From 209a2bddba4ff56b89450c8e1441b31fbffa67d0 Mon Sep 17 00:00:00 2001
From: Daniel-VM <danielvmillares@gmail.com>
Date: Tue, 31 Oct 2023 17:58:47 +0100
Subject: [PATCH 01/10] patch dragonflye module to allow short-reads polishing
 of draft genome

---
 conf/modules.config                        |  2 +-
 modules.json                               |  3 +-
 modules/nf-core/dragonflye/dragonflye.diff | 39 ++++++++++++++++++++++
 modules/nf-core/dragonflye/main.nf         |  6 ++--
 modules/nf-core/dragonflye/meta.yml        |  2 +-
 workflows/bacass.nf                        |  7 ++--
 6 files changed, 51 insertions(+), 8 deletions(-)
 create mode 100644 modules/nf-core/dragonflye/dragonflye.diff

diff --git a/conf/modules.config b/conf/modules.config
index d33ea8de..46308d77 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -96,7 +96,7 @@ process {
 
     withName: 'DRAGONFLYE' {
         ext.args = {
-            if ( $meta.gsize || $meta.gsize != 'NA' ){
+            if ( $meta.gsize && $meta.gsize != 'NA' ){
                 if ( !params.dragonflye_args.contains("--gsize") ) {
                     "--gsize ${meta.gsize} ${params.dragonflye_args}"
                 } else {
diff --git a/modules.json b/modules.json
index 205b7a79..2c61af54 100644
--- a/modules.json
+++ b/modules.json
@@ -28,7 +28,8 @@
                     "dragonflye": {
                         "branch": "master",
                         "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/dragonflye/dragonflye.diff"
                     },
                     "fastp": {
                         "branch": "master",
diff --git a/modules/nf-core/dragonflye/dragonflye.diff b/modules/nf-core/dragonflye/dragonflye.diff
new file mode 100644
index 00000000..4122edb3
--- /dev/null
+++ b/modules/nf-core/dragonflye/dragonflye.diff
@@ -0,0 +1,39 @@
+Changes in module 'nf-core/dragonflye'
+--- modules/nf-core/dragonflye/meta.yml
++++ modules/nf-core/dragonflye/meta.yml
+@@ -18,7 +18,7 @@
+         e.g. [ id:'test', single_end:false ]
+   - reads:
+       type: file
+-      description: Input Nanopore FASTQ file
++      description: Input Nanopore FASTQ file. Optional, additional Illumina FASTQ files can be provided to perform short reads polishing.
+       pattern: "*.fastq.gz"
+ output:
+   - meta:
+
+--- modules/nf-core/dragonflye/main.nf
++++ modules/nf-core/dragonflye/main.nf
+@@ -8,7 +8,7 @@
+         'biocontainers/dragonflye:1.0.11--hdfd78af_0' }"
+ 
+     input:
+-    tuple val(meta), path(reads)
++    tuple val(meta), path(shortreads), path(longreads)
+ 
+     output:
+     tuple val(meta), path("contigs.fa")                                        , emit: contigs
+@@ -24,9 +24,11 @@
+     script:
+     def args = task.ext.args ?: ''
+     def memory = task.memory.toGiga()
++    def short_polishing = shortreads ? "--R1 ${shortreads[0]} --R2 ${shortreads[1]}" : '' 
+     """
+     dragonflye \\
+-        --reads ${reads} \\
++        --reads ${longreads} \\
++        $short_polishing \\
+         $args \\
+         --cpus $task.cpus \\
+         --ram $memory \\
+
+************************************************************
diff --git a/modules/nf-core/dragonflye/main.nf b/modules/nf-core/dragonflye/main.nf
index bc3527a7..9e60df14 100644
--- a/modules/nf-core/dragonflye/main.nf
+++ b/modules/nf-core/dragonflye/main.nf
@@ -8,7 +8,7 @@ process DRAGONFLYE {
         'biocontainers/dragonflye:1.0.11--hdfd78af_0' }"
 
     input:
-    tuple val(meta), path(reads)
+    tuple val(meta), path(shortreads), path(longreads)
 
