Docker Hub -> ECR

DOH-JDJ0303 · Jun 25, 2024 · f8424bf · f8424bf
1 parent ce9405b
commit f8424bf
Show file tree

Hide file tree

Showing 7 changed files with 33 additions and 81 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -18,7 +18,7 @@ process {
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
     withName: TAR2REFS {
-        container = 'docker.io/jdj0303/vaper-base:1.0'
+        container = 'public.ecr.aws/o8h2f0o1/vaper-base:1.0'
         publishDir = [
             path: { "${params.outdir}/" },
             pattern: "none"
@@ -73,7 +73,7 @@ process {
         ]
     }
     withName: 'FASTP2TBL' {
-        container = 'docker.io/jdj0303/vaper-base:1.0'
+        container = 'public.ecr.aws/o8h2f0o1/vaper-base:1.0'
         ext.args            = ""
         ext.when            = {  }
         publishDir          = [
@@ -147,7 +147,7 @@ process {
         ]
     }
     withName: 'SUMMARIZE_TAXA' {
-        container = 'docker.io/jdj0303/vaper-base:1.0'
+        container = 'public.ecr.aws/o8h2f0o1/vaper-base:1.0'
         ext.args            = ""
         ext.when            = {  }
         publishDir          = [
@@ -163,6 +163,29 @@ process {
             ]
         ]
     }
+    withName: 'SM2REFS' {
+        container = 'public.ecr.aws/o8h2f0o1/vaper-base:1.0'
+        ext.args            = ""
+        ext.when            = {  }
+        publishDir          = [
+            [
+                path: { "${params.outdir}/${meta.id}/taxonomy/" },
+                pattern: "*.csv",
+                mode: 'copy'
+            ],
+        ]
+    }
+    withName: 'NCBI_DATASETS' {
+        ext.args            = ""
+        ext.when            = {  }
+        publishDir          = [
+            [
+                path: { "${params.outdir}/${meta.id}/taxonomy/" },
+                pattern: "*.csv",
+                mode: 'copy'
+            ],
+        ]
+    }
     withName: 'BWA_MEM' {
         ext.args            = ""
         ext.when            = {  }
@@ -236,7 +259,7 @@ process {
         ]
     }
     withName: 'NEXTCLADE_CONFIG' {
-        container = 'docker.io/jdj0303/vaper-base:1.0'
+        container = 'public.ecr.aws/o8h2f0o1/vaper-base:1.0'
         ext.args            = ""
         ext.when            = {  }
         publishDir = [
@@ -247,7 +270,7 @@ process {
         ]
     }
     withName: 'SUMMARYLINE' {
-        container = 'docker.io/jdj0303/vaper-base:1.0'
+        container = 'public.ecr.aws/o8h2f0o1/vaper-base:1.0'
         ext.args            = ""
         ext.when            = {  }
         publishDir          = [
@@ -257,7 +280,7 @@ process {
         ]
     }
     withName: 'COMBINE_SUMMARYLINES' {
-        container = 'docker.io/jdj0303/vaper-base:1.0'
+        container = 'public.ecr.aws/o8h2f0o1/vaper-base:1.0'
         ext.args            = ""
         ext.when            = {  }
         publishDir          = [
@@ -304,7 +327,7 @@ process {
         ]
     }
     withName: 'REPORT' {
-        container = 'docker.io/jdj0303/vaper-base:1.0'
+        container = 'public.ecr.aws/o8h2f0o1/vaper-base:1.0'
         ext.args            = ""
         ext.when            = {  }
         publishDir          = [

diff --git a/modules/local/irma.nf b/modules/local/irma.nf
@@ -3,7 +3,7 @@ process IRMA {
     label 'process_high'
     stageInMode 'copy'
 
-    container "docker.io/staphb/irma:1.1.4"
+    container "public.ecr.aws/o8h2f0o1/irma:1.1.4"
 
     input:
     tuple val(meta), path(refs), path(reads)

diff --git a/modules/local/ivar_consensus.nf b/modules/local/ivar_consensus.nf
@@ -3,7 +3,7 @@ process IVAR_CONSENSUS {
     label 'process_high'
 
     conda "bioconda::ivar"
-    container "staphb/ivar:1.4.2"
+    container "public.ecr.aws/o8h2f0o1/ivar:1.4.2"
 
     input:
     tuple val(meta), val(ref_id), path(bam)

diff --git a/modules/local/kraken2.nf b/modules/local/kraken2.nf
diff --git a/modules/local/ncbi-datasets.nf b/modules/local/ncbi-datasets.nf
@@ -1,6 +1,7 @@
 process NCBI_DATASETS {
     tag "${ref_id}"
     label 'process_low'
+    container 'public.ecr.aws/o8h2f0o1/ncbi-datasets:16.15.0'
 
     input:
     tuple val(ref_id), val(accession)

diff --git a/modules/local/samtoolstats2tbl.nf b/modules/local/samtoolstats2tbl.nf
diff --git a/modules/local/sm2refs.nf b/modules/local/sm2refs.nf
@@ -1,8 +1,6 @@
 process SM2REFS {
     label 'process_low'
 
-    container 'docker.io/jdj0303/vaper-base:beta'
-
     input:
     tuple val(meta), path(sm_species)