fixed path to new indexes

tiagofilipe12 · May 29, 2018 · 8cc7dee · 8cc7dee
1 parent 3693d20
commit 8cc7dee
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Showing 2 changed files with 10 additions and 10 deletions.
diff --git a/main.nf b/main.nf
@@ -38,7 +38,7 @@ if (params.mash_screen || params.mapping) {
 if (params.mash_screen || params.assembly) {
     // creates two channels for each approach
     Channel
-        .value("/ngstools/data/patlas.msh")
+        .value("/ngstools/data/patlas_mash_sketch.msh")
         .into { refSketchChannel; refSketchChannel2 }
 }
 else {
@@ -67,9 +67,9 @@ if (params.mapping) {
 //    samtoolsIndex = "/ngstools/data/indexes/fasta/samtools.fasta.fai"   // maindb_path
 //    lengthJson = "/ngstools/data/reads_sample_result_length.json"
     bowtieStuffChannel = Channel
-        .value("/ngstools/data/indexes/bowtie2idx/bowtie2")
+        .value("/ngstools/data/indexes/patlas_bowtie_index")
     samtoolsStuffChannel = Channel
-        .value("/ngstools/data/indexes/fasta/samtools.fasta.fai")
+        .value("/ngstools/data/indexes/master_fasta_patlas_version_18042018.fas.fai")
     lengthJsonChannel = Channel
         .value("/ngstools/data/reads_sample_result_length.json")
 }

diff --git a/nextflow.config b/nextflow.config
@@ -39,13 +39,13 @@ params {
 }
 
 process {
-    $mashScreen.container = 'tiagofilipe12/patlasflow_mash_screen:1.1'
-    $mashOutputJson.container = 'tiagofilipe12/patlasflow_mash_screen:1.1'
-    $runMashDist.container = 'tiagofilipe12/patlasflow_mash_screen:1.1'
-    $mashDistOutputJson.container = 'tiagofilipe12/patlasflow_mash_screen:1.1'
-    $mappingBowtie.container = 'tiagofilipe12/patlasflow_mapping:1.1.4'
-    $samtoolsView.container = 'tiagofilipe12/patlasflow_mapping:1.1.4'
-    $jsonDumpingMapping.container = 'tiagofilipe12/patlasflow_mapping:1.1.4'
+    $mashScreen.container = 'tiagofilipe12/patlasflow_mash_screen:1.1.1'
+    $mashOutputJson.container = 'tiagofilipe12/patlasflow_mash_screen:1.1.1'
+    $runMashDist.container = 'tiagofilipe12/patlasflow_mash_screen:1.1.1'
+    $mashDistOutputJson.container = 'tiagofilipe12/patlasflow_mash_screen:1.1.1'
+    $mappingBowtie.container = 'tiagofilipe12/patlasflow_mapping:1.1.5'
+    $samtoolsView.container = 'tiagofilipe12/patlasflow_mapping:1.1.5'
+    $jsonDumpingMapping.container = 'tiagofilipe12/patlasflow_mapping:1.1.5'
 }
 
 // this should be passed with the -profile mash_screen