Merge pull request #341 from PGScatalog/dev

v2.0.0-beta.2

.gitignore

@@ -11,3 +11,5 @@ assets/report/renv/
 assets/report/report.Rproj
 .Rprofile
 tests/.venv/
+docs/.venv/
+docs/_build

CITATIONS.md

@@ -33,9 +33,6 @@
 * [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)
     > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.
 
-* [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)
-    > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.
-
 * [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)
 
 * [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)

assets/report/report.qmd

@@ -443,7 +443,7 @@ uscores_plot <- uscores[1:min(length(uscores), 6)] # plot max 6 PGS
 
 # Plot multiple adjustment methods at once per PGS
 for(current_pgs in uscores_plot){
-  long_scores <- scores %>% select(!percentile_MostSimilarPop) %>% filter(PGS == current_pgs) %>% gather(Method, score, -sampleset, -IID, -PGS)
+  long_scores <- scores %>% select(!percentile_MostSimilarPop) %>% filter(PGS == current_pgs) %>% gather(Method, score, -sampleset, -FID, -IID, -PGS)
   long_scores %>%
   ggplot(aes(x = score, fill = sampleset)) +
     geom_density(alpha = 0.3) +

conf/modules.config

@@ -38,12 +38,12 @@ process {
         ext.conda = "$projectDir/environments/pgscatalog_utils/environment.yml"
         ext.docker = 'ghcr.io/pgscatalog/pygscatalog'
         ext.singularity = 'oras://ghcr.io/pgscatalog/pygscatalog'
-        ext.docker_version = ':pgscatalog-utils-1.1.2'
-        ext.singularity_version = ':pgscatalog-utils-1.1.2-singularity'
+        ext.docker_version = ':pgscatalog-utils-1.2.0'
+        ext.singularity_version = ':pgscatalog-utils-1.2.0-singularity'
     }
 
     withLabel: plink2 {
-        ext.conda = "bioconda::plink2==2.00a5.10"
+        ext.conda = "$projectDir/environments/plink2/environment.yml"
         ext.docker = 'ghcr.io/pgscatalog/plink2'
         ext.singularity = 'oras://ghcr.io/pgscatalog/plink2'
         ext.docker_version = ':2.00a5.10'
@@ -52,22 +52,22 @@ process {
 
     withLabel: zstd {
         ext.conda = "$projectDir/environments/zstd/environment.yml"
-        ext.singularity = 'oras://dockerhub.ebi.ac.uk/gdp-public/pgsc_calc/singularity/zstd'
-        ext.singularity_version = ':amd64-1.4.8'
-        ext.docker = 'dockerhub.ebi.ac.uk/gdp-public/pgsc_calc/zstd'
-        ext.docker_version = ':1.4.8'
+        ext.singularity = 'oras://ghcr.io/pgscatalog/zstd'
+        ext.singularity_version = ':2-beta-singularity'
+        ext.docker = 'ghcr.io/pgscatalog/zstd'
+        ext.docker_version = ':2-beta'
     }
 
     withLabel: report {
         ext.conda = "$projectDir/environments/report/environment.yml"
-        ext.singularity = 'oras://dockerhub.ebi.ac.uk/gdp-public/pgsc_calc/singularity/report'
-        ext.singularity_version = ':2.00a5'
-        ext.docker = 'dockerhub.ebi.ac.uk/gdp-public/pgsc_calc/report'
-        ext.docker_version = ':2.00a5'
+        ext.singularity = 'oras://ghcr.io/pgscatalog/report'
+        ext.singularity_version = ':2-beta-singularity'
+        ext.docker = 'ghcr.io/pgscatalog/report'
+        ext.docker_version = ':2-beta'
     }
 
     withLabel: pyyaml {
-        ext.conda = "conda-forge::pyyaml==6.0"
+        ext.conda = "$projectDir/environments/pyyaml/environment.yml"
         ext.singularity = 'oras://ghcr.io/pgscatalog/pyyaml'
         ext.singularity_version = ':6.0-singularity'
         ext.docker = 'ghcr.io/pgscatalog/pyyaml'
@@ -77,9 +77,9 @@ process {
     withLabel: fraposa {
         ext.conda = "$projectDir/environments/fraposa/environment.yml"
         ext.singularity = 'oras://ghcr.io/pgscatalog/fraposa_pgsc'
-        ext.singularity_version = ':v0.1.0-singularity'
+        ext.singularity_version = ':v1.0.0-singularity'
         ext.docker = 'ghcr.io/pgscatalog/fraposa_pgsc'
-        ext.docker_version = ':v0.1.1'
+        ext.docker_version = ':v1.0.0'
     }
 
     // output configuration

docs/_templates/globaltoc.html

@@ -22,7 +22,7 @@ <h3>Contents</h3>
 <h3>About the project</h3>
 
 <ul>
-  <li><a href="{{ pathto('changelog') }}">Changelog</a></li>
+  <li><a href="https://github.com/PGScatalog/pgsc_calc/releases">Changelog</a></li>
   <li><a href="{{ pathto('license') }}">License</a></li>
 </ul>
 
@@ -35,7 +35,7 @@ <h3>Useful links</h3>
       <li><a href="https://github.com/pgscatalog/pgsc_calc/issues">Issue tracker</a></li>
       <li><a href="https://github.com/PGScatalog/pgsc_calc/discussions">Discussion board</a></li>
   </ul>
-  <li><a href="https://github.com/PGScatalog/pgscatalog_utils">pgscatalog_utils Github</a></li>
+  <li><a href="https://github.com/PGScatalog/pygscatalog">pgscatalog-utils GitHub</a></li>
 </ul>
 
 <hr>