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Nf sma failure #160

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Merged
aw-watson merged 6 commits into from
Oct 21, 2025
Merged

Nf sma failure #160

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29dc00b
added monitoring tools to antismash image. changed antismash base ima…
aw-watson Sep 30, 2025
e37f7c2
manually update image versions on branch
aw-watson Sep 30, 2025
9f67cb8
actually add reporting tools to image
aw-watson Oct 1, 2025
2f8c85e
reverting base image version until discussing updates
aw-watson Oct 1, 2025
61c9062
annotation workflow no longer causes failed runs from filling up bin …
aw-watson Oct 15, 2025
018c41f
opaver_anno.pl script no longer fills up bin space
aw-watson Oct 21, 2025
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2 changes: 1 addition & 1 deletion workflows/Nextflow/configs/container.config
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Original file line number Diff line number Diff line change
Expand Up @@ -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'
Expand Down
16 changes: 8 additions & 8 deletions workflows/Nextflow/modules/runAnnotation/resources/usr/bin/opaver_anno.pl
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Expand Up @@ -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;
Expand Down Expand Up @@ -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" ){
Expand All @@ -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";
}
}
Expand Down Expand Up @@ -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 $/;
Expand Down
10 changes: 5 additions & 5 deletions workflows/Nextflow/modules/runAnnotation/runAnnotation.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand All @@ -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: "${settings["annotationOutDir"]}",
mode: 'copy'
Expand Down Expand Up @@ -88,7 +88,7 @@ process prokkaAnnotate {
process rattAnnotate {
label 'annotation'
label 'small'
containerOptions '--compat --bind .:/venv/bin/ec_info'
containerOptions '--compat --bind \$PWD:/venv/bin/ec_info'
publishDir(
path: "${settings["annotationOutDir"]}",
mode: 'copy'
Expand Down Expand Up @@ -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: "${settings["annotationOutDir"]}",
mode: 'copy'
Expand All @@ -154,7 +154,7 @@ process annPlot {
process keggPlots {
label 'annotation'
label 'tiny'
containerOptions '--compat --bind .:/venv/bin/ec_info'
containerOptions '--compat --bind \$PWD:/venv/bin/ec_info'
publishDir(
path: "${settings["annotationOutDir"]}",
mode: 'copy'
Expand Down
4 changes: 3 additions & 1 deletion workflows/Nextflow/modules/runAntiSmash/Dockerfile
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Original file line number Diff line number Diff line change
@@ -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"]
Expand Down
2 changes: 1 addition & 1 deletion workflows/Nextflow/nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -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'
Expand Down