nextflow-io/nf-schema

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Functionality for working with pipeline and sample sheet schema files in Nextflow pipelines

Stars: 57
Forks: 31
Open beginner issues: 0
Indexed issues: 39
Avg merge: 3d 17h
Merged PRs (30d): 1

Dominant language: Groovy
License: Apache-2.0
Last GitHub push: Aug 24, 2026
Latest indexed: Sep 19, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed

Beginner friendly Everything

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39 open issues indexed

Feature request: periodic progress logging during samplesheet validation Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 48/100

nextflow-io/nf-schema#224 · 2 comments · Opened Sep 15, 2026
Add `writeToSamplesheet` option using the json schema Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

nextflow-io/nf-schema#214 · 1 comment · Opened May 4, 2026
Feature: Publish methods as separate Maven package Open

feature request

Difficulty 5/5 Over a week Newbie friendliness 25/100

nextflow-io/nf-schema#203 · 1 reaction · Opened Feb 9, 2026
Clarify support for external $ref in nextflow_schema.json Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nextflow-io/nf-schema#202 · 9 comments · Opened Feb 8, 2026
Add `samplesheetToRecords` function Open

feature request

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nextflow-io/nf-schema#196 · Opened Jan 28, 2026
filter out containers from paramsSummaryLog Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nextflow-io/nf-schema#194 · 1 comment · Opened Jan 27, 2026
Comment out samplesheet line Open

enhancement

nextflow-io/nf-schema#193 · 3 comments · 1 assignee · Opened Jan 7, 2026
Expand numbers in scientific notation Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nextflow-io/nf-schema#190 · Opened Dec 9, 2025
Schema integrity check is not performed Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nextflow-io/nf-schema#187 · 5 comments · Opened Nov 8, 2025
Feature request: `samplesheetToMaps` function Open

feature request

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nextflow-io/nf-schema#186 · 5 comments · 1 reaction · Opened Nov 6, 2025
Support workbook format Open

enhancement

nextflow-io/nf-schema#177 · 3 comments · 1 reaction · 1 assignee · Opened Sep 12, 2025
Use `patternProperties` to match columns with a certain `prefix` Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 42/100

nextflow-io/nf-schema#176 · Opened Sep 10, 2025
Using --params-file command line option should raise an error but only a warning is raised Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nextflow-io/nf-schema#171 · 2 comments · Opened Aug 20, 2025
Top level `validate` function broken for `Path` type schema signature Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nextflow-io/nf-schema#169 · Opened Aug 15, 2025
Support `patternProperties` for data/samplesheet validation Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nextflow-io/nf-schema#164 · 3 comments · Opened Jul 23, 2025
(non default) option to only warn when validating URL Open

enhancement

nextflow-io/nf-schema#161 · 13 comments · 1 assignee · Opened Jul 7, 2025
Only fully empty column should be sanitised in CSV/TSV Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nextflow-io/nf-schema#160 · Opened Jul 7, 2025
samplesheetToList converting string values to integer in scientific notation Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nextflow-io/nf-schema#153 · 6 comments · Opened Jul 1, 2025
Implement localization of descriptive fields Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nextflow-io/nf-schema#152 · Opened Jun 27, 2025
required boolean parameter fails validation when set to false Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nextflow-io/nf-schema#143 · 3 comments · Opened May 21, 2025
`formatEntry` is broken when using `defs` in a samplesheet schema. Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 42/100

nextflow-io/nf-schema#136 · 6 comments · Opened May 6, 2025
Cryptic error message when input schema file is missing Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 48/100

nextflow-io/nf-schema#131 · 1 comment · Opened Apr 16, 2025
Add tests for cloud storage files Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nextflow-io/nf-schema#128 · Opened Apr 7, 2025
Automatically replace `params` values in files during validation Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nextflow-io/nf-schema#127 · Opened Mar 26, 2025
Allow unspecified columns in samplesheet Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nextflow-io/nf-schema#126 · 1 comment · Opened Mar 24, 2025
Can we have a function to check spec version for the samplesheet? Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

nextflow-io/nf-schema#125 · 3 comments · Opened Mar 24, 2025
No possibility to read a single sample in yaml format for now. Open

Difficulty 3/5 1-2 days Newbie friendliness 38/100

nextflow-io/nf-schema#124 · 2 comments · Opened Mar 24, 2025
Warning message being created with nested parameters Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nextflow-io/nf-schema#119 · 3 comments · Opened Mar 13, 2025
Consider replacing `uniqueEntries` with the already standardised `uniqueKeys` Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

nextflow-io/nf-schema#107 · 4 comments · Opened Feb 13, 2025
Check schema against meta-schema Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

nextflow-io/nf-schema#101 · 2 comments · Opened Feb 3, 2025
Parameter -resume doesn't work after --help execution Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nextflow-io/nf-schema#96 · 9 comments · Opened Jan 31, 2025
Improve docs with more 'applied' examples Open

documentation

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nextflow-io/nf-schema#94 · 3 comments · Opened Jan 22, 2025
improvement for error/warning message for wrong delimiter Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 38/100

nextflow-io/nf-schema#88 · Opened Jan 16, 2025
Add a `listToSamplesheet` function Open

feature request

nextflow-io/nf-schema#87 · 2 comments · 1 reaction · 1 assignee · Opened Jan 16, 2025
Idea: Validate parameters when the parameter has been changed Open

feature request

Difficulty 5/5 Over a week Newbie friendliness 25/100

nextflow-io/nf-schema#51 · 9 comments · 1 reaction · Opened Sep 3, 2024
Add smarter typecasting to the samplesheet converter Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 45/100

nextflow-io/nf-schema#50 · Opened Aug 27, 2024
Make validateParameters function assigns (optionally) default values defined in the schema Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nextflow-io/nf-schema#35 · 1 comment · 4 reactions · Opened May 27, 2024
Feature request: param concatenation into array Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nextflow-io/nf-schema#20 · 1 comment · Opened Sep 18, 2023
Class used in plugin can't be used in a `resume` run Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nextflow-io/nf-schema#23 · 18 comments · Opened Jun 9, 2023

nextflow-io/nf-schema

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