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

znorgaard · 2026-03-23T22:09:17Z

Closes #137

PR Overview

This PR adds an option to use non-random (or fixed) UMIs with fastqourum.
This is supported by an optional new column in the samplesheet which points to a file of known UMI sequences.
This allows the fixed list to be used for some samples but not all of them, or to use different fixed lists for different samples.

Pulled from the updated Usage.md:

When using UMI correction, consider setting --groupreadsbyumi_strategy Identity (or Paired with --groupreadsbyumi_edits 0 for duplex sequencing), since UMIs have already been corrected to exact known sequences. The pipeline will emit a warning if a fuzzy-matching strategy is used with corrected UMIs.

The pipeline will also report an error if you supply different UMI lists for the same "sample" (note for #147, this should be based on "library_id").

Test Data Overview

The test data for this was created by taking the existing randomer data for SRR6109255 and replacing the existing 10bp UMI and 1 constant base with an 8bp UMI from the xGen™ cfDNA & FFPE DNA Library Preparation Kit. Then a random 1bp substitution was introduced in ~10% of the UMI sequences.

In the final output test data, we expect to have fewer consensus reads due to the reduced number of available UMIs. However, the drop shouldn't be too drastic.

Running the Test Data

nextflow run main.nf -profile test,docker --outdir results_random
nextflow run main.nf -profile test_nonrandom,docker --outdir results_nonrandom

Evaluating the UMI Correction (and Synthetic data creation)

Non-Random Correct UMI Metrics

% cat SRR6109255.correct-umis-metrics.txt
umi	total_matches	perfect_matches	one_mismatch_matches	two_mismatch_matches	other_matches	fraction_of_matches	representation
AAGCACTG	1162	1050	112	0	0	0.02934	0.938895
ACCACGAT	1258	1090	168	0	0	0.031764	1.016463
ACGACTTG	1274	1148	126	0	0	0.032168	1.029391
ACGGAACA	1302	1146	156	0	0	0.032875	1.052015
ACGTTCAG	1214	1062	152	0	0	0.030653	0.980911
ACTAGGAG	1240	1134	106	0	0	0.03131	1.001919
ACTGAGGT	1232	1118	114	0	0	0.031108	0.995455
AGCGTGTT	1226	1110	116	0	0	0.030956	0.990607
ATCCAGAG	1240	1130	110	0	0	0.03131	1.001919
CAATGTGG	1202	1086	116	0	0	0.03035	0.971215
CGCATGAT	1228	1100	128	0	0	0.031007	0.992223
CGGCTAAT	1132	1032	100	0	0	0.028583	0.914655
CTGTTGAC	1204	1092	112	0	0	0.030401	0.972831
CTTAGGAC	1248	1114	134	0	0	0.031512	1.008383
GAAGGAAG	1312	1174	138	0	0	0.033128	1.060095
GAGACGAT	1190	1088	102	0	0	0.030047	0.961519
GATCGAGT	1144	1034	110	0	0	0.028886	0.924351
GATGTGTG	1204	1094	110	0	0	0.030401	0.972831
GATTACCG	1222	1094	128	0	0	0.030855	0.987375
GCACAACT	1274	1108	166	0	0	0.032168	1.029391
GCGTCATT	1284	1166	118	0	0	0.032421	1.037471
GCTATCCT	1292	1154	138	0	0	0.032623	1.043935
GTCGAAGA	1310	1188	122	0	0	0.033077	1.058479
GTGCCATA	1182	1080	102	0	0	0.029845	0.955055
GTTACGCA	1248	1128	120	0	0	0.031512	1.008383
NNNNNNNN	0	0	0	0	0	0	0
TCGCTGTT	1290	1182	108	0	0	0.032572	1.042319
TGAAGACG	1236	1140	96	0	0	0.031209	0.998687
TGGACTCT	1222	1096	126	0	0	0.030855	0.987375
TTCCAAGG	1200	1048	152	0	0	0.0303	0.969599
TTCGTTGG	1244	1114	130	0	0	0.031411	1.005151
TTGCAGAC	1272	1120	152	0	0	0.032118	1.027775
TTGCGAAG	1316	1186	130	0	0	0.033229	1.063327

We observe all the expected UMIs and they all have ~10% representation from reads with 1 mismatch.

Comparing the Grouping

Random

% cat SRR6109255.grouped-family-sizes.txt
family_size	count	fraction	fraction_gt_or_eq_family_size
1	6219	0.870399	1
2	799	0.111826	0.129601
3	104	0.014556	0.017775
4	22	0.003079	0.003219
5	1	0.00014	0.00014

Non-Random

% cat SRR6109255.grouped-family-sizes.txt

family_size	count	fraction	fraction_gt_or_eq_family_size
1	4185	0.735113	1
2	932	0.16371	0.264887
3	315	0.055331	0.101177
4	149	0.026172	0.045846
5	69	0.01212	0.019673
6	24	0.004216	0.007553
7	9	0.001581	0.003337
8	8	0.001405	0.001757
9	1	0.000176	0.000351
11	1	0.000176	0.000176

We (as expected) observe larger family sizes in the non-random data because we're using fewer UMIs resulting in more reads sharing coordinates and UMIs.

