Snippy parameters added: mincov, minfrac, minqual

metashot · Jun 30, 2022 · 2d6eb91 · 2d6eb91
1 parent 7cba2a5
commit 2d6eb91
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Showing 5 changed files with 8 additions and 21 deletions.
diff --git a/modules/bbtools.nf b/modules/bbtools.nf
@@ -1,8 +1,6 @@
 nextflow.enable.dsl=2
 
 
-// Params:
-//     - none
 process deinterleave {      
         tag "${id}"
 

diff --git a/modules/gubbins.nf b/modules/gubbins.nf
@@ -1,10 +1,6 @@
 nextflow.enable.dsl=2
 
 
-// Params:
-//   - outdir
-//   - gubbins_tree_builder
-//   - gubbins_iterations
 process gubbins {
     publishDir "${params.outdir}/gubbins/" , mode: 'copy'
 
@@ -26,11 +22,7 @@ process gubbins {
     """
 }
 
-// Params:
-//   - outdir
-//   - raxml_mode
-//   - raxml_nsearch
-//   - raxml_nboot
+
 process raxml {
     publishDir "${params.outdir}/raxml" , mode: 'copy'
     publishDir "${params.outdir}" , mode: 'copy' ,

diff --git a/modules/snippy.nf b/modules/snippy.nf
@@ -1,11 +1,6 @@
 nextflow.enable.dsl=2
 
 
-// Params:
-//   - outdir
-//   - single_end
-//   - targets
-//   - report
 process snippy {
     tag "${id}"
 
@@ -32,15 +27,16 @@ process snippy {
         $param_input \
         $param_targets \
         $param_report \
+        --mincov ${params.mincov} \
+        --minfrac ${params.minfrac} \
+        --minqual ${params.minqual} \
         --force \
         --tmpdir tmp
     rm -rf tmp
     """
 }
 
 
-// Params:
-//   - outdir
 process snippy_core {
     publishDir "${params.outdir}/snippy_core" , mode: 'copy'
     publishDir "${params.outdir}" , mode: 'copy' ,

diff --git a/modules/snp_sites.nf b/modules/snp_sites.nf
@@ -1,8 +1,6 @@
 nextflow.enable.dsl=2
 
 
-// Params:
-//   - outdir
 process snp_sites {
     publishDir "${params.outdir}/gubbins/" , mode: 'copy'
 

diff --git a/nextflow.config b/nextflow.config
@@ -9,6 +9,9 @@ params {
 
     /* snippy options */
     report = false                    // generate a snps.report.txt
+    mincov = 10                       // minimum site depth to for calling alleles
+    minfrac = 0                       // minumum proportion for variant evidence (0=AUTO)
+    minqual = 100                     // minumum QUALITY in VCF column 6
 
     /* gubbins options */
     skip_gubbins = false              // skip gubbins
@@ -46,7 +49,7 @@ manifest {
     homePage = 'metashot.github.io'
     description = 'SNVs identification and phylogenetic tree inference from prokaryotic isolates'
     mainScript = 'main.nf'
-    version = '1.0.0'
+    version = '1.1.0'
 }