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Merge pull request #120 from Plant-Food-Research-Open/typo
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Updated citation and fixed typos
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GallVp authored Jul 30, 2024
2 parents 41e6331 + ea2d1c9 commit c5165fe
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5 changes: 0 additions & 5 deletions .github/version_checks.sh
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Expand Up @@ -12,8 +12,3 @@ fi

head -10 CHANGELOG.md | grep "## v$config_version - " >/dev/null \
|| (echo 'Failed to match CHANGELOG version'; exit 1)

# Check README version

grep "assembly quality ($config_version)" README.md >/dev/null \
|| (echo 'Failed to match README version'; exit 1)
17 changes: 10 additions & 7 deletions CHANGELOG.md
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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).

## v2.1.0+dev - [30-July-2024]
## v2.1.0+dev - [31-July-2024]

### `Added`

Expand All @@ -24,10 +24,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
5. Now `LTRRETRIEVER_LTRRETRIEVER` does not crash when the input assembly does not contain any LTRs [#92](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/92)
6. Now `LTRRETRIEVER_LTRRETRIEVER` does not crash when the input assembly is not writable [#98](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/98)
7. Now soft masked regions are unmasked before computing LAI [#117](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/117)
8. Changed `NextFlow` to `Nextflow`
9. Updated citation to Bioinformatics

### `Dependencies`

1. NextFlow!>=23.04.0
1. Nextflow!>=23.04.0
2. [email protected]

### `Deprecated`
Expand All @@ -37,6 +39,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
3. Moved `docs/contributors.sh` to `.github/contributors.sh`
4. Removed dependency on <https://github.com/PlantandFoodResearch/nxf-modules.git>
5. Replaced `nf-core/fastq_trim_fastp_fastqc` with `nf-core/fastq_fastqc_umitools_fastp` which has nf-test unit tests
6. Removed version check on README.md

## v2.0.0 - [04-June-2024]

Expand Down Expand Up @@ -72,11 +75,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
8. Updated `FASTA_LTRRETRIEVER_LAI` to fix a pipeline crash when `ch_monoploid_seqs` was `[ meta, [] ]` [#83](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/83)
9. Improved input assembly documentation [#86](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/86)
10. Added assembly tag to synteny warning message regarding missing `synteny_labels` file
11. Now copying files in `NCBI_FCS_GX_SETUP_SAMPLE` rather than symlinking in an attempt to support NextFlow Fusion
11. Now copying files in `NCBI_FCS_GX_SETUP_SAMPLE` rather than symlinking in an attempt to support Nextflow Fusion

### `Dependencies`

1. NextFlow!>=23.04.0
1. Nextflow!>=23.04.0
2. [email protected]

### `Deprecated`
Expand Down Expand Up @@ -115,7 +118,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Dependencies`

1. NextFlow!>=23.04.0
1. Nextflow!>=23.04.0
2. [email protected]

### `Deprecated`
Expand Down Expand Up @@ -165,7 +168,7 @@ For a ~600 MB assembly, EDTA (without sensitive flag) takes ~25 hours of compute
## v1.0.1 [07-Sep-2023]

1. Now pipeline timeline, report, and trace are enabled by default.
2. Included `procps` package where needed to allow NextFlow to collect system statistics.
2. Included `procps` package where needed to allow Nextflow to collect system statistics.

