# HG changeset patch
# User kkonganti
# Date 1656545075 14400
# Node ID a047ee0e34ae6c5daa1c1915c39b4cc0776c1a8f
# Parent  1d6557e7db7223a06dd42ba8b5eae84d0a3f25a0
"planemo upload"

diff -r 1d6557e7db72 -r a047ee0e34ae 0.2.1/conf/modules.config
--- a/0.2.1/conf/modules.config	Wed Jun 29 19:08:47 2022 -0400
+++ b/0.2.1/conf/modules.config	Wed Jun 29 19:24:35 2022 -0400
@@ -18,62 +18,50 @@
 
     withLabel: 'process_femto' {
         cpus = 2
-        memory = 64.GB
     }
 
     withLabel: 'process_pico' {
         cpus = 2
-        memory = 64.GB
     }
 
     withLabel: 'process_nano' {
         cpus = 4
-        memory = 64.GB
     }
 
     withLabel: 'process_micro' {
         cpus = 8
-        memory = 64.GB
     }
 
     withLabel: 'process_only_mem_low' {
         cpus = 2
-        memory = 64.GB
     }
 
     withLabel: 'process_only_mem_medium' {
         cpus = 2
-        memory = 64.GB
     }
 
     withLabel: 'process_only_mem_high' {
         cpus = 2
-        memory = 64.GB
     }
 
     withLabel: 'process_low' {
         cpus = 8
-        memory = 64.GB
     }
 
     withLabel: 'process_medium' {
         cpus = 8
-        memory = 64.GB
     }
 
     withLabel: 'process_high' {
         cpus = 8
-        memory = 64.GB
     }
 
     withLabel: 'process_higher' {
         cpus = 8
-        memory = 64.GB
     }
 
     withLabel: 'process_gigantic' {
         cpus = 8
-        memory = 64.GB
     }
 }
 
diff -r 1d6557e7db72 -r a047ee0e34ae 0.2.1/modules/spades/assemble/main.nf
--- a/0.2.1/modules/spades/assemble/main.nf	Wed Jun 29 19:08:47 2022 -0400
+++ b/0.2.1/modules/spades/assemble/main.nf	Wed Jun 29 19:24:35 2022 -0400
@@ -23,7 +23,7 @@
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def maxmem = task.memory.toGiga()
+    def maxmem = task.memory ? "--memory ${task.memory.toGiga()}" : ""
     def illumina_reads = illumina ? ( meta.single_end ? "-s $illumina" : "-1 ${illumina[0]} -2 ${illumina[1]}" ) : ""
     def pacbio_reads = !(pacbio.simpleName ==~ 'dummy_file.*') ? "--pacbio $pacbio" : ""
     def nanopore_reads = !(nanopore.simpleName ==~ 'dummy_file.*') ? "--nanopore $nanopore" : ""
@@ -32,7 +32,7 @@
     spades.py \\
         $args \\
         --threads $task.cpus \\
-        --memory $maxmem \\
+        $maxmem \\
         $custom_hmms \\
         $illumina_reads \\
         $pacbio_reads \\
diff -r 1d6557e7db72 -r a047ee0e34ae 0.2.1/nextflow.config
--- a/0.2.1/nextflow.config	Wed Jun 29 19:08:47 2022 -0400
+++ b/0.2.1/nextflow.config	Wed Jun 29 19:24:35 2022 -0400
@@ -28,7 +28,7 @@
 
 // Nextflow runtime profiles
 conda.cacheDir = '/data/cfsan-centriflaken-db/0/kondagac_cache'
-singularity.cacheDir = '/data/cfsan-centriflaken-db/0/cingularitygac_cache'
+singularity.cacheDir = 'cingularitygac_cache'
 
 profiles {
     standard {