feat: add non-random UMI support by znorgaard · Pull Request #145 · nf-core/fastquorum

znorgaard · 2026-03-23T22:09:17Z

Closes #137

PR checklist

github-actions · 2026-03-23T22:10:51Z

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

Posted for pipeline commit 44c9a71

+| ✅ 205 tests passed       |+
#| ❔  10 tests were ignored |#
!| ❗   1 tests had warnings |!

Details

❗ Test warnings:

files_unchanged - LICENSE does not match the template

❔ 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: conf/modules/modules.config
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
files_unchanged - File ignored due to lint config: assets/nf-core-fastquorum_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-fastquorum_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
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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
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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
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files_exist - File found: .github/actions/get-shards/action.yml
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files_exist - File found: .github/workflows/linting_comment.yml
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files_exist - File found: assets/nf-core-fastquorum_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
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files_exist - File found: docs/images/nf-core-fastquorum_logo_light.png
files_exist - File found: docs/images/nf-core-fastquorum_logo_dark.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
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files_exist - File found: docs/usage.md
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files_exist - File found: tests/default.nf.test
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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: modules.json
files_exist - File found: ro-crate-metadata.json
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
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files_exist - File not found check: conf/aws.config
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files_exist - File not found check: lib/Checks.groovy
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files_exist - File not found check: lib/Workflow.groovy
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files_exist - File not found check: lib/WorkflowFastquorum.groovy
files_exist - File not found check: parameters.settings.json
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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
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nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
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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/
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nextflow_config - Config dag.file ended with .html
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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.mode= rd
nextflow_config - Config default value correct: params.correct_umis_max_mismatches= 2
nextflow_config - Config default value correct: params.correct_umis_min_distance= 1
nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
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
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files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/CONTRIBUTING.md matches the template
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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/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 - docs/images/nf-core-fastquorum_logo_light.png matches the template
files_unchanged - docs/README.md matches the template
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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_todos - No TODO strings found
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: branch.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
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actions_schema_validation - Workflow validation passed: nf-test.yml
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actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: release-announcements.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'
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 - BWA_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_FAIDX found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_DICT found in conf/modules.config and Nextflow scripts.
modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
modules_config - FASTQTOBAM found in conf/modules.config and Nextflow scripts.
modules_config - CORRECTUMIS found in conf/modules.config and Nextflow scripts.
modules_config - ALIGN_RAW_BAM found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_BAM found in conf/modules.config and Nextflow scripts.
modules_config - GROUPREADSBYUMI found in conf/modules.config and Nextflow scripts.
modules_config - COLLECTDUPLEXSEQMETRICS found in conf/modules.config and Nextflow scripts.
modules_config - CALLDDUPLEXCONSENSUSREADS found in conf/modules.config and Nextflow scripts.
modules_config - CALLANDFILTERDUPLEXCONSENSUSREADS found in conf/modules.config and Nextflow scripts.
modules_config - FILTERCONSENSUSREADS found in conf/modules.config and Nextflow scripts.
modules_config - ALIGN_CONSENSUS_BAM found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC 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: 3.5.2
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.5.2
Run at 2026-03-23 22:55:20

…arams

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

…pport - Add nonrandom.nf.test: tests R&D and HT modes with fixed UMIs - Add mixed_umis.nf.test: tests mixed fixed/random UMI samples - Update test configs to use nf-core/test-datasets URLs - Use Paired strategy with edits=0 for nonrandom test Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

The previous approach parsed the CSV with new File() which silently fails for URL inputs. Now the warning fires from the workflow itself by checking the first item in the correct branch channel, which works regardless of whether the samplesheet is a local path or URL. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

znorgaard force-pushed the zn_nonrandom_umi_support branch from 190f274 to 9548ab5 Compare March 23, 2026 22:10

znorgaard changed the base branch from dev to nh13/switch-master-to-main March 23, 2026 22:12

Base automatically changed from nh13/switch-master-to-main to dev March 23, 2026 22:13

znorgaard and others added 16 commits March 23, 2026 15:26

feat: add optional umi_file column to samplesheet schema

30939d5

feat: validate umi_file consistency across runs of same sample

3b8abbb

feat: add FGBIO_CORRECTUMIS module

59dace6

feat: add CORRECTUMIS publishing config

bb05743

feat: add correct_umis_max_mismatches and correct_umis_min_distance p…

3d06cff

…arams

feat: wire CorrectUmis into workflow between FastqToBam and alignment

5771a58

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

feat: warn when grouping strategy may be suboptimal for corrected UMIs

d542a65

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

docs: document non-random UMI support and CorrectUmis outputs

21e064c

feat: add test configs for non-random and mixed UMI runs

f58df3f

fix branch reference

ccbaed3

chore: prettier

14695fb

fix: rename

826c827

docs: clarify strategy/edits reasoning in test configs

5b68fbd

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

refactor: consolidate CORRECTUMIS publishDir patterns

93fd81c

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

znorgaard force-pushed the zn_nonrandom_umi_support branch from 84097ec to 93fd81c Compare March 23, 2026 22:26

znorgaard and others added 3 commits March 23, 2026 15:38

chore: fix rename

0694370

docs: add changelog entry for non-random UMI support

f4aa6aa

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

test: add nf-test snapshots for nonrandom and mixed UMI tests

44c9a71

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

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feat: add non-random UMI support#145

feat: add non-random UMI support#145
znorgaard wants to merge 19 commits intodevfrom
zn_nonrandom_umi_support

znorgaard commented Mar 23, 2026 •

edited by clintval

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nf-core pipelines lint overall result: Passed ✅ ⚠️

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znorgaard commented Mar 23, 2026 •

edited by clintval

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