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Fix single bin size #21

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Merged
nvnieuwk merged 3 commits into from
Feb 16, 2026
Merged

Fix single bin size #21

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584bc71
fix single bin size
nvnieuwk Feb 16, 2026
a0de8ec
fix lint
nvnieuwk Feb 16, 2026
4c500a2
fix files_unchanged
nvnieuwk Feb 16, 2026
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6 changes: 3 additions & 3 deletions .github/workflows/linting.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ jobs:
pre-commit:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
- uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5

- name: Set up Python 3.14
uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
Expand All @@ -28,7 +28,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Check out pipeline code
uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5

- name: Install Nextflow
uses: nf-core/setup-nextflow@v2
Expand Down Expand Up @@ -71,7 +71,7 @@ jobs:

- name: Upload linting log file artifact
if: ${{ always() }}
uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
with:
name: linting-logs
path: |
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46 changes: 0 additions & 46 deletions .github/workflows/template-version-comment.yml
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1 change: 0 additions & 1 deletion .nf-core.yml
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Expand Up @@ -22,7 +22,6 @@ lint:
- manifest.name
- manifest.homePage
nf_test_content: false
included_configs: false
nf_core_version: 3.4.1
repository_type: pipeline
template:
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6 changes: 6 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -3,6 +3,12 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## dev

### Fixes

1. Fixed a bug where an integer value of `--bin_sizes` would cause the pipeline to fail. The parameter can now take either a comma-delimited list of bin sizes or a single integer value.

## v1.3.0 - Skilled Worker - [18 November 2025]

### New features
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2 changes: 1 addition & 1 deletion main.nf
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Expand Up @@ -57,7 +57,7 @@ workflow {
PIPELINE_INITIALISATION.out.samplesheet,
params.fasta,
params.fai,
params.bin_sizes.tokenize(","),
params.bin_sizes in String ? params.bin_sizes.tokenize(",") : [params.bin_sizes as String],
params.prefix,
params.outdir,
params.multiqc_config,
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4 changes: 2 additions & 2 deletions nextflow_schema.json
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Expand Up @@ -54,9 +54,9 @@
"default": "",
"properties": {
"bin_sizes": {
"type": "string",
"type": ["string", "integer"],

@matthdsm matthdsm Feb 16, 2026

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Wouldn't it be cleaner to just make this a List[int] ?

@nvnieuwk nvnieuwk Feb 16, 2026

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Yes, but that sadly won't work with parameters

"description": "A comma-delimited list of bin sizes in kilobases to use for the analysis",
"default": "1000,500,50,30,15,10,5,1"
"default": "500,100,50,15,10,5"
}
}
},
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