     output:
     tuple val(meta), path("contigs.fa")                                        , emit: contigs
@@ -24,9 +24,11 @@ process DRAGONFLYE {
     script:
     def args = task.ext.args ?: ''
     def memory = task.memory.toGiga()
+    def short_polishing = shortreads ? "--R1 ${shortreads[0]} --R2 ${shortreads[1]}" : '' 
     """
     dragonflye \\
-        --reads ${reads} \\
+        --reads ${longreads} \\
+        $short_polishing \\
         $args \\
         --cpus $task.cpus \\
         --ram $memory \\
diff --git a/modules/nf-core/dragonflye/meta.yml b/modules/nf-core/dragonflye/meta.yml
index 13b9ad66..4c3b9405 100644
--- a/modules/nf-core/dragonflye/meta.yml
+++ b/modules/nf-core/dragonflye/meta.yml
@@ -18,7 +18,7 @@ input:
         e.g. [ id:'test', single_end:false ]
   - reads:
       type: file
-      description: Input Nanopore FASTQ file
+      description: Input Nanopore FASTQ file. Optional, additional Illumina FASTQ files can be provided to perform short reads polishing.
       pattern: "*.fastq.gz"
 output:
   - meta:
diff --git a/workflows/bacass.nf b/workflows/bacass.nf
index 708ce8c4..aba591c5 100644
--- a/workflows/bacass.nf
+++ b/workflows/bacass.nf
@@ -226,7 +226,7 @@ workflow BACASS {
     ch_assembly = Channel.empty()
 
     //
-    // MODULE: Unicycler, genome assembly, nf-core module allows only short assembly
+    // MODULE: Unicycler, genome assembly, nf-core module allows only short, long and hybrid assembly
     //
     if ( params.assembler == 'unicycler' ) {
         UNICYCLER (
@@ -236,6 +236,7 @@ workflow BACASS {
         ch_versions = ch_versions.mix( UNICYCLER.out.versions.ifEmpty(null) )
     }
 
+
     //
     // MODULE: Canu, genome assembly, long reads
     //
@@ -294,11 +295,11 @@ workflow BACASS {
     }
 
     //
-    // MODULE: Dragonflye, genome assembly, long reads
+    // MODULE: Dragonflye, genome assembly of long reads. Short reads polishing of the draft genome is available, when both short and long reads are present.
     //
     if( params.assembler == 'dragonflye' ){
         DRAGONFLYE(
-            ch_for_assembly.map { meta, sr, lr -> tuple(meta, lr) }
+            ch_for_assembly
         )
         ch_assembly = ch_assembly.mix( DRAGONFLYE.out.contigs.dump(tag: 'dragonflye') )
         ch_versions = ch_versions.mix( DRAGONFLYE.out.versions.ifEmpty(null) )

From 1a01a47a4208a42c885741b6ccdedf0373500b19 Mon Sep 17 00:00:00 2001
From: Daniel-VM <danielvmillares@gmail.com>
Date: Thu, 2 Nov 2023 17:44:02 +0100
Subject: [PATCH 02/10] porechop patch to prevent input file from being
 overwritten with output file

---
 modules.json                                  |  3 ++-
 modules/nf-core/porechop/porechop/main.nf     |  4 ++--
 .../porechop/porechop/porechop-porechop.diff  | 23 +++++++++++++++++++
 3 files changed, 27 insertions(+), 3 deletions(-)
 create mode 100644 modules/nf-core/porechop/porechop/porechop-porechop.diff

diff --git a/modules.json b/modules.json
index 2c61af54..8a3cf78d 100644
--- a/modules.json
+++ b/modules.json
@@ -75,7 +75,8 @@
                     "porechop/porechop": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/porechop/porechop/porechop-porechop.diff"
                     },
                     "prokka": {
                         "branch": "master",
diff --git a/modules/nf-core/porechop/porechop/main.nf b/modules/nf-core/porechop/porechop/main.nf
index 8fe0dd2e..f4bfd21c 100644
--- a/modules/nf-core/porechop/porechop/main.nf
+++ b/modules/nf-core/porechop/porechop/main.nf
@@ -11,7 +11,7 @@ process PORECHOP_PORECHOP {
     tuple val(meta), path(reads)
 
     output:
-    tuple val(meta), path("*.fastq.gz"), emit: reads
+    tuple val(meta), path("*.porechop.fastq.gz"), emit: reads
     tuple val(meta), path("*.log")     , emit: log
     path "versions.yml"                , emit: versions
 
