T20:45:43Z

`nf-core lint` overall result: Failed ❌

Posted for pipeline commit c4603b5

+| ✅ 157 tests passed       |+
!| ❗   5 tests had warnings |!
-| ❌   4 tests failed       |-

Details

❌ Test failures:

files_unchanged - .github/CONTRIBUTING.md does not match the template
files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
files_unchanged - .github/workflows/linting.yml does not match the template
files_unchanged - lib/NfcoreTemplate.groovy does not match the template

❗ Test warnings:

pipeline_todos - TODO string in README.md: Add full-sized test dataset and amend the paragraph below if applicable
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 awsfulltest.yml: You can customise AWS full pipeline tests as required
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

✅ 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-viralintegration_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-viralintegration_logo_light.png
files_exist - File found: docs/images/nf-core-viralintegration_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/WorkflowViralintegration.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: 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-viralintegration_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: 0.1.1dev
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
nextflow_config - nextflow.config contains configuration profile test
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/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/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 - assets/nf-core-viralintegration_logo_light.png matches the template
files_unchanged - docs/images/nf-core-viralintegration_logo_light.png matches the template
files_unchanged - docs/images/nf-core-viralintegration_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 - .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
readme - README Zenodo placeholder was replaced with DOI.
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/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: clean-up.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: branch.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: awsfulltest.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' 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 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.11
Run at 2023-12-20 00:54:27

Co-authored-by: Mariana Dias Guilardi <mariguilardi@users.noreply.github.com>

Co-authored-by: Mariana Guilardi <diasgmariana@gmail.com>

Co-authored-by: Mariana Dias Guilardi <mariguilardi@users.noreply.github.com>

Co-authored-by: Mariana Guilardi <diasgmariana@gmail.com>

No reason to diverge from upstream on these, it's just a STAR problem.

lpantano · 2026-03-05T18:59:50Z

Hi, I am closing this PR since is too old. Feel free to reopen with updated code to get the tests passing. Sorry we didn't get to merge on time.

alyssa-ab marked this pull request as ready for review November 28, 2023 15:47

edmundmiller self-requested a review December 19, 2023 20:40

edmundmiller assigned alyssa-ab Dec 19, 2023

alyssa-ab and others added 26 commits December 19, 2023 15:03

Build: HOST_STAR Subworkflow

46a4dcc

Co-authored-by: Mariana Dias Guilardi <mariguilardi@users.noreply.github.com>

Build: HOST_STAR Subworkflow

74b253c

Co-authored-by: Mariana Dias Guilardi <mariguilardi@users.noreply.github.com>

host: add trimmers

eb09470

Build: PLUS subworkflow

c66345c

Co-authored-by: Mariana Guilardi <diasgmariana@gmail.com>

HOST: remove unneeded emissions

6016ea8

PLUS: add junction emission

6afdead

PLUS: Add samtools

f714429

plus: add join bam_bai_junction

dd510ee

Co-authored-by: Mariana Dias Guilardi <mariguilardi@users.noreply.github.com>

reorganize workflow with subworkflows

bf3680d

Co-authored-by: Mariana Guilardi <diasgmariana@gmail.com>

subworkflows: rename STAR to match args

a3344a4

Co-authored-by: Mariana Guilardi <diasgmariana@gmail.com>

clean up main workflow

de860aa

build INSERTION_SITES subworkflow

4185391

build: validate subworkflow

77fc465

fix(validate): Add log_final to make Multiqc happy

9f35672

fix(host): add mqc_log for TRIMMOMATIC in MultiQC

136c021

build chimeric reads subworkflow

88ee4e3

Template update for nf-core/tools version 2.8

818c0fb

Template update for nf-core/tools version 2.9

aac112c

bug fix: rollback star and samtools version

487a09a

star/samtools: use matching mulled containers

fd28f0c

fix: Remove samtools diffs

09b7b5c

No reason to diverge from upstream on these, it's just a STAR problem.

fix prettier

f1eb5cc

fix prettier

818e702

fix prettier + html functionality

427cb74

chore: bump date

f9e7b8e

update README and modules.json

bef7644

alyssa-ab and others added 16 commits December 19, 2023 15:11

run prettier

613c306

add nf-validaiton for input

9347341

clean up README + CHANGELOG

43b7211

update gitignore

d51216e

fix linting

82ba614

fix linting

bf9a9bf

fix nf-test config/names/snapshot

3077283

fix linting

6364077

Template update for nf-core/tools version 2.8

cf3305b

Template update for nf-core/tools version 2.9

d00e2f0

bug fix: rollback star and samtools version

8021014

star/samtools: use matching mulled containers

f922b2f

update README and modules.json

6ff6146

update modules

b5bb0ef

update snapshots of passing tests + script paths

630060e

fix prettier

c4603b5

edmundmiller force-pushed the star-subworkflows branch from 7a3aa1d to c4603b5 Compare December 20, 2023 00:53

lpantano closed this Mar 5, 2026

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Organize into subworkflows - #59

Organize into subworkflows#59
alyssa-ab wants to merge 42 commits into
devfrom
star-subworkflows

alyssa-ab commented Mar 28, 2023

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github-actions Bot commented Mar 28, 2023 •

edited

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❌ Test failures:

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lpantano commented Mar 5, 2026

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alyssa-ab commented Mar 28, 2023

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nf-core lint overall result: Failed ❌

❌ Test failures:

❗ Test warnings:

✅ Tests passed:

Run details

Uh oh!

lpantano commented Mar 5, 2026

Uh oh!

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github-actions Bot commented Mar 28, 2023 •

edited

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`nf-core lint` overall result: Failed ❌