## v1 [25-Jul-2023]

Expand Down Expand Up @@ -257,7 +260,7 @@ Same as v1rc6c

## v0.10.4 [16-May-2023]

1. Moved the main workflow into `workflows/assembly_qc.nf` so that it can be imported by other NextFlow pipelines.
1. Moved the main workflow into `workflows/assembly_qc.nf` so that it can be imported by other Nextflow pipelines.
2. Fixed a bug in synteny due to which the pipeline did not resume properly sometimes.
3. The included binaries now have unique versions to avoid collision with binaries with same names already present on local PATH.
4. Now using a unique name for the conda environment to have better interoperability across pipelines.
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12 changes: 8 additions & 4 deletions CITATION.cff
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Expand Up @@ -16,12 +16,16 @@ authors:
given-names: "Marcus"
- family-names: "Chen"
given-names: "Ting-Hsuan"
- family-names: "Carvajal"
given-names: "Ignacio"
- family-names: "Bailey"
given-names: "Sarah"
- family-names: "Thomson"
given-names: "Susan"
- family-names: "Deng"
given-names: "Cecilia"
title: "AssemblyQC: A NextFlow pipeline for evaluating assembly quality"
title: "AssemblyQC: A Nextflow pipeline for reproducible reporting of assembly quality"
version: 2.1.0+dev
date-released: 2024-02-12
url: "https://github.com/Plant-Food-Research-Open/assembly_qc"
doi: 10.5281/zenodo.10647870
date-released: 2024-07-30
url: "https://github.com/Plant-Food-Research-Open/assemblyqc"
doi: 10.1093/bioinformatics/btae477
16 changes: 10 additions & 6 deletions README.md
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@@ -1,5 +1,5 @@
[![GitHub Actions CI Status](https://github.com/plant-food-research-open/assemblyqc/actions/workflows/ci.yml/badge.svg)](https://github.com/plant-food-research-open/assemblyqc/actions/workflows/ci.yml)
[![GitHub Actions Linting Status](https://github.com/plant-food-research-open/assemblyqc/actions/workflows/linting.yml/badge.svg)](https://github.com/plant-food-research-open/assemblyqc/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.10647870-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.10647870)
[![GitHub Actions Linting Status](https://github.com/plant-food-research-open/assemblyqc/actions/workflows/linting.yml/badge.svg)](https://github.com/plant-food-research-open/assemblyqc/actions/workflows/linting.yml)[![Cite Article](http://img.shields.io/badge/DOI-10.1093/bioinformatics/btae477-1073c8?labelColor=000000)](https://doi.org/10.1093/bioinformatics/btae477)
[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)

[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
Expand All @@ -10,7 +10,7 @@

## Introduction

**plant-food-research-open/assemblyqc** is a [NextFlow](https://www.nextflow.io/docs/latest/index.html) pipeline which evaluates assembly quality with multiple QC tools and presents the results in a unified html report. The tools are shown in the [Pipeline Flowchart](#pipeline-flowchart) and their references are listed in [CITATIONS.md](./CITATIONS.md).
**plant-food-research-open/assemblyqc** is a [Nextflow](https://www.nextflow.io/docs/latest/index.html) pipeline which evaluates assembly quality with multiple QC tools and presents the results in a unified html report. The tools are shown in the [Pipeline Flowchart](#pipeline-flowchart) and their references are listed in [CITATIONS.md](./CITATIONS.md).

## Pipeline Flowchart

Expand Down Expand Up @@ -123,7 +123,7 @@ plant-food-research-open/assemblyqc was originally written by Usman Rashid ([@ga

Ross Crowhurst ([@rosscrowhurst](https://github.com/rosscrowhurst)), Chen Wu ([@christinawu2008](https://github.com/christinawu2008)) and Marcus Davy ([@mdavy86](https://github.com/mdavy86)) generously contributed their QC scripts.

Mahesh Binzer-Panchal ([@mahesh-panchal](https://github.com/mahesh-panchal)) helped port the pipeline modules and sub-workflows to [nf-core](https://nf-co.re) schema.
Mahesh Binzer-Panchal ([@mahesh-panchal](https://github.com/mahesh-panchal)) and Simon Pearce ([@SPPearce](https://github.com/SPPearce)) helped port the pipeline modules and sub-workflows to [nf-core](https://nf-co.re) schema.

