Replace plink container with galaxyproject container and switch to ve…

…rsion 1.90b6.21
NBISweden · Jun 17, 2024 · 09b02a2 · 09b02a2
1 parent bca2e56
commit 09b02a2
Show file tree

Hide file tree

Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/workflow/rules/10_pca.smk b/workflow/rules/10_pca.smk
@@ -49,7 +49,7 @@ rule vcf2plink_pca:
     log:
         "results/logs/10_pca/{dataset}/" + REF_NAME + ".{dataset}_fmissing{fmiss}.{chr}_vcf2plink_pca.log",
     singularity:
-        "docker://quay.io/biocontainers/plink:1.90b6.12--heea4ae3_0"
+        "https://depot.galaxyproject.org/singularity/plink%3A1.90b6.21--hec16e2b_4"
     shell:
         """
         plink --vcf {input.vcf} --make-bed --allow-extra-chr --out {params.bfile} 2> {log}
@@ -71,7 +71,7 @@ rule plink_eigenvec:
     log:
         "results/logs/10_pca/{dataset}/" + REF_NAME + ".{dataset}_fmissing{fmiss}.{chr}_plink_eigenvec.log",
     singularity:
-        "docker://quay.io/biocontainers/plink:1.90b6.12--heea4ae3_0"
+        "https://depot.galaxyproject.org/singularity/plink%3A1.90b6.21--hec16e2b_4"
     shell:
         """
         samples=`cat {input.fam} | wc -l`

diff --git a/workflow/rules/11_ROH.smk b/workflow/rules/11_ROH.smk
@@ -98,7 +98,7 @@ rule vcf2plink_hwe:
     log:
         "results/logs/11_ROH/{dataset}/" + REF_NAME + ".{dataset}_fmissing{fmiss}.{chr}_vcf2plink_hwe.log",
     singularity:
-        "docker://quay.io/biocontainers/plink:1.90b6.12--heea4ae3_0"
+        "https://depot.galaxyproject.org/singularity/plink%3A1.90b6.21--hec16e2b_4"
     shell:
         """
         plink --vcf {input.vcf} --make-bed --allow-extra-chr --out {params.bfile} 2> {log}
@@ -127,7 +127,7 @@ rule ROHs:
     log:
         "results/logs/11_ROH/{dataset}/" + REF_NAME + ".{dataset}_fmissing{fmiss}.{chr}.homsnp{homsnp}.homkb{homkb}.homwinsnp{homwinsnp}.homwinhet{homwinhet}.homwinmis{homwinmis}.homhet{homhet}_ROHs.log",
     singularity:
-        "docker://quay.io/biocontainers/plink:1.90b6.12--heea4ae3_0"
+        "https://depot.galaxyproject.org/singularity/plink%3A1.90b6.21--hec16e2b_4"
     shell:
         """
         plink --bfile {params.bfile} --homozyg --homozyg-window-threshold 0.05 --allow-extra-chr \