feat(docker): use host network instead of docker bridge

metagenomics · Oct 28, 2024 · cf5c770 · cf5c770
1 parent 7fb762b
commit cf5c770
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Showing 8 changed files with 24 additions and 12 deletions.
diff --git a/lib/Utils.groovy b/lib/Utils.groovy
@@ -31,6 +31,11 @@ class Utils {
       }
   }
 
+  static String getDockerNetwork(){
+    return " --net=host ";
+  }
+
+
   static String getCreateDatabaseDirCommand(db){
     return "if [ ! -z " + db + " ]; then mkdir " + db + " -p; fi"
   }

diff --git a/modules/annotation/module.nf b/modules/annotation/module.nf
@@ -59,7 +59,7 @@ process pMMseqs2 {
       // Another mount flag is used to get a key file (aws format) into the docker-container. 
 
       // This file is then used by s5cmd. The necessary mount points are generated by “constructParametersObject()”. 
-      containerOptions constructParametersObject("mmseqs2") + " --entrypoint='' "
+      containerOptions constructParametersObject("mmseqs2") + " --entrypoint='' " + Utils.getDockerNetwork()
 
       tag "Sample: $sample, Database: $dbType"
 
@@ -104,7 +104,7 @@ process pMMseqs2_taxonomy {
       // Therefore this place has to be mounted to the docker container to be accessible during run time.
       // Another mount flag is used to get a key file (aws format) into the docker-container. 
       // This file is then used by s5cmd. The necessary mount points are generated by “constructParametersObject()”. 
-      containerOptions constructParametersObject("mmseqs2_taxonomy") + " --entrypoint='' "
+      containerOptions constructParametersObject("mmseqs2_taxonomy") + " --entrypoint='' " + Utils.getDockerNetwork()
 
       tag "Sample: $sample, Database_taxonomy: $dbType"
 
@@ -148,7 +148,7 @@ process pResistanceGeneIdentifier {
 
    container "${params.rgi_image}"
 
-   containerOptions Utils.getDockerMount(params?.steps?.annotation?.rgi?.database, params)
+   containerOptions Utils.getDockerMount(params?.steps?.annotation?.rgi?.database, params) + Utils.getDockerNetwork()
 
    tag "Sample: $sample, BinID: $binID"
 
@@ -296,7 +296,7 @@ process pHmmSearch {
       // Re-Use the gtdb-tk container for Prodigal to safe space
       container "${params.gtdbtk_image}"
 
-      containerOptions Utils.getDockerMount(params?.steps?.binning?.magscot?.hmmSearch?.database, params)
+      containerOptions Utils.getDockerMount(params?.steps?.binning?.magscot?.hmmSearch?.database, params) + Utils.getDockerNetwork()
 
       tag "Sample: $sample"
 
@@ -370,7 +370,8 @@ process pKEGGFromMMseqs2 {
       // Another mount flag is used to get a key file (aws format) into the docker-container. 
       // This file is then used by s5cmd. 
 
-      containerOptions Utils.getDockerMount(params.steps?.annotation?.keggFromMMseqs2?.database, params)
+      containerOptions Utils.getDockerMount(params.steps?.annotation?.keggFromMMseqs2?.database, params) + Utils.getDockerNetwork()
+
       publishDir params.output, mode: "${params.publishDirMode}", saveAs: { filename -> getOutput("${sample}", params.runid, "keggFromMMseqs2", filename) }, \
          pattern: "{**.tsv}"
 

diff --git a/modules/fragmentRecruitment/mashScreen.nf b/modules/fragmentRecruitment/mashScreen.nf
@@ -38,6 +38,8 @@ process pMashScreen {
 
     container "${params.mash_image}"
 
+    containerOptions Utils.getDockerNetwork()
+
     when params?.steps?.fragmentRecruitment?.mashScreen != null
 
     input:

diff --git a/modules/magAttributes/module.nf b/modules/magAttributes/module.nf
@@ -49,7 +49,7 @@ process pCheckM {
     when params.steps.containsKey("magAttributes") && params.steps.magAttributes.containsKey("checkm") \
 	&& !params.steps.magAttributes.containsKey("checkm2")
 
-    containerOptions Utils.getDockerMount(params.steps?.magAttributes?.checkm?.database, params) 
+    containerOptions Utils.getDockerMount(params.steps?.magAttributes?.checkm?.database, params) + Utils.getDockerNetwork()
 
     beforeScript Utils.getCreateDatabaseDirCommand("${params.polished.databases}")
 
