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Update nfcore modules in spatialaxe #184

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Update nfcore modules in spatialaxe #184

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845219d
fixed warning, added missing meta.yml, zenodo id
khersameesh24 Jun 26, 2026
5e4c88c
lint fix for template file
khersameesh24 Jun 26, 2026
ed9764a
added nf-core baysor module, updated baysor subworkflows
khersameesh24 Jun 26, 2026
6d50015
updated input channels, meta yml files
khersameesh24 Jun 26, 2026
98b9aaf
added nf-core module opt, updated subworkflow
khersameesh24 Jun 26, 2026
83e3f97
added nf-core module proseg
khersameesh24 Jun 26, 2026
ee8eeeb
fixed output channel for baysor preview
khersameesh24 Jun 26, 2026
8c5cef3
updated nf-test snapshot
khersameesh24 Jun 26, 2026
5b8cf20
fix(xenium_patch): restore --min-transcripts-per-cell in stitch script
an-altosian Jun 27, 2026
7b02685
Merge pull request #11 from an-altosian/fix/stitch-min-transcripts-pr184
khersameesh24 Jun 27, 2026
394ccdc
restructured modules directory
khersameesh24 Jun 27, 2026
aa552a3
added module for baysor scale estimation, minor fixes, tool-based con…
khersameesh24 Jul 12, 2026
0945ab2
lint fix
khersameesh24 Jul 12, 2026
292baeb
added nf-test for estimate-scale-factor
khersameesh24 Jul 12, 2026
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4 changes: 2 additions & 2 deletions .nf-core.yml
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
lint:
actions_ci: false
files_exist:
- .github/workflows/awsfulltest.yml
- .github/workflows/awstest.yml
- conf/igenomes.config
- conf/igenomes_ignored.config
files_unchanged:
- .gitignore
- assets/nf-core-spatialaxe_logo_light.png
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4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -7,7 +7,7 @@

[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/spatialaxe)
[![GitHub Actions CI Status](https://github.com/nf-core/spatialaxe/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/spatialaxe/actions/workflows/nf-test.yml)
[![GitHub Actions Linting Status](https://github.com/nf-core/spatialaxe/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/spatialaxe/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/spatialaxe/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
[![GitHub Actions Linting Status](https://github.com/nf-core/spatialaxe/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/spatialaxe/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/spatialaxe/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.20733817-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.20733817)
[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)

[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
Expand Down Expand Up @@ -181,7 +181,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `#

## Citations

<!-- If you use nf-core/spatialaxe for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
<!-- If you use nf-core/spatialaxe for your analysis, please cite it using the following doi: [10.5281/zenodo.20733817](https://doi.org/10.5281/zenodo.20733817) -->

An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.

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2 changes: 1 addition & 1 deletion assets/email_template.html
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Expand Up @@ -4,7 +4,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1">

<meta name="description" content="nf-core/spatialaxe: A pipeline for spatialomics 10x Xenium In Situ data.">
<meta name="description" content="nf-core/spatialaxe: A pipeline to process spatialomics data from 10x Xenium In Situ or 10x Atera.">
<title>nf-core/spatialaxe Pipeline Report</title>
</head>
<body>
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10 changes: 3 additions & 7 deletions bin/baysor_create_dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -46,11 +46,9 @@ def generate_dataset(
reader = csv.reader(infile)
writer = csv.writer(outfile)

# get the header line
header = next(reader)
writer.writerow(header)

# randomize csv rows to write
for row in reader:
if random.random() < float(sample_fraction):
writer.writerow(row)
Expand All @@ -59,9 +57,7 @@ def generate_dataset(


def main() -> None:
"""
Run create dataset as nf module
"""

parser = argparse.ArgumentParser(
description="Create sampled dataset for Baysor preview"
)
Expand All @@ -79,11 +75,11 @@ def main() -> None:
)
args = parser.parse_args()

sampled_transcripts = "sampled_transcripts.csv"
sampled_transcripts = Path("sampled_transcripts.csv")

# generate dataset
BaysorPreview.generate_dataset(
transcripts=args.transcripts,
transcripts=Path(args.transcripts),
sampled_transcripts=sampled_transcripts,
sample_fraction=args.sample_fraction,
prefix=args.prefix
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