Mercurial > repos > kkonganti > cfsan_centriflaken

changeset 37:a047ee0e34ae

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"planemo upload"
author kkonganti
date Wed, 29 Jun 2022 19:24:35 -0400
parents 1d6557e7db72
children d7c07f2456b4
files 0.2.1/conf/modules.config 0.2.1/modules/spades/assemble/main.nf 0.2.1/nextflow.config
diffstat 3 files changed, 3 insertions(+), 15 deletions(-) [+]
line wrap: on
line diff
--- 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
     }
 }
 
--- 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 \\
--- 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 {