Comparing the Consensus BAMs

Random

% samtools flagstat SRR6109255.cons.unmapped.bam
13350 + 0 in total (QC-passed reads + QC-failed reads)
13350 + 0 primary
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
0 + 0 mapped (0.00% : N/A)
0 + 0 primary mapped (0.00% : N/A)
13350 + 0 paired in sequencing
6675 + 0 read1
6675 + 0 read2
0 + 0 properly paired (0.00% : N/A)
0 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

Non-random

% samtools flagstat SRR6109255.cons.unmapped.bam

9474 + 0 in total (QC-passed reads + QC-failed reads)
9474 + 0 primary
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
0 + 0 mapped (0.00% : N/A)
0 + 0 primary mapped (0.00% : N/A)
9474 + 0 paired in sequencing
4737 + 0 read1
4737 + 0 read2
0 + 0 properly paired (0.00% : N/A)
0 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

~30% reduction in consensus sequences in the non-random data as expected with the larger family sizes.

Comparing Filtered Aligned Consensus BAM

Random

% samtools flagstat SRR6109255.mapped.bam
13402 + 0 in total (QC-passed reads + QC-failed reads)
13350 + 0 primary
0 + 0 secondary
52 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
13293 + 0 mapped (99.19% : N/A)
13241 + 0 primary mapped (99.18% : N/A)
13350 + 0 paired in sequencing
6675 + 0 read1
6675 + 0 read2
13166 + 0 properly paired (98.62% : N/A)
13180 + 0 with itself and mate mapped
61 + 0 singletons (0.46% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

Non-Random

% samtools flagstat SRR6109255.mapped.bam
9525 + 0 in total (QC-passed reads + QC-failed reads)
9474 + 0 primary
0 + 0 secondary
51 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
9423 + 0 mapped (98.93% : N/A)
9372 + 0 primary mapped (98.92% : N/A)
9474 + 0 paired in sequencing
4737 + 0 read1
4737 + 0 read2
9302 + 0 properly paired (98.18% : N/A)
9314 + 0 with itself and mate mapped
58 + 0 singletons (0.61% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

We observe a similar map rate (slightly worse makes sense because we've created consensus across molecules by reducing the number of UMIs available -- more UMI collisions).

PR checklist

github-actions · 2026-03-23T22:10:51Z

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

Posted for pipeline commit 4060202

+| ✅ 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
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-fastquorum_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-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
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: 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-fastquorum_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/WorkflowFastquorum.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 ends in dev: 1.3.0dev
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
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
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 - .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/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
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_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: download_pipeline.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: branch.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: release-announcements.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: clean-up.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 2026-03-27 22:15:37

…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>

Verifies the pipeline fails with an informative error when multiple runs of the same sample specify different umi_file values in the samplesheet. 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 4 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>

test: add validation test for mismatched umi_file across sample runs

b4df205

Verifies the pipeline fails with an informative error when multiple runs of the same sample specify different umi_file values in the samplesheet. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

znorgaard marked this pull request as ready for review March 27, 2026 16:41

znorgaard requested a review from nh13 March 27, 2026 16:41

znorgaard assigned nh13 Mar 27, 2026

docs: update doc string

a06cb28

nh13 approved these changes Mar 27, 2026

View reviewed changes

Comment thread conf/test_mixed_umis.config Outdated

Comment thread subworkflows/local/utils_nfcore_fastquorum_pipeline/main.nf Outdated

doc: fix doc strings

4060202

znorgaard merged commit 4d3d4ab into dev Mar 27, 2026
20 checks passed

znorgaard deleted the zn_nonrandom_umi_support branch March 27, 2026 23:05

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

feat: add non-random UMI support#145

feat: add non-random UMI support#145
znorgaard merged 22 commits intodevfrom
zn_nonrandom_umi_support

znorgaard commented Mar 23, 2026 •

edited

Loading

Uh oh!

github-actions Bot commented Mar 23, 2026 •

edited

Loading

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

Conversation

znorgaard commented Mar 23, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

PR Overview

Test Data Overview

Running the Test Data

Evaluating the UMI Correction (and Synthetic data creation)

Comparing the Grouping

Comparing the Consensus BAMs

Comparing Filtered Aligned Consensus BAM

PR checklist

Uh oh!

github-actions Bot commented Mar 23, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

znorgaard commented Mar 23, 2026 •

edited

Loading

github-actions Bot commented Mar 23, 2026 •

edited

Loading

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