Make snippy report optional (#14)

* make snippy report optional

* flipped logic to skip_report instead for backward compatibility

* removed defaults channel from env

* Bump version

---------

Co-authored-by: Dan Fornika <dfornika@gmail.com>

Author: jpalmer37

environments/environment.yml

@@ -2,7 +2,6 @@ name: snippy-nf
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - python=3
   - csvkit=1.0.5

modules/snippy.nf

@@ -44,14 +44,15 @@ process snippy {
 
     script:
     ram = task.memory ? ram = "--ram ${task.memory}" : "" 
+    report = params.skip_report ? "" : "--report"
     """
     mkdir tmp
 
     snippy \
       --tmpdir ./tmp \
       --cpus ${task.cpus} \
       ${ram} \
-      --report \
+      ${report} \
       --prefix ${sample_id} \
       --mincov ${params.mincov} \
       --basequal ${params.basequal} \

nextflow.config

@@ -1,7 +1,7 @@
 manifest {
   author = 'Dan Fornika'
   name = 'BCCDC-PHL/snippy-nf'
-  version = '0.1.0'
+  version = '0.1.1'
   description = 'BCCDC-PHL Nextflow wrapper for Snippy'
   mainScript = 'main.nf'
   nextflowVersion = '>=20.01.0'
@@ -19,6 +19,7 @@ params {
   mapqual = 60
   minfrac = 0
   outdir = 'results'
+  skip_report = false
   pipeline_short_name = parsePipelineName(manifest.toMap().get('name'))
   pipeline_minor_version = parseMinorVersion(manifest.toMap().get('version'))
 }