Merge pull request #17 from BCCDC-PHL/fix_gubbins

remove testing num isolates within snippy core module

README.md

@@ -38,7 +38,7 @@ Note: the process WITHOUT gubbins occurs if --skip_gubbins is true, or if there
 ## Usage
 
 ```
-nextflow run BCCDC-PHL/snippy-phylogenomics-nf \
+nextflow run BCCDC-PHL/snippy-core-phylogenomics \
   --snippy_dirs </path/to/snippy_output_dirs> \
   --ref ref.fa \
   [--mask mask.bed] \

main.nf

@@ -34,12 +34,9 @@ workflow {
 
 
   if (!params.skip_gubbins) {
-    gubbins(snippy_core.out.clean_full_alignment, snippy_core.out.run_gubbins)
-    if (snippy_core.out.run_gubbins == "true") {
-      ch_alignment = gubbins.out.filtered_polymorphic_sites
-    } else {
-      ch_alignment = snippy_core.out.clean_full_alignment
-    }
+    gubbins(snippy_core.out.clean_full_alignment)
+    ch_alignment = gubbins.out.filtered_polymorphic_sites
+
   } else {
     ch_alignment = snippy_core.out.clean_full_alignment
   }

modules/gubbins.nf

@@ -6,15 +6,12 @@ process gubbins {
 
   input:
   path(alignment)
-  val(run_gubbins)
 
   output:
   path('gubbins.filtered_polymorphic_sites.fasta'), emit: filtered_polymorphic_sites
   path('gubbins.recombination_predictions.gff'),    emit: recombination_predictions_gff
   path('gubbins.per_branch_statistics.tsv'),        emit: per_branch_statistics
 
-  when:
-  run_gubbins == "true"
 
   script:
   """

modules/snippy_core.nf

@@ -12,7 +12,6 @@ process snippy_core {
     path('core.tsv'), emit: core_stats
     path('core.full.aln'), emit: full_alignment
     path('clean.full.aln'), emit: clean_full_alignment
-    val('run_gubbins'), emit: run_gubbins
 
 
     script:
@@ -26,13 +25,6 @@ process snippy_core {
 
     add_percent_used.py core.txt > core.tsv
 
-    num_isolates=\$(echo "\$snippy_dirs" | tr -s ' ' | wc -w)
-    if [ "\$num_isolates" -ge 3 ]; then
-        run_gubbins='true'
-    else
-        run_gubbins='false'
-    fi
-    
     """
 }