From d21bfb034467d134095b83545453c2ca016de67d Mon Sep 17 00:00:00 2001
From: Dan Fornika <dfornika@gmail.com>
Date: Tue, 28 Nov 2023 16:26:39 -0800
Subject: [PATCH] Add support for flye `--meta` flag (#11)

* bump version

* Add support for --meta flag
---
 README.md             | 12 ++++++++++++
 modules/dragonflye.nf | 11 +++++++++++
 nextflow.config       |  3 ++-
 3 files changed, 25 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index a794ed2..45364f5 100644
--- a/README.md
+++ b/README.md
@@ -83,6 +83,18 @@ nextflow run BCCDC-PHL/dragonflye-nf \
   --outdir <output directory>
 ```
 
+The `--meta` flag can be passed through to flye by adding the `--flye_meta` flag. The `--meta` flag is intended for use with metagenome assemblies,
+but may be helpful in other scenarios such as plasmid assembly:
+
+```
+nextflow run BCCDC-PHL/dragonflye-nf \
+  --hybrid \
+  --flye_meta \
+  --fastq_input <short-read fastq input directory> \
+  --fastq_input_long <long-read fastq input directory> \
+  --outdir <output directory>
+```
+
 ## Output
 An output directory will be created for each sample under the directory provided with the `--outdir` flag. The directory will be named by sample ID, inferred from
 the fastq files (all characters before the first underscore in the fastq filenames), or the `ID` field of the samplesheet, if one is used.
diff --git a/modules/dragonflye.nf b/modules/dragonflye.nf
index fc32351..e4eda1c 100644
--- a/modules/dragonflye.nf
+++ b/modules/dragonflye.nf
@@ -18,14 +18,25 @@ process dragonflye {
       hybrid_long_reads = assembly_mode == "hybrid" ? "--reads ${reads[2]}" : ""
       long_reads        = assembly_mode == "long"   ? "--reads ${reads[0]}" : ""
       polypolish        = assembly_mode == "hybrid" ? "--polypolish" : ""
+      meta              = params.flye_meta ? "--opts '--meta'" : ""
       """
       printf -- "- process_name: dragonflye\\n"                                                 >> ${sample_id}_dragonflye_${assembly_mode}_provenance.yml
       printf -- "  tools:\\n"                                                                   >> ${sample_id}_dragonflye_${assembly_mode}_provenance.yml
       printf -- "    - tool_name: dragonflye\\n"                                                >> ${sample_id}_dragonflye_${assembly_mode}_provenance.yml
       printf -- "      tool_version: \$(dragonflye --version | cut -d ' ' -f 2 | tr -d 'v')\\n" >> ${sample_id}_dragonflye_${assembly_mode}_provenance.yml
+      printf -- "      parameters:\\n"                                                          >> ${sample_id}_dragonflye_${assembly_mode}_provenance.yml
+      printf -- "        - parameter: --tmpdir\\n"                                              >> ${sample_id}_dragonflye_${assembly_mode}_provenance.yml
+      printf -- "          value: ./tmp\\n"                                                     >> ${sample_id}_dragonflye_${assembly_mode}_provenance.yml
+
+      if [ "${params.flye_meta}" == "true" ]; then
+        printf -- "        - parameter: --opts\\n"                                              >> ${sample_id}_dragonflye_${assembly_mode}_provenance.yml
+        printf -- "          value: '--meta'\\n"                                                >> ${sample_id}_dragonflye_${assembly_mode}_provenance.yml
+      fi
+    
 
       dragonflye --cpus ${task.cpus} \
         --tmpdir './tmp' \
+	${meta} \
         ${short_reads} \
         ${hybrid_long_reads} \
 	${long_reads} \
diff --git a/nextflow.config b/nextflow.config
index 8d07c7c..5493d93 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -1,7 +1,7 @@
 manifest {
   author = 'Dan Fornika'
   name = 'BCCDC-PHL/dragonflye-nf'
-  version = '0.1.2'
+  version = '0.1.3'
   description = 'Nextflow wrapper for Dragonflye Assembler'
   mainScript = 'main.nf'
   nextflowVersion = '>=20.01.0'
@@ -25,6 +25,7 @@ params {
   fastq_input_long = 'NO_FILE'
   filtlong_min_length = 1000
   filtlong_keep_percent = 90
+  flye_meta = false
   samplesheet_input = 'NO_FILE'
   versioned_outdir = false
   collect_outputs = false