Features for 1.3.0 by atrull314 · Pull Request #100 · nf-core/scnanoseq

atrull314 · 2026-05-07T14:11:20Z

This PR contains the following new features for 1.3.0:

Added chopper as an alternative to Nanofilt
Reduced the amount of storage in teh work directory by minimizing the amount of times FASTQs are modified (i.e. splitting + uncompression)
Update template to 3.5.1
Update pipeline to use strict syntax
Upgraded IsoQuant and updated downstream steps to work with new output format.
Due to updates to Isoquant we also removed the splitting and merging of bams done for this step
ToulligQC, FastQC, and Nanocomp are now disabled by default due to not scaling well with updated Nanopore chemistries

PR checklist

…ting done in Isoquant subworkflow

gzip compression of temp fastq files and replaced nanofilt with chopper

…rmat

…-3.5.1

…ixing issue where multiqc was not being output correctly

Feature isoquant upgrade

…sta being a process channel

… parameter

Features for 1.3.0

nf-core-bot · 2026-05-07T14:12:05Z

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

github-actions · 2026-05-07T14:13:50Z

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

Posted for pipeline commit cea013b

+| ✅ 204 tests passed       |+
#| ❔   4 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   6 tests had warnings |!
-| ❌   1 tests failed       |-

Details

❌ Test failures:

version_consistency - The versioning is not consistent between container, release tag and config. Found manifest.version = 1.2.2, nfcore_yml.version = 1.0.0

❗ Test warnings:

pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
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!
included_configs - Pipeline config does not include custom configs. Please add the includeConfig line.

❔ Tests ignored:

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 fixed:

rocrate_readme_sync - Mismatch fixed: RO-Crate description updated from README.md.

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
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/nf-test.yml
files_exist - File found: .github/actions/get-shards/action.yml
files_exist - File found: .github/actions/nf-test/action.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: nf-test.config
files_exist - File found: tests/default.nf.test
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 found: ro-crate-metadata.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: 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 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 variable (correctly) not found: validation.failUnrecognisedParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedHeaders
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 does not contain dev for release: 1.2.2
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.no_blaze_demux= true
nextflow_config - Config default value correct: params.dedup_tool= umitools
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.skip_bam_nanocomp= 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/
nf_test_content - 'tests/default.nf.test' contains outdir parameter
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/nextflow.config' contains modules_testdata_base_path
nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
nf_test_content - 'nf-test.config' sets a testsDir
nf_test_content - 'nf-test.config' sets a workDir
nf_test_content - 'nf-test.config' sets a configFile
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-scnanoseq_logo_light.png matches the template
files_unchanged - docs/README.md matches the template
actions_nf_test - '.github/workflows/nf-test.yml' is triggered on expected events
actions_nf_test - '.github/workflows/nf-test.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: 25.04.0, Config: 25.04.0
readme - README nf-core template version badge found.
readme - README Zenodo placeholder was replaced with DOI.
pipeline_if_empty_null - No ifEmpty(null) strings found
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_comment.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: release-announcements.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 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'
local_component_structure - local subworkflows directory structure is correct 'subworkflows/local/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: 3.5.1
rocrate_readme_sync - RO-Crate description matches the README.md.

Run details

nf-core/tools version 3.5.1
Run at 2026-05-07 14:13:23

lianov · 2026-05-08T13:16:00Z

@atrull314 : metro needs to be updated to reflect the change from nanofilt to chopper

nick-youngblut and others added 30 commits May 13, 2025 14:05

Added chopper; gzip'd split fastq files

6a6b967

fixed '--split_amount 0' bug for CHOPPER

bfe3388

Template update for nf-core/tools version 3.3.1

8b9154c

Template update for nf-core/tools version 3.3.2

ad6eca7

Template update for nf-core/tools version 3.4.1

f8fa4cd

Template update for nf-core/tools version 3.5.1

09b8c33

Merge branch 'dev' into dev-compress-fq

9dfeca2

Removing redundant modules and clean up

59d0b0d

Cleanup cat_fastq

cceb0e8

Fixing linting

0996a38

(#93) Initial work to upgrade isoquant and remove the chromsome split…

032f7ad

…ting done in Isoquant subworkflow

Adding patch for cat/fastq

9c44fb6

fixes issue #83

6b2707f

Adding missing split_seq into modules.conf

83099b8

Linting

ce8ead3

Merge pull request #65 from nick-youngblut/dev-compress-fq

a69a591

gzip compression of temp fastq files and replaced nanofilt with chopper

added no_blaze_demux option, closes issue #87

4c41ab5

changed skip_bam_nanocomp default

c78a0b2

Merge branch 'dev' of https://github.com/nf-core/scnanoseq into dev

2fdab8c

Fixing silent error that resulted in files not being split correctly

2447ec7

Adding work so that Seurat is able to read the new Isoquant matrix fo…

2ff34f9

…rmat

Removing debug

c425d60

Fixing isoquant flags

b6fe288

updated all modules and subworkflows, mostly for syntax needs

66715b5

re-added module patches and changed to strict syntax where needed

84eecc0

updates to strict syntax in al local modules and subworkflows

4b55b24

Merge remote-tracking branch 'origin/dev' into nf-core-template-merge…

dac11a3

…-3.5.1

Reordering structure of modules

784846c

Reorging subworkflows

94252d5

initial pass for module.config syntax changes

e6c855c

atrull314 and others added 23 commits April 22, 2026 20:17

Merge branch 'dev' into feature_isoquant_upgrade

936d7a0

Fixing issues with isoquant upgrade

5e023fc

Merge branch 'dev' into feature_isoquant_upgrade

a49e18d

Fixing issues where umitools dedup would not merge bams correctly + F…

aaa9d50

…ixing issue where multiqc was not being output correctly

Merge pull request #8 from U-BDS/feature_isoquant_upgrade

4cf2734

Feature isoquant upgrade

Linting

11111de

Reverting isoquant versions

de9f1d4

Prettier modules.json

6efcace

Fixing manifest version

5db6bfb

Fixing linting

cadfd10

Updating fastqc

2bad313

Upgrading isoquant

692487a

Fixing issue where not all samples were being processed due to the fa…

c70484a

…sta being a process channel

Adding versions to multiqc

d76812e

Fixing isoquant results organization and fixing warning about genomes…

2ff2e80

… parameter

Upgrading process label on Isoquant and fixing conda version

d8a4a5f

Disabling fastqc and nanocomp by default due to runtime issues

0ca451b

Removing trailing whitespace

2cfea94

Increasing minimum nextflow version

9612227

Committing test snapshot and reverting minimum nextflow version

9239543

Temporarily disabling nf-test for now

266c6d7

Prettier-ing nf-core.yml

17da1d5

Merge pull request #98 from U-BDS/dev

cea013b

Features for 1.3.0

atrull314 assigned atrull314 and unassigned atrull314 May 7, 2026

atrull314 requested a review from lianov May 7, 2026 16:40

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Features for 1.3.0#100

Features for 1.3.0#100
atrull314 wants to merge 61 commits intomasterfrom
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atrull314 commented May 7, 2026

Uh oh!

nf-core-bot commented May 7, 2026

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github-actions Bot commented May 7, 2026

❌ Test failures:

❗ Test warnings:

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

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lianov commented May 8, 2026 •

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atrull314 commented May 7, 2026

PR checklist

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github-actions Bot commented May 7, 2026

nf-core pipelines lint overall result: Failed ❌

❌ Test failures:

❗ Test warnings:

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

Run details

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lianov commented May 8, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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

lianov commented May 8, 2026 •

edited

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