Update nextflow.config

dsarov · Sep 23, 2019 · 11a4eed · 11a4eed
1 parent a722ae1
commit 11a4eed
Showing 1 changed file with 10 additions and 15 deletions.
diff --git a/nextflow.config b/nextflow.config
@@ -3,11 +3,7 @@ params {
     fastq               =   "*_{1,2}.fastq.gz"
     database            =   "Burkholderia_pseudomallei_k96243"
     ref                 =   "k96243.fasta"
-    reference           =   "${baseDir}/Databases/${database}/${ref}"
-    resistance_db       =   "${baseDir}/Databases/${database}/${database}.db"
-    card_db             =   "${baseDir}/Databases/${database}/${database}_CARD.db"
     patientMetaData     =   "${baseDir}/Reports/data/patientMetaData.csv"
-    sweaveReport        =   "${baseDir}/Databases/${database}/sweaveTB-WGS-Micro-Report.Rnw"
     gwas                =   false
     matrix              =   true
     annotate            =   true
@@ -21,7 +17,6 @@ params {
     indel_merge         =   true
     tri_tetra_allelic   =   false
     size                =   1000000
-    snpeff              =   "${database}"
     phred               =   "-phred33"
     org                 =   "haploid"
     logo                =   "${baseDir}/Reports/data/ARDaP_logo.png"
@@ -55,35 +50,35 @@ process {
     withLabel: spandx_default {
         cpus = 2
         memory = "4G"
-        time = "2h"
+        time = "24h"
     }
 
     withLabel: spandx_alignment {
-        cpus = 4
+        cpus = 1
         memory = "4G"
-        time = "2h"
+        time = "24h"
     }
     withLabel: spandx_gatk_haplo {
         cpus = 4
         memory = "8G"
-        time = "8h"
+        time = "24h"
     }
 	withLabel: spandx_gatk {
         cpus = 4
         memory = "8G"
-        time = "8h"
+        time = "24h"
     }
 
     withLabel: spandx_snpeff {
         cpus = 1
         memory = "8G"
-        time = "2h"
+        time = "24h"
     }
 
     withLabel: spandx_pindel {
         cpus = 2
         memory = "8G"
-        time = "8h"
+        time = "96h"
     }
 
     withLabel: genomic_queries {
@@ -107,18 +102,18 @@ process {
 	withLabel: master_vcf {
         cpus = 1
         memory = "4G"
-        time = "2h"
+        time = "24h"
     }
 	withLabel: SNP_matrix {
         cpus = 1
         memory = "4G"
-        time = "2h"
+        time = "24h"
     }
 }
 
 manifest {
     homePage = 'http://github.com/dsarov/ARDaP'
     description = 'Comprehensive resistance detection from WGS'
     mainScript = 'main.nf'
-    version = '1.5.a4'
+    version = '1.5.a6'
 }