We thank the following people for their extensive assistance in the development of this pipeline:

Expand All @@ -145,19 +145,19 @@ The pipeline uses nf-core modules contributed by following authors:
<a href="https://github.com/maxulysse"><img src="https://github.com/maxulysse.png" width="50" height="50"></a>
<a href="https://github.com/matthdsm"><img src="https://github.com/matthdsm.png" width="50" height="50"></a>
<a href="https://github.com/joseespinosa"><img src="https://github.com/joseespinosa.png" width="50" height="50"></a>
<a href="https://github.com/grst"><img src="https://github.com/grst.png" width="50" height="50"></a>
<a href="https://github.com/ewels"><img src="https://github.com/ewels.png" width="50" height="50"></a>
<a href="https://github.com/sofstam"><img src="https://github.com/sofstam.png" width="50" height="50"></a>
<a href="https://github.com/sateeshperi"><img src="https://github.com/sateeshperi.png" width="50" height="50"></a>
<a href="https://github.com/robsyme"><img src="https://github.com/robsyme.png" width="50" height="50"></a>
<a href="https://github.com/priyanka-surana"><img src="https://github.com/priyanka-surana.png" width="50" height="50"></a>
<a href="https://github.com/phue"><img src="https://github.com/phue.png" width="50" height="50"></a>
<a href="https://github.com/muffato"><img src="https://github.com/muffato.png" width="50" height="50"></a>
<a href="https://github.com/lescai"><img src="https://github.com/lescai.png" width="50" height="50"></a>
<a href="https://github.com/kevinmenden"><img src="https://github.com/kevinmenden.png" width="50" height="50"></a>
<a href="https://github.com/jvhagey"><img src="https://github.com/jvhagey.png" width="50" height="50"></a>
<a href="https://github.com/joon-klaps"><img src="https://github.com/joon-klaps.png" width="50" height="50"></a>
<a href="https://github.com/jeremy1805"><img src="https://github.com/jeremy1805.png" width="50" height="50"></a>
<a href="https://github.com/heuermh"><img src="https://github.com/heuermh.png" width="50" height="50"></a>
<a href="https://github.com/grst"><img src="https://github.com/grst.png" width="50" height="50"></a>
<a href="https://github.com/friederikehanssen"><img src="https://github.com/friederikehanssen.png" width="50" height="50"></a>
<a href="https://github.com/fellen31"><img src="https://github.com/fellen31.png" width="50" height="50"></a>
<a href="https://github.com/felixkrueger"><img src="https://github.com/felixkrueger.png" width="50" height="50"></a>
Expand All @@ -174,7 +174,11 @@ If you would like to contribute to this pipeline, please see the [contributing g

If you use plant-food-research-open/assemblyqc for your analysis, please cite it as:

> Rashid, U., Wu, C., Shiller, J., Smith, K., Crowhurst, R., Davy, M., Chen, T.-H., Thomson, S., & Deng, C. (2024). AssemblyQC: A NextFlow pipeline for evaluating assembly quality (2.1.0+dev). Zenodo. https://doi.org/10.5281/zenodo.10647870
> **AssemblyQC: A Nextflow pipeline for reproducible reporting of assembly quality.**
>
> Usman Rashid, Chen Wu, Jason Shiller, Ken Smith, Ross Crowhurst, Marcus Davy, Ting-Hsuan Chen, Ignacio Carvajal, Sarah Bailey, Susan Thomson & Cecilia H Deng.
>
> _Bioinformatics_. 2024 July 30. doi: [10.1093/bioinformatics/btae477](https://doi.org/10.1093/bioinformatics/btae477).
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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<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1">

