Merge pull request #46 from nf-core/pipeline-credits

Add citations

CITATIONS.md

@@ -8,11 +8,24 @@
 
 > Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.
 
-## Pipeline tools
+## Base pipeliines
+
+- [panpipes](https://doi.org/10.1101/2023.03.11.532085)
+
+  > Curion F, Rich-Griffin C, Agarwal D, et al. Panpipes: a pipeline for multiomic single-cell and spatial transcriptomic data analysis. Published online December 18, 2023:2023.03.11.532085. doi:10.1101/2023.03.11.532085
+
+- [scFlow](https://doi.org/10.1101/2021.08.16.456499)
 
-- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
+  > Khozoie C, Fancy N, Marjaneh MM, Murphy AE, Matthews PM, Skene N. scFlow: A Scalable and Reproducible Analysis Pipeline for Single-Cell RNA Sequencing Data. Published online August 19, 2021:2021.08.16.456499. doi:10.1101/2021.08.16.456499
 
-  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
+- [SIMBA](https://github.com/Mye-InfoBank/SIMBA)
+
+  > Trummer, N. et al. 2024. SIMBA (Single-cell Integration Methods pipeline for Big Atlases)
+
+- [YASCP](https://github.com/wtsi-hgi/yascp)
+  > Ozols, M. et al. 2023. YASCP (Yet Another Single Cell Pipeline)
+
+## Pipeline tools
 
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 

README.md

@@ -21,6 +21,13 @@
 
 **nf-core/scdownstream** is a bioinformatics pipeline that can be used to process already quantified single-cell RNA-seq data. It takes a samplesheet and h5ad-, SingleCellExperiment/Seurat- or CSV files as input and performs quality control, integration, dimensionality reduction and clustering. It produces an integrated h5ad and SingleCellExperiment file and an extensive QC report.
 
+The pipeline is based on the learnings and implementations from the following pipelines (alphabetical):
+
+- [panpipes](https://github.com/DendrouLab/panpipes)
+- [scFlow](https://combiz.github.io/scFlow/)
+- [SIMBA](https://github.com/Mye-InfoBank/SIMBA)
+- [YASCP](https://github.com/wtsi-hgi/yascp)
+
 # ![nf-core/scdownstream](docs/images/metromap.png)
 
 Not all of the steps shown in the metromap have already been implemented, as this pipeline is still under development. However, the following steps are already functional:
@@ -99,12 +106,20 @@ For more details about the output files and reports, please refer to the
 
 ## Credits
 
-nf-core/scdownstream was originally written by Nico Trummer.
+nf-core/scdownstream was originally written by [Nico Trummer](https://github.com/nictru).
 
-<!-- TODO nf-core: If applicable, make list of people who have also contributed
+We thank the following people for their extensive assistance in the development of this pipeline (alphabetical):
 
-We thank the following people for their extensive assistance in the development of this pipeline:
- -->
+- [Fabiola Curion](https://github.com/bio-la)
+- [Gregor Sturm](https://github.com/grst)
+- [Jonathan Talbot-Martin](https://github.com/jtalbotmartin)
+- [Lukas Heumos](https://github.com/zethson)
+- [Matiss Ozols](https://github.com/maxozo)
+- [Nathan Skene](https://github.com/NathanSkene)
+- [Nurun Fancy](https://github.com/nfancy)
+- [Riley Grindle](https://github.com/Riley-Grindle)
+- [Ryan Seaman](https://github.com/RPSeaman)
+- [Wojtek Sowinski](https://github.com/WojtekSowinski)
 
 ## Contributions and Support