applied reviewer suggestions #104

README.md

@@ -30,7 +30,7 @@ This pipeline is primarily for bacterial assembly of next-generation sequencing
 ### Long Read Assembly
 
 For users that only have Nanopore data, the pipeline quality trims these using [PoreChop](https://github.com/rrwick/Porechop) and assesses basic sequencing QC utilizing [NanoPlot](https://github.com/wdecoster/NanoPlot) and [PycoQC](https://github.com/a-slide/pycoQC).
-The pipeline can then perform long read assembly utilizing [Unicycler](https://github.com/rrwick/Unicycler), [Miniasm](https://github.com/lh3/miniasm) in combination with [Racon](https://github.com/isovic/racon), [Canu](https://github.com/marbl/canu) or [Flye](https://github.com/fenderglass/Flye) by using the [Dragonflye](https://github.com/rpetit3/dragonflye)\* pipeline. Long reads assembly can be polished using [Medaka](https://github.com/nanoporetech/medaka) or [NanoPolish](https://github.com/jts/nanopolish) with Fast5 files.
+The pipeline can then perform long read assembly utilizing [Unicycler](https://github.com/rrwick/Unicycler), [Miniasm](https://github.com/lh3/miniasm) in combination with [Racon](https://github.com/isovic/racon), [Canu](https://github.com/marbl/canu) or [Flye](https://github.com/fenderglass/Flye) by using the [Dragonflye](https://github.com/rpetit3/dragonflye)(\*) pipeline. Long reads assembly can be polished using [Medaka](https://github.com/nanoporetech/medaka) or [NanoPolish](https://github.com/jts/nanopolish) with Fast5 files.
 
 > **\*Note**: Dragonflye is a comprehensive pipeline designed for genome assembly of Oxford Nanopore Reads. It facilitates the utilization of Flye (default), Miniasm, and Raven assemblers, along with Racon(default) and Medaka polishers. For more information, visit the [Dragonflye GitHub](https://github.com/rpetit3/dragonflye) repository.
 

conf/modules.config

@@ -96,21 +96,21 @@ process {
 
     withName: 'DRAGONFLYE' {
         ext.args = {
-            if ( $meta.gsize && $meta.gsize != 'NA' ){
+            if ( !$meta.gsize?.equals('NA') ){
                 if ( !params.dragonflye_args.contains("--gsize") ) {
                     "--gsize ${meta.gsize} ${params.dragonflye_args}"
                 } else {
-                    params.dragonflye_args ? params.dragonflye_args : ''
+                    params.dragonflye_args ?: ''
                 }
             } else {
-                params.dragonflye_args ? params.dragonflye_args : ''
+                params.dragonflye_args ?: ''
             }
         }
 
         publishDir = [
             path: { "${params.outdir}/Dragonflye" },
             mode: params.publish_dir_mode,
-            pattern: '*.fa',
+            pattern: "*.{fa,log}",
             saveAs: { filename ->
                 if (filename.equals('versions.yml')) {
                     null

docs/output.md

@@ -148,6 +148,9 @@ Check out the [Miniasm documentation](https://github.com/lh3/miniasm) for more i
 
 - `Dragonflye/`
   - `*.contigs.fa`: Assembly in Fasta format
+  - `*.dragonflye.log`: Log file containing the report of the dragonflye process
+
+Checkout the [Dragonflye](https://github.com/rpetit3/dragonflye) documentation for more information of the Dragonflye output.
 
 </details>