@@ -88,7 +88,7 @@ process pCheckM2 {
 
     when params.steps.containsKey("magAttributes") && params.steps.magAttributes.containsKey("checkm2")
 
-    containerOptions Utils.getDockerMount(params.steps?.magAttributes?.checkm2?.database, params)
+    containerOptions Utils.getDockerMount(params.steps?.magAttributes?.checkm2?.database, params) + Utils.getDockerNetwork()
 
     beforeScript "mkdir -p ${params.polished.databases}"
 
@@ -128,7 +128,7 @@ process pGtdbtk {
 
     when params.steps.containsKey("magAttributes") && params.steps.magAttributes.containsKey("gtdb")
 
-    containerOptions Utils.getDockerMount(params?.steps?.magAttributes?.gtdb?.database, params)
+    containerOptions Utils.getDockerMount(params?.steps?.magAttributes?.gtdb?.database, params) + Utils.getDockerNetwork()
 
     beforeScript Utils.getCreateDatabaseDirCommand("${params.polished.databases}")
 

diff --git a/modules/plasmids/module.nf b/modules/plasmids/module.nf
@@ -69,7 +69,7 @@ process pPLSDB {
 	saveAs: { filename -> getOutput("${sample}", params.runid, "PLSDB", filename) }, \
         pattern: "{**.tsv}"
 
-    containerOptions Utils.getDockerMount(params.steps?.plasmid?.PLSDB?.database, params)
+    containerOptions Utils.getDockerMount(params.steps?.plasmid?.PLSDB?.database, params) + Utils.getDockerNetwork()
 
     when params.steps.containsKey("plasmid") && params.steps.plasmid.containsKey("PLSDB")
 

diff --git a/modules/plasmids/processes.nf b/modules/plasmids/processes.nf
@@ -24,7 +24,7 @@ process pViralVerifyPlasmid {
 
     shell = ['/bin/bash']
 
-    containerOptions Utils.getDockerMount(params?.steps?.plasmid?.ViralVerifyPlasmid?.database, params)
+    containerOptions Utils.getDockerMount(params?.steps?.plasmid?.ViralVerifyPlasmid?.database, params) + Utils.getDockerNetwork()
 
     container "${params.viralVerify_image}"
 
@@ -121,7 +121,7 @@ process pMobTyper {
 
     beforeScript Utils.getCreateDatabaseDirCommand("${params.polished.databases}")
 
-    containerOptions Utils.getDockerMount(params.steps?.plasmid?.MobTyper?.database, params)
+    containerOptions Utils.getDockerMount(params.steps?.plasmid?.MobTyper?.database, params) + Utils.getDockerNetwork()
 
     secret { "${S3_MobTyper_ACCESS}"!="" ? ["S3_MobTyper_ACCESS", "S3_MobTyper_SECRET"] : [] } 
 
@@ -183,7 +183,7 @@ process pPlaton {
 
     tag "Sample: $sample, BinId: $binID"
 
-    containerOptions " --user root:root " + Utils.getDockerMount(params.steps?.plasmid?.Platon?.database, params)
+    containerOptions " --user root:root " + Utils.getDockerMount(params.steps?.plasmid?.Platon?.database, params) + Utils.getDockerNetwork()
 
     publishDir params.output, mode: "${params.publishDirMode}", saveAs: { filename -> getOutput("${sample}", params.runid, "Platon", filename) }, \
         pattern: "{**.tsv}"

diff --git a/modules/qualityControl/ontQC.nf b/modules/qualityControl/ontQC.nf
@@ -59,6 +59,8 @@ process pPorechopDownload {
 
     container "${params.porechop_image}"
 
+    containerOptions Utils.getDockerNetwork()
+
     input:
     tuple val(sample), env(readUrl)
 

diff --git a/modules/qualityControl/shortReadQC.nf b/modules/qualityControl/shortReadQC.nf
@@ -204,6 +204,8 @@ process pFastpSplitDownload {
 
     container "${params.fastp_image}"
 
+    containerOptions Utils.getDockerNetwork()
+
     input:
     tuple val(sample), env(read1Url), env(read2Url)
-Original file line number
+Diff line change
@@ Expand Up / @@ -38,6 +38,8 @@ process pMashScreen { @@
         container "${params.mash_image}"
+        containerOptions Utils.getDockerNetwork()
         when params?.steps?.fragmentRecruitment?.mashScreen != null
         input:
@@ Expand Down @@