Add param to configure global repository for containers

guigolab · Jun 14, 2024 · 899598e · 899598e
1 parent 7fb1865
commit 899598e
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Showing 12 changed files with 16 additions and 14 deletions.
diff --git a/modules/bamStats/bamstats/main.nf b/modules/bamStats/bamstats/main.nf
@@ -1,5 +1,5 @@
 params.bamstatsVersion = '0.3.5--he881be0_0'
-params.container = "quay.io/biocontainers/bamstats:${params.bamstatsVersion}"
+params.container = "${params.containerRepo}/bamstats:${params.bamstatsVersion}"
 params.bamStatsMaxBuf = '1000000'
 params.bamStatsLogLevel = 'info'
 

diff --git a/modules/bigwig/star/main.nf b/modules/bigwig/star/main.nf
@@ -1,8 +1,8 @@
 params.starVersion = "2.4.0j--h9ee0642_2"
 // params.starVersion = "2.7.10a--h9ee0642_0"
 params.ucscVersion = '455--h2a80c09_1'
-params.starContainer = "quay.io/biocontainers/star:${params.starVersion}"
-params.bgtobwContainer = "quay.io/biocontainers/ucsc-bedgraphtobigwig:${params.ucscVersion}"
+params.starContainer = "${params.containerRepo}/star:${params.starVersion}"
+params.bgtobwContainer = "${params.containerRepo}/ucsc-bedgraphtobigwig:${params.ucscVersion}"
 params.wigRefPrefix = '-'
 
 process signal {

diff --git a/modules/fastaIndex/samtools/main.nf b/modules/fastaIndex/samtools/main.nf
@@ -1,5 +1,5 @@
 params.samtoolsVersion = '1.19.2--h50ea8bc_1'
-params.container = "quay.io/biocontainers/samtools:${params.samtoolsVersion}"
+params.container = "${params.containerRepo}/samtools:${params.samtoolsVersion}"
 
 process fastaIndex {
 

diff --git a/modules/inferExp/rseqc/main.nf b/modules/inferExp/rseqc/main.nf
@@ -1,8 +1,8 @@
 params.rseqcVersion = '2.6.4--py27hf8a1672_2'
 params.ucscVersion = '447--h2a80c09_1'
-params.gtfToGenePredContainer = "quay.io/biocontainers/ucsc-gtftogenepred:${params.ucscVersion}"
-params.genePredContainer = "quay.io/biocontainers/ucsc-genepredtobed:${params.ucscVersion}"
-params.rseqcContainer = "quay.io/biocontainers/rseqc:${params.rseqcVersion}"
+params.gtfToGenePredContainer = "${params.containerRepo}/ucsc-gtftogenepred:${params.ucscVersion}"
+params.genePredContainer = "${params.containerRepo}/ucsc-genepredtobed:${params.ucscVersion}"
+params.rseqcContainer = "${params.containerRepo}/rseqc:${params.rseqcVersion}"
 params.inferExpThreshold = '0.8'
 
 process gtfToGenePred {

diff --git a/modules/mapping/star/main.nf b/modules/mapping/star/main.nf
@@ -1,6 +1,6 @@
 params.starVersion = "2.4.0j--h9ee0642_2"
 // params.starVersion = "2.7.10a--h9ee0642_0"
-params.container = "quay.io/biocontainers/star:${params.starVersion}"
+params.container = "${params.containerRepo}/star:${params.starVersion}"
 
 def getIndexBases(genome) {
     int size = genome.size()

diff --git a/modules/markdup/sambamba/main.nf b/modules/markdup/sambamba/main.nf
@@ -1,5 +1,5 @@
 params.sambambaVersion = '0.7.1--h984e79f_3'
-params.container = "quay.io/biocontainers/sambamba:${params.sambambaVersion}"
+params.container = "${params.containerRepo}/sambamba:${params.sambambaVersion}"
 
 process markdup {
 

diff --git a/modules/mergeBam/sambamba/main.nf b/modules/mergeBam/sambamba/main.nf
@@ -1,5 +1,5 @@
 params.sambambaVersion = '0.7.1--h984e79f_3'
-params.container = "quay.io/biocontainers/sambamba:${params.sambambaVersion}"
+params.container = "${params.containerRepo}/sambamba:${params.sambambaVersion}"
 
 process mergeBam {
 

diff --git a/modules/mergeBam/samtools/main.nf b/modules/mergeBam/samtools/main.nf
@@ -1,5 +1,5 @@
 params.samtoolsVersion = '1.19.2--h50ea8bc_1'
-params.container = "quay.io/biocontainers/samtools:${params.samtoolsVersion}"
+params.container = "${params.containerRepo}/samtools:${params.samtoolsVersion}"
 
 process mergeBam {
 

diff --git a/modules/quantification/rsem/main.nf b/modules/quantification/rsem/main.nf
@@ -1,5 +1,5 @@
 params.rsemVersion = '1.3.3--pl5321h0033a41_7'
-params.container = "quay.io/biocontainers/rsem:${params.rsemVersion}"
+params.container = "${params.containerRepo}/rsem:${params.rsemVersion}"
 params.rsemCalcCI = false
 params.rsemPlotModel = false
 

diff --git a/modules/sortBam/sambamba/main.nf b/modules/sortBam/sambamba/main.nf
@@ -1,5 +1,5 @@
 params.sambambaVersion = '0.7.1--h984e79f_3'
-params.container = "quay.io/biocontainers/sambamba:${params.sambambaVersion}"
+params.container = "${params.containerRepo}/sambamba:${params.sambambaVersion}"
 
 process sortBam {
     tag "${sample}"

diff --git a/modules/sortBam/samtools/main.nf b/modules/sortBam/samtools/main.nf
@@ -1,5 +1,5 @@
 params.samtoolsVersion = '1.19.2--h50ea8bc_1'
-params.container = "quay.io/biocontainers/samtools:${params.samtoolsVersion}"
+params.container = "${params.containerRepo}/samtools:${params.samtoolsVersion}"
 
 process sortBam {
     tag "${sample}"

diff --git a/nextflow.config b/nextflow.config
@@ -11,6 +11,8 @@ params {
         annotation = "$baseDir/data/annotation.gtf"
 }
 
+params.containerRepo = "public.ecr.aws/biocontainers"
+
 // Docker is disabled by default and uses the following options when activated
 docker {
     sudo = false