@@ -26,7 +26,7 @@ process PORECHOP_PORECHOP {
         -i $reads \\
         -t $task.cpus \\
         $args \\
-        -o ${prefix}.fastq.gz \\
+        -o ${prefix}.porechop.fastq.gz \\
         > ${prefix}.log
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/porechop/porechop/porechop-porechop.diff b/modules/nf-core/porechop/porechop/porechop-porechop.diff
new file mode 100644
index 00000000..528a4031
--- /dev/null
+++ b/modules/nf-core/porechop/porechop/porechop-porechop.diff
@@ -0,0 +1,23 @@
+Changes in module 'nf-core/porechop/porechop'
+--- modules/nf-core/porechop/porechop/main.nf
++++ modules/nf-core/porechop/porechop/main.nf
+@@ -11,7 +11,7 @@
+     tuple val(meta), path(reads)
+ 
+     output:
+-    tuple val(meta), path("*.fastq.gz"), emit: reads
++    tuple val(meta), path("*.porechop.fastq.gz"), emit: reads
+     tuple val(meta), path("*.log")     , emit: log
+     path "versions.yml"                , emit: versions
+ 
+@@ -26,7 +26,7 @@
+         -i $reads \\
+         -t $task.cpus \\
+         $args \\
+-        -o ${prefix}.fastq.gz \\
++        -o ${prefix}.porechop.fastq.gz \\
+         > ${prefix}.log
+     cat <<-END_VERSIONS > versions.yml
+     "${task.process}":
+
+************************************************************

From ed3d296975d1f1d3437cadb661057bf0223d6009 Mon Sep 17 00:00:00 2001
From: Daniel-VM <danielvmillares@gmail.com>
Date: Fri, 3 Nov 2023 10:41:46 +0100
Subject: [PATCH 03/10] update dragonflye version and fix output file name

---
 modules/nf-core/dragonflye/dragonflye.diff | 35 +++++++++++++++++++---
 modules/nf-core/dragonflye/environment.yml |  2 +-
 modules/nf-core/dragonflye/main.nf         | 10 ++++---
 3 files changed, 38 insertions(+), 9 deletions(-)

diff --git a/modules/nf-core/dragonflye/dragonflye.diff b/modules/nf-core/dragonflye/dragonflye.diff
index 4122edb3..73237c1c 100644
--- a/modules/nf-core/dragonflye/dragonflye.diff
+++ b/modules/nf-core/dragonflye/dragonflye.diff
@@ -1,4 +1,13 @@
 Changes in module 'nf-core/dragonflye'
+--- modules/nf-core/dragonflye/environment.yml
++++ modules/nf-core/dragonflye/environment.yml
+@@ -3,4 +3,4 @@
+   - bioconda
+   - defaults
+ dependencies:
+-  - bioconda::dragonflye=1.0.11
++  - bioconda::dragonflye=1.1.2
+
 --- modules/nf-core/dragonflye/meta.yml
 +++ modules/nf-core/dragonflye/meta.yml
 @@ -18,7 +18,7 @@
@@ -13,18 +22,34 @@ Changes in module 'nf-core/dragonflye'
 
 --- modules/nf-core/dragonflye/main.nf
 +++ modules/nf-core/dragonflye/main.nf
-@@ -8,7 +8,7 @@
-         'biocontainers/dragonflye:1.0.11--hdfd78af_0' }"
+@@ -4,17 +4,17 @@
+ 
+     conda 'modules/nf-core/dragonflye/environment.yml'
+     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+-        'https://depot.galaxyproject.org/singularity/dragonflye:1.0.11--hdfd78af_0' :
+-        'biocontainers/dragonflye:1.0.11--hdfd78af_0' }"
++        'https://depot.galaxyproject.org/singularity/dragonflye:1.1.2--hdfd78af_0' :
++        'biocontainers/dragonflye:1.1.2--hdfd78af_0' }"
  
