correct for TEMPLATE issues

CITATIONS.md

@@ -14,8 +14,6 @@
 
   > Liao W, Asri M, Ebler J, Doerr D, Haukness M, Hickey G, Lu S, Lucas J K, Monlong J, Abel H J, Buonaiuto S, Chang X H, Cheng H, Chu J, Colonna V, Eizenga J M, Feng X, Fischer C, Fulton R S, Garg S, Groza C, Guarracino A, Harvey W T, Heumos S, Howe K, Jain M, Lu T, Markello C, Martin F J, Mitchell M W, Munson K M, Mwaniki M N, Novak A M, Olsen H E, Pesout T, Porubsky D, Prins P, Sibbesen J A, Tomlinson C, Villani F, Vollger M R, Human Pangenome Reference Consortium, Bourque G, Chaisson M J P, Flicek P, Phillippy A M, Zook J M, Eichler E E,Haussler D, Jarvis E D, Miga K H, Wang T, Garrison E, Marschall T, Hall I, Li H, Paten B. A Draft Human Pangenome Reference. Nature 617, 312–324 (2023). https://doi.org/10.1038/s41586-023-05896-x.
 
-  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
-
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
   > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: https://10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
@@ -76,7 +74,7 @@
 
 - [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)
 
-  > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.
+  > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: https://10.5555/2600239.2600241.
 
 - [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
   > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: https://10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.

nextflow.config

@@ -245,13 +245,6 @@ env {
 // Capture exit codes from upstream processes when piping
 process.shell = ['/bin/bash', '-euo', 'pipefail']
 
-// Set default registry for Docker, Singularity and Podman independent of -profile
-// Will not be used unless Docker, Singularity and Podman are enabled
-// Set to your registry if you have a mirror of containers
-docker.registry      = 'quay.io'
-podman.registry      = 'quay.io'
-singularity.registry = 'quay.io'
-
 def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
 timeline {
     enabled = true