add bootstrap parametrization

hoelzer-lab · Mar 6, 2022 · 6544492 · 6544492
1 parent 50547cb
commit 6544492
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Showing 3 changed files with 4 additions and 2 deletions.
diff --git a/modules/raxml.nf b/modules/raxml.nf
@@ -12,8 +12,8 @@ process raxml {
 
   script:
     """
-    #raxmlHPC-PTHREADS-SSE3 -T ${task.cpus} -f a -x 1234 -p 1234 -s coreGenome_mafft.aln -n aa -m PROTGAMMAWAG -N 100 
-    raxml-ng --all --threads ${task.cpus} --msa coreGenome_mafft.aln --prefix coreGenome_mafft --msa-format FASTA --model PROTGTR+G --bs-trees 100 
+    #raxmlHPC-PTHREADS-SSE3 -T ${task.cpus} -f a -x 1234 -p 1234 -s ${aln} -n aa -m PROTGAMMAWAG -N ${params.bootstrap}
+    raxml-ng --all --threads ${task.cpus} --msa ${aln} --prefix coreGenome_mafft --msa-format FASTA --model PROTGTR+G --bs-trees ${params.bootstrap} 
     """
 }
 
diff --git a/nextflow.config b/nextflow.config
@@ -21,6 +21,7 @@ params {
   heigth = 8
   width = 10
   tree = false
+  bootstrap = 100
   sets = false
   tmlim = 240 // ILP solve time limit in seconds
 

diff --git a/ribap.nf b/ribap.nf
@@ -214,6 +214,7 @@ def helpMSG() {
     --tree              build tree based on the core genome? 
                         Sure thing, We will use RAxML for this. 
                         Be aware, this will take a lot of time. [default: $params.tree]
+    --bootstrap         Bootstrap value for tree building (increases time!). [default $params.bootstrap] 
 
     ${c_yellow}UpSet plot:${c_reset}
     --sets              FASTA simpleNames for genomes that should be