updated bowtie process and images in config

tiagofilipe12 · Jul 4, 2018 · 1dcd864 · 1dcd864
1 parent c69f3b2
commit 1dcd864
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Showing 4 changed files with 9 additions and 13 deletions.
diff --git a/README.md b/README.md
@@ -84,7 +84,6 @@ Usage: nextflow run tiagofilipe12/pATLASflow [options] or nextflow run main.nf [
    Fasta options:
        --fasta     Provide fasta file pattern to be searched by nextflow.  Default: 'fasta/*.fas'
    Bowtie2 options:
-       --max_k     Provide the maximum number of alignments allowed per read.  Default: 10949 (the number of plasmids present in pATLAS)
        --trim5     Provide parameter -5 to bowtie2 allowing to trim 5' end.    Default: 0
        --cov_cutoff    Provide a cutoff value to filter results for coverage results.  Default: 0.60
 

diff --git a/lib/Helper.groovy b/lib/Helper.groovy
@@ -46,8 +46,6 @@ class Help{
         println("       --fasta     Provide fasta file pattern to be searched by " +
             "nextflow.  Default: 'fasta/*.fas'")
         println("   Bowtie2 options:")
-        println("       --max_k     Provide the maximum number of alignments allowed " +
-            "per read.  Default: 10949 (the number of plasmids present in pATLAS)")
         println("       --trim5     Provide parameter -5 to bowtie2 allowing to trim " +
             "5' end.    Default: 0")
         println("       --cov_cutoff    Provide a cutoff value to filter results for " +

diff --git a/main.nf b/main.nf
@@ -185,8 +185,8 @@ process mappingBowtie {
     }
 
     """
-    bowtie2 -x ${bowtie2Index} ${readsString} -p ${task.cpus} -k \
-    ${params.max_k} -5 ${params.trim5} -S mappingBowtie_${sample}.sam
+    bowtie2 -x ${bowtie2Index} ${readsString} -p ${task.cpus} -a \
+    -5 ${params.trim5} -S mappingBowtie_${sample}.sam
     """
 }
 

diff --git a/nextflow.config b/nextflow.config
@@ -22,7 +22,6 @@ params {
     shared_hashes = 0.8
     noWinner = false
     //bowtie2 unique options
-    max_k = 10949   // sets k parameter of bowtie2 -k, allowing the same read to map against more than 1 read. Default value is 1.
     trim5 = 0
     cov_cutoff = 0.60    // cutoff for the coverage in mapping approach
     plasmid_length_dict ='jsons/*_length.json'
@@ -39,13 +38,13 @@ params {
 }
 
 process {
-    $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'
+    $mashScreen.container = 'tiagofilipe12/patlasflow_mash_screen:1.4.1'
+    $mashOutputJson.container = 'tiagofilipe12/patlasflow_mash_screen:1.4.1'
+    $runMashDist.container = 'tiagofilipe12/patlasflow_mash_screen:1.4.1'
+    $mashDistOutputJson.container = 'tiagofilipe12/patlasflow_mash_screen:1.4.1'
+    $mappingBowtie.container = 'tiagofilipe12/patlasflow_mapping:1.4.1'
+    $samtoolsView.container = 'tiagofilipe12/patlasflow_mapping:1.4.1'
+    $jsonDumpingMapping.container = 'tiagofilipe12/patlasflow_mapping:1.4.1'
 }
 
 // this should be passed with the -profile mash_screen