diff --git a/README.md b/README.md index c279d69e..79af8cb4 100644 --- a/README.md +++ b/README.md @@ -112,22 +112,22 @@ sbatch ./pfr_assemblyqc ## Credits -plant-food-research-open/assemblyqc was originally written by Usman Rashid and Ken Smith. Ross Crowhurst, Chen Wu and Marcus Davy generously contributed their QC scripts. +plant-food-research-open/assemblyqc was originally written by Usman Rashid ([@gallvp](https://github.com/gallvp)) and Ken Smith ([@hzlnutspread](https://github.com/hzlnutspread)). + +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. We thank the following people for their extensive assistance in the development of this pipeline: -- Cecilia Deng [@CeciliaDeng](https://github.com/CeciliaDeng) -- Chen Wu [@christinawu2008](https://github.com/christinawu2008) -- Ignacio Carvajal [@ignacio3437](https://github.com/ignacio3437) -- Jason Shiller [@jasonshiller](https://github.com/jasonshiller) -- Mahesh Binzer-Panchal [@mahesh-panchal](https://github.com/mahesh-panchal) -- Marcus Davy [@mdavy86](https://github.com/mdavy86) -- Ross Crowhurst [@rosscrowhurst](https://github.com/rosscrowhurst) -- Sarah Bailey [@SarahBailey1998](https://github.com/SarahBailey1998) -- Susan Thomson [@cflsjt](https://github.com/cflsjt) -- Ting-Hsuan Chen [@ting-hsuan-chen](https://github.com/ting-hsuan-chen) +- [Cecilia Deng](https://github.com/CeciliaDeng) +- [Ignacio Carvajal](https://github.com/ignacio3437) +- [Jason Shiller](https://github.com/jasonshiller) +- [Sarah Bailey](https://github.com/SarahBailey1998) +- [Susan Thomson](https://github.com/cflsjt) +- [Ting-Hsuan Chen](https://github.com/ting-hsuan-chen) -The pipeline uses nf-core modules contributed by following authors. +The pipeline uses nf-core modules contributed by following authors: @@ -164,7 +164,9 @@ If you would like to contribute to this pipeline, please see the [contributing g ## Citations -If you use plant-food-research-open/assemblyqc for your analysis, please cite it using the following doi: [10.5281/zenodo.10647870](https://doi.org/10.5281/zenodo.10647870) +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 (2.0.0-rc.1). Zenodo. https://doi.org/10.5281/zenodo.10647870 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. diff --git a/docs/output.md b/docs/output.md index ff7a724f..3cb7c048 100644 --- a/docs/output.md +++ b/docs/output.md @@ -205,9 +205,13 @@ Hi-C contact mapping experiments measure the frequency of physical contact betwe [Circos](https://circos.ca) and linear synteny plots are created from genome-wide alignments performed with [MUMMER](https://github.com/mummer4/mummer?tab=readme-ov-file) and [`dnadiff.pl`](https://github.com/mummer4/mummer/blob/master/scripts/dnadiff.pl). -
AssemblyQC - Circos synteny plot
AssemblyQC - Circos synteny plot
-
AssemblyQC - Dotplot synteny plot
AssemblyQC - Dotplot synteny plot
-
AssemblyQC - Plotsr synteny plot
AssemblyQC - Plotsr synteny plot
+
+AssemblyQC - Circos synteny plot +AssemblyQC - Plotsr synteny plot +AssemblyQC - Dotplot synteny plot +
+AssemblyQC - Synteny plots +
### Merqury diff --git a/version_check.sh b/version_check.sh index 23cf619c..ca34d57e 100755 --- a/version_check.sh +++ b/version_check.sh @@ -12,3 +12,8 @@ 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)