<meta name="description" content="plant-food-research-open/assemblyqc: A NextFlow pipeline which evaluates assembly quality with multiple QC tools and presents the results in a unified html report.">
<meta name="description" content="plant-food-research-open/assemblyqc: A Nextflow pipeline which evaluates assembly quality with multiple QC tools and presents the results in a unified html report.">
<title>plant-food-research-open/assemblyqc Pipeline Report</title>
</head>
<body>
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33 changes: 16 additions & 17 deletions bin/report_modules/templates/params/params.html
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@@ -1,19 +1,18 @@
<div id="PARAMS" class="tabcontent" style="display: none">
<div class="section-para-wrapper">
<p class="section-para">
AssemblyQC is a Nextflow pipeline which evaluates assembly quality with well established tools and presents
the results in a unified html report.
</p>
<p class="section-para"><b>Reference:</b></p>
<p class="section-para">
Rashid, U., Wu, C., Shiller, J., Smith, K., Crowhurst, R., Davy, M., Chen, T.-H., Thomson, S., & Deng, C.
(2024). AssemblyQC: A NextFlow pipeline for evaluating assembly quality ({{
all_stats_dicts['VERSIONS']['Workflow']['plant-food-research-open/assemblyqc'] }}). Zenodo.
<a href="https://doi.org/10.5281/zenodo.10647870" target="_blank">10.5281/zenodo.10647870</a>. GitHub.
<a href="https://github.com/Plant-Food-Research-Open/assemblyqc" target="_blank"
>https://github.com/Plant-Food-Research-Open/assemblyqc</a
>
</p>
</div>
{% include 'params/contents.html' %}
<div class="section-para-wrapper">
<p class="section-para">
AssemblyQC is a Nextflow pipeline which evaluates assembly quality with well established tools and presents
the results in a unified html report.
</p>
<p class="section-para"><b>Reference:</b></p>
<p class="section-para">
Rashid, U., Wu, C., Shiller, J., Smith, K., Crowhurst, R., Davy, M., Chen, T.-H., Carvajal, I., Bailey, S.,
Thomson, S., & Deng, C.H.
(2024). AssemblyQC: A Nextflow pipeline for reproducible reporting of assembly quality. Bioinformatics.
DOI <a href="https://doi.org/10.1093/bioinformatics/btae477" target="_blank">10.1093/bioinformatics/btae477</a>.
GitHub <a href="https://github.com/Plant-Food-Research-Open/assemblyqc"
target="_blank">https://github.com/Plant-Food-Research-Open/assemblyqc</a>.
</p>
</div>
{% include 'params/contents.html' %}
</div>
2 changes: 1 addition & 1 deletion docs/parameters.md
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@@ -1,6 +1,6 @@
# plant-food-research-open/assemblyqc pipeline parameters

A NextFlow pipeline which evaluates assembly quality with multiple QC tools and presents the results in a unified html report.
A Nextflow pipeline which evaluates assembly quality with multiple QC tools and presents the results in a unified html report.

## Input/output options

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4 changes: 2 additions & 2 deletions nextflow.config
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Expand Up @@ -280,11 +280,11 @@ manifest {
name = 'plant-food-research-open/assemblyqc'
author = """Usman Rashid, Ken Smith, Ross Crowhurst, Chen Wu, Marcus Davy"""
homePage = 'https://github.com/plant-food-research-open/assemblyqc'
description = """A NextFlow pipeline which evaluates assembly quality with multiple QC tools and presents the results in a unified html report."""
description = """A Nextflow pipeline which evaluates assembly quality with multiple QC tools and presents the results in a unified html report."""
mainScript = 'main.nf'
nextflowVersion = '!>=23.04.0'
version = '2.1.0+dev'
doi = 'https://doi.org/10.5281/zenodo.10647870'
doi = 'https://doi.org/10.1093/bioinformatics/btae477'
}

// Load modules.config for DSL2 module specific options
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2 changes: 1 addition & 1 deletion nextflow_schema.json
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"$schema": "http://json-schema.org/draft-07/schema",
"$id": "https://raw.githubusercontent.com/plant-food-research-open/assemblyqc/main/nextflow_schema.json",
"title": "plant-food-research-open/assemblyqc pipeline parameters",
"description": "A NextFlow pipeline which evaluates assembly quality with multiple QC tools and presents the results in a unified html report.",
"description": "A Nextflow pipeline which evaluates assembly quality with multiple QC tools and presents the results in a unified html report.",
"type": "object",
"definitions": {
"input_output_options": {
Expand Down

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