validations and fixes for singularity setup

bin/download_singularity.sh

@@ -1,6 +1,14 @@
-grep "withLabel:" $1 | cut -f2 -d "'" > .container_list.tmp
+grep "withLabel:" $1 | cut -f2 -d "'"  > .container_list.tmp
 cachedir="$2"
 
 while read container; do
-	singularity pull --dir $cachedir docker://${container}
+	name=${container//[\:\/]/-}
+
+	if [ -e ${cachedir}/${name}.img ]
+	then
+		echo "${name}.img image exists"
+	else
+		singularity pull --name ${name}.img --dir "${cachedir}" "docker://${container}"
+	fi
+
 done < ".container_list.tmp"

modules/setup_container.nf

@@ -1,5 +1,9 @@
 process setup_container {
         label 'noContainer'
+        def slash = "/"
+        def cachdirloc = workflow.launchDir + slash + params.cachedir
+        println cachdirloc
+        println slash
     input:
         file(config_file)
     output:
@@ -12,8 +16,9 @@ process setup_container {
         touch everything_done.txt
         """
         else if (workflow.profile.contains('singularity'))
+
         """
-        download_singularity.sh ${config_file}
+        download_singularity.sh ${config_file} ${workflow.launchDir}/${params.cachedir} 
 
         touch everything_done.txt
         """

phage.nf

@@ -38,8 +38,9 @@ println "  $params.databases\u001B[0m"
 if (workflow.profile.contains('singularity')) {
 println "\033[2mSingularity cache location [--cachedir]:"
 println "  $params.cachedir"
+println "  "
 println "\u001B[33m  WARNING: Singularity image building sometimes fails!"
-println "  Rerun WtP via -resume to retry the failed image build"
+println "  Please download all images first via --setup --cachedir IMAGE-LOCATION"
 println "  Manually remove faulty images in $params.cachedir for a rebuild\u001B[0m"
 }
 println " "
@@ -691,6 +692,8 @@ def helpMSG() {
     """.stripIndent()
 }
 
-workflow.onComplete { 
-	log.info ( workflow.success ? "\nDone! Results are stored here --> $params.output \n" : "Oops .. something went wrong" )
-}
+if (!params.setup) {
+    workflow.onComplete { 
+        log.info ( workflow.success ? "\nDone! Results are stored here --> $params.output \n" : "Oops .. something went wrong" )
+    }
+}