Updated citation and fixed typos

.github/version_checks.sh

@@ -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)

CHANGELOG.md

@@ -3,7 +3,7 @@
 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`
 
@@ -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`
@@ -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]
 
@@ -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`
@@ -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`
@@ -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]
 
@@ -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.

CITATION.cff

@@ -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

README.md

@@ -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/)
@@ -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
 
@@ -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:
 
@@ -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>
@@ -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.
 

assets/email_template.html

@@ -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="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>

bin/report_modules/templates/params/params.html

@@ -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>

docs/parameters.md

@@ -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
 

nextflow.config

@@ -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

nextflow_schema.json

@@ -2,7 +2,7 @@
     "$schema": "http://json-schema.org/draft-07/schema",
     "$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": {