use metaFlye for mag assembly

jimmyliu1326 · Jun 21, 2023 · 8da69ab · 8da69ab
1 parent d253cdf
commit 8da69ab
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Showing 2 changed files with 21 additions and 10 deletions.
diff --git a/modules/local/nanopore-assembly.nf b/modules/local/nanopore-assembly.nf
@@ -1,16 +1,21 @@
 // assembly methods for Nanopore workflows
-process flye {
-    tag "Flye assembly on ${sample_id}"
+process metaflye {
+    tag "MetaFlye assembly on ${sample_id}"
     label "process_medium"
+    publishDir "$params.outdir"+"/assembly/", mode: "copy"
+    errorStrategy 'ignore'
 
     input:
         tuple val(sample_id), path(reads)
+        val(flye_opts)
     output:
-        tuple val(sample_id), file("flye/${sample_id}.fasta")
+        tuple val(sample_id), file("${sample_id}.fasta"), emit: fasta
+        tuple val(sample_id), file("${sample_id}.gfa"), emit: gfa
     shell:
         """
-        flye --nano-raw ${reads} -t ${task.cpus} -i 2 --out-dir flye
-        mv flye/assembly.fasta flye/${sample_id}.fasta
+        flye --nano-raw ${reads} -t ${task.cpus} -i 0 --meta --keep-haplotypes --no-alt-contigs --out-dir flye ${flye_opts}
+        mv flye/assembly.fasta ${sample_id}.fasta
+        mv flye/assembly_graph.gfa ${sample_id}.gfa
         """
 }
 

diff --git a/subworkflow/genome_assembly.nf b/subworkflow/genome_assembly.nf
@@ -1,5 +1,5 @@
 // import modules
-include { flye; dragonflye } from '../modules/local/nanopore-assembly.nf'
+include { metaflye; dragonflye } from '../modules/local/nanopore-assembly.nf'
 include { medaka; medaka_gpu } from '../modules/local/nanopore-polish.nf'
 include { shovill } from '../modules/local/illumina-assembly.nf'
 
@@ -8,23 +8,29 @@ workflow ASSEMBLY_nanopore {
     main:
         // define assembly opts for target wgs and metagenomics
         flye_opts=""
-        if (params.meta) { flye_opts = flye_opts + "--depth 0 --opts '--meta --keep-haplotypes -i 0'" }
+        //if (params.meta) { flye_opts = flye_opts + "--depth 0 --opts '--meta --keep-haplotypes -i 0'" }
         if( params.nanohq ) { flye_opts = flye_opts + " --nanohq" }
 
         // run assembly workflow
-        dragonflye(reads, flye_opts)
+        if ( params.meta ) {
+            metaflye(reads, flye_opts)
+            assembly = metaflye.out.fasta
+        } else {
+            dragonflye(reads, flye_opts)
+            assembly = dragonflye.out.fasta
+        }
 
         if (params.gpu) {
 
-            dragonflye.out.fasta \
+            assembly \
                 | join(reads) \
                 | medaka_gpu
 
             assembly_out = medaka_gpu.out
 
         } else {
 
-            dragonflye.out.fasta \
+            assembly \
                 | join(reads) \
                 | medaka