Fixes antismash and annotation workflow failures (#160)

* added monitoring tools to antismash image

* manually update image versions on branch

* add reporting tools to image

* annotation workflow no longer causes failed runs from filling up bin space

* opaver_anno.pl script no longer fills up bin space

Author: aw-watson

workflows/Nextflow/configs/container.config

@@ -53,7 +53,7 @@ process {
         container = 'ghcr.io/lanl-bioinformatics/edge_phage_finder:1.2.0'
     }
     withLabel: 'sma' {
-        container = 'ghcr.io/lanl-bioinformatics/edge_sma:0.14.0'
+        container = 'ghcr.io/lanl-bioinformatics/edge_sma:0.15.2'
     }
     withLabel: 'binning' {
         container = 'ghcr.io/lanl-bioinformatics/edge_binning:1.0.0'

workflows/Nextflow/modules/runAnnotation/resources/usr/bin/opaver_anno.pl

@@ -43,9 +43,9 @@
 
 #init directory
 `mkdir -p $outdir`;
-`mkdir -p $Bin/ec_info`;
+`mkdir -p ./ec_info`;
 die "[ERROR] Can't create output directory $outdir: $!\n" unless -d $outdir;
-die "[ERROR] Can't create ec_info directory $Bin/ec_info: $!\n" unless -d "$Bin/ec_info";
+die "[ERROR] Can't create ec_info directory ./ec_info: $!\n" unless -d "./ec_info";
 
 #init KEGG info
 $ecinfo = &retrieveKoInfoJson( $kojson ) if -s $kojson;
@@ -74,9 +74,9 @@
 print STDERR "[INFO] Retrieve pathway image and KGML...";
 foreach my $mapid ( keys %$map ){
     print STDERR "[INFO] download map$mapid...";
-    if( -e "$Bin/ec_info/ec$mapid.png" && -e "$Bin/ec_info/ec$mapid.xml" ){
-    `cp $Bin/ec_info/ec$mapid.png $outdir/ec$mapid.png`;
-    `cp $Bin/ec_info/ec$mapid.xml $outdir/ec$mapid.xml`;
+    if( -e "./ec_info/ec$mapid.png" && -e "./ec_info/ec$mapid.xml" ){
+    `cp ./ec_info/ec$mapid.png $outdir/ec$mapid.png`;
+    `cp ./ec_info/ec$mapid.xml $outdir/ec$mapid.xml`;
     }
 
     if( !-e "$outdir/ec$mapid.png" || !-e "$outdir/ec$mapid.xml" ){
@@ -86,8 +86,8 @@
             print STDERR "[WARNING] Failed to download map$mapid image/KGML from KEGG.\n";
         }
         else{
-        `cp $outdir/ec$mapid.png  $Bin/ec_info/ec$mapid.png`;
-        `cp $outdir/ec$mapid.xml $Bin/ec_info/ec$mapid.xml`;
+        `cp $outdir/ec$mapid.png ./ec_info/ec$mapid.png`;
+        `cp $outdir/ec$mapid.xml ./ec_info/ec$mapid.xml`;
             print STDERR "Done.\n";
         }
     }
@@ -220,7 +220,7 @@ sub getECinfo {
         my $info;
         my $url = "https://rest.kegg.jp/get";
         my $content;
-        my $ec_info_file = "$Bin/ec_info/$ec";
+        my $ec_info_file = "./ec_info/$ec";
 
         if( -e $ec_info_file ){
             local $/;

workflows/Nextflow/modules/runAnnotation/runAnnotation.nf

@@ -4,7 +4,7 @@
 process autodetectKingdom {
     label 'annotation'
     label 'tiny'
-    containerOptions '--compat --bind .:/venv/bin/ec_info'
+    containerOptions '--compat --bind \$PWD:/venv/bin/ec_info'
     input:
     path contigs
 
@@ -25,7 +25,7 @@ process autodetectKingdom {
 process prokkaAnnotate {
     label 'annotation'
     label 'small'
-    containerOptions '--compat --bind .:/venv/bin/ec_info'
+    containerOptions '--compat --bind \$PWD:/venv/bin/ec_info'
     publishDir(
         path: "${settings["annotationOutDir"]}",
         mode: 'copy'
@@ -88,7 +88,7 @@ process prokkaAnnotate {
 process rattAnnotate {
     label 'annotation'
     label 'small'
-    containerOptions '--compat --bind .:/venv/bin/ec_info'
+    containerOptions '--compat --bind \$PWD:/venv/bin/ec_info'
     publishDir(
         path: "${settings["annotationOutDir"]}",
         mode: 'copy'
@@ -127,7 +127,7 @@ process rattAnnotate {
 process annPlot {
     label 'annotation'
     label 'tiny'
-    containerOptions '--compat --bind .:/venv/bin/ec_info'
+    containerOptions '--compat --bind \$PWD:/venv/bin/ec_info'
     publishDir(
         path: "${settings["annotationOutDir"]}",
         mode: 'copy'
@@ -154,7 +154,7 @@ process annPlot {
 process keggPlots {
     label 'annotation'
     label 'tiny'
-    containerOptions '--compat --bind .:/venv/bin/ec_info'
+    containerOptions '--compat --bind \$PWD:/venv/bin/ec_info'
     publishDir(
         path: "${settings["annotationOutDir"]}",
         mode: 'copy'

workflows/Nextflow/modules/runAntiSmash/Dockerfile

@@ -1,6 +1,8 @@
 # syntax=docker/dockerfile:1
 FROM antismash/standalone-lite-nonfree:7.1.0
-ENV version=0.14.0
+ENV version=0.15.2
+
+RUN apt-get update && apt-get install procps -y && apt-get clean
 
 #we override the base image's entrypoint for appropriate interaction with Nextflow
 ENTRYPOINT ["/usr/bin/env"]

workflows/Nextflow/nextflow.config

@@ -305,7 +305,7 @@ process {
         container = 'ghcr.io/lanl-bioinformatics/edge_phage_finder:1.2.0'
     }
     withLabel: 'sma' {
-        container = 'ghcr.io/lanl-bioinformatics/edge_sma:0.14.0'
+        container = 'ghcr.io/lanl-bioinformatics/edge_sma:0.15.2'
     }
     withLabel: 'binning' {
         container = 'ghcr.io/lanl-bioinformatics/edge_binning:1.0.0'