1.2.0 Updates #42

atrull314 · 2024-12-24T05:21:39Z

PR Checklist

This PR contains the following updates for v1.2.0 of the pipeline:

Adding oarfish as an additional quantifier
Parallelization of isoquant by splitting on chromosome
Upgrading isoquant
Allowing read counts to utilize nanocount stats
First pass at "modularizing" the pipeline by moving code to subworkflows

Updating dev versions to 1.1.0dev

…ization

…all na values are correctly set to 0

1.1.0 Updates

…run on just the genome, jsut the transcriptome, or both

Add in oarfish as additional quantification method

github-actions · 2024-12-24T05:23:52Z

`nf-core pipelines lint` overall result: Failed ❌

Posted for pipeline commit 5c964ec

+| ✅ 188 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗   3 tests had warnings |!
-| ❌   3 tests failed       |-

❌ Test failures:

nextflow_config - Config manifest.version should not contain dev for a release: 1.1.0dev
version_consistency - manifest.version was not numeric: 1.1.0dev!
included_configs - Pipeline config does not include custom configs. Please uncomment the includeConfig line.

❗ Test warnings:

pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
files_unchanged - File ignored due to lint config: docs/images/nf-core-scnanoseq_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-scnanoseq_logo_dark.png
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
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: 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-scnanoseq_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-scnanoseq_logo_light.png
files_exist - File found: docs/images/nf-core-scnanoseq_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: 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: conf/igenomes_ignored.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: modules.json
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: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
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: docs/images/nf-core-scnanoseq_logo.png
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/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowScnanoseq.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Found nf-schema plugin
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: validation.help.enabled
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 found: validation.help.beforeText
nextflow_config - Config variable found: validation.help.afterText
nextflow_config - Config variable found: validation.help.command
nextflow_config - Config variable found: validation.summary.beforeText
nextflow_config - Config variable found: validation.summary.afterText
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 variable (correctly) not found: params.max_cpus
nextflow_config - Config variable (correctly) not found: params.max_memory
nextflow_config - Config variable (correctly) not found: params.max_time
nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
nextflow_config - Config variable (correctly) not found: params.validationLenientMode
nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
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 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
nextflow_config - Config default value correct: params.igenomes_ignore= true
nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
nextflow_config - Config default value correct: params.split_amount= 0
nextflow_config - Config default value correct: params.min_length= 1
nextflow_config - Config default value correct: params.min_q_score= 10
nextflow_config - Config default value correct: params.kmer_size= 14
nextflow_config - Config default value correct: params.save_transcript_secondary_alignment= true
nextflow_config - Config default value correct: params.retain_introns= true
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
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 - 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-scnanoseq_logo_light.png matches the template
files_unchanged - docs/README.md 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: 24.04.2, Config: 24.04.2
readme - README Zenodo placeholder was replaced with DOI.
plugin_includes - No wrong validation plugin imports have been 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
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: template_version_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: ci.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 found and not ignored.
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 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'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 3.0.2
version_consistency - Version tags are numeric and consistent between container, release tag and config.

Run details

nf-core/tools version 3.0.2
Run at 2024-12-24 05:23:34

atrull314 and others added 30 commits October 7, 2024 10:40

Updating dev versions to 1.1.0dev

e2c8668

Template update for nf-core/tools version 3.0.0

474ca48

Template update for nf-core/tools version 3.0.1

d263368

Template update for nf-core/tools version 3.0.2

6b0496a

Merge pull request #2 from U-BDS/1.1.0_update

ba39bb4

Updating dev versions to 1.1.0dev

Implementing chromosome splitting of Isoquant to assist with parallel…

c7ba955

…ization

Modifications to reference file splitting

f0b1000

Changing mtx_merge to use barcodes as key to join on and making sure …

7845de0

…all na values are correctly set to 0

Adjusting outputs and cleanup

6a4093f

Fixing BLAZE custom config in README

54984fb

Fixing nodes in metro diagram

5aba04a

Upgrade isoquant version

bbfd70c

Merge branch 'feature_isoquant_performance' into dev

8233fc7

Allowing read counts to run if FastQC is disabled

5629165

Increasing resources for seurat step

2b9251d

Fixing linting errors

5a73588

Updating Documentation

3a40ec7

Update CHANGELOG.md

75e0240

Merging Template Update

068781a

Fixing linting issues

a7a3129

Fixing Harshil alignment

9732fd6

Merge pull request #40 from U-BDS/dev

e4b681d

1.1.0 Updates

Initial work to add in OARFISH and allow the pipeline to selectively …

fd93533

…run on just the genome, jsut the transcriptome, or both

Fixing multiQC issues

74e95fb

Removing comments and unused modules/subworkflows

8d6a241

Increasing memory for tag_barcodes

6a94f29

Adding check for genome_fa when preparing references

cf31ba3

Fixing order of creating genome fai

911087d

Various Fixes for multiqc report and test configs

3a9bef2

Fixing linting

7b81f3c

atrull314 and others added 25 commits December 13, 2024 11:00

Fixing prettier

86df3a6

Update output.md

48186b5

Update README.md

6bdbae0

Updating metro

fc09a47

Fixing markdown linting

057c3ac

Updating metro

674d689

Fixing issue when skip_dedup is used

3023e3a

Adding recommended flags for oarfish

c4db265

Add transcript fasta to test_full config

ed8d926

Temporary addition of new params

42c66de

Correcting variable name

78f5c29

Fixing umitools dedup issue

461407c

Fixing UMITOOLS_DEDUP issue

9059a41

Splitting save_secondary parameter between genome and transcriptome

3477e01

Fixing linting issues

c43897c

Update output.md

b0a8ddf

Updating CHANGELOG

f017f6f

Update usage.md

7363e6a

Update README.md

7fa82b4

Fixing dedup issue

5c2f8d4

Fixing alignment on tube map

4ea8c39

Update CITATIONS.md

902f5b1

documentation updates

7fdfd14

fixi harshil alignment and removal commented code

f1f1524

Merge pull request #41 from U-BDS/dev

5c964ec

Add in oarfish as additional quantification method

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1.2.0 Updates #42

1.2.0 Updates #42

atrull314 commented Dec 24, 2024

github-actions bot commented Dec 24, 2024

❌ Test failures:

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

1.2.0 Updates #42

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1.2.0 Updates #42

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atrull314 commented Dec 24, 2024

PR Checklist

github-actions bot commented Dec 24, 2024

nf-core pipelines lint overall result: Failed ❌

❌ Test failures:

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

`nf-core pipelines lint` overall result: Failed ❌