      input:
 -    tuple val(meta), path(reads)
 +    tuple val(meta), path(shortreads), path(longreads)
  
      output:
-     tuple val(meta), path("contigs.fa")                                        , emit: contigs
-@@ -24,9 +24,11 @@
+-    tuple val(meta), path("contigs.fa")                                        , emit: contigs
++    tuple val(meta), path("*.contigs.fa")                                      , emit: contigs
+     tuple val(meta), path("dragonflye.log")                                    , emit: log
+     tuple val(meta), path("{flye,miniasm,raven}.fasta")                        , emit: raw_contigs
+-    tuple val(meta), path("{miniasm,raven}-unpolished.gfa"), optional:true     , emit: gfa
++    tuple val(meta), path("{flye,miniasm,raven}-unpolished.gfa"), optional:true, emit: gfa
+     tuple val(meta), path("flye-info.txt"), optional:true                      , emit: txt
+     path "versions.yml"                                                        , emit: versions
+ 
+@@ -23,11 +23,15 @@
+ 
      script:
      def args = task.ext.args ?: ''
++    def prefix = task.ext.prefix ?: "${meta.id}"
      def memory = task.memory.toGiga()
 +    def short_polishing = shortreads ? "--R1 ${shortreads[0]} --R2 ${shortreads[1]}" : '' 
      """
@@ -33,7 +58,9 @@ Changes in module 'nf-core/dragonflye'
 +        --reads ${longreads} \\
 +        $short_polishing \\
          $args \\
++        --prefix ${prefix}.contigs \\
          --cpus $task.cpus \\
          --ram $memory \\
+         --outdir ./ \\
 
 ************************************************************
diff --git a/modules/nf-core/dragonflye/environment.yml b/modules/nf-core/dragonflye/environment.yml
index 8a7ad456..7899d46d 100644
--- a/modules/nf-core/dragonflye/environment.yml
+++ b/modules/nf-core/dragonflye/environment.yml
@@ -3,4 +3,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::dragonflye=1.0.11
+  - bioconda::dragonflye=1.1.2
diff --git a/modules/nf-core/dragonflye/main.nf b/modules/nf-core/dragonflye/main.nf
index 9e60df14..4ed9f7f0 100644
--- a/modules/nf-core/dragonflye/main.nf
+++ b/modules/nf-core/dragonflye/main.nf
@@ -4,17 +4,17 @@ process DRAGONFLYE {
 
     conda 'modules/nf-core/dragonflye/environment.yml'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/dragonflye:1.0.11--hdfd78af_0' :
-        'biocontainers/dragonflye:1.0.11--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/dragonflye:1.1.2--hdfd78af_0' :
+        'biocontainers/dragonflye:1.1.2--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(shortreads), path(longreads)
 
     output:
-    tuple val(meta), path("contigs.fa")                                        , emit: contigs
+    tuple val(meta), path("*.contigs.fa")                                      , emit: contigs
     tuple val(meta), path("dragonflye.log")                                    , emit: log
     tuple val(meta), path("{flye,miniasm,raven}.fasta")                        , emit: raw_contigs
-    tuple val(meta), path("{miniasm,raven}-unpolished.gfa"), optional:true     , emit: gfa
+    tuple val(meta), path("{flye,miniasm,raven}-unpolished.gfa"), optional:true, emit: gfa
     tuple val(meta), path("flye-info.txt"), optional:true                      , emit: txt
     path "versions.yml"                                                        , emit: versions
 
@@ -23,6 +23,7 @@ process DRAGONFLYE {
 
     script:
     def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
     def memory = task.memory.toGiga()
     def short_polishing = shortreads ? "--R1 ${shortreads[0]} --R2 ${shortreads[1]}" : '' 
     """
@@ -30,6 +31,7 @@ process DRAGONFLYE {
         --reads ${longreads} \\
         $short_polishing \\
         $args \\
+        --prefix ${prefix}.contigs \\
         --cpus $task.cpus \\
         --ram $memory \\
         --outdir ./ \\

From 1bfafe9ce72d347119990238f9fdc816d7009e2f Mon Sep 17 00:00:00 2001
From: Daniel-VM <danielvmillares@gmail.com>
Date: Fri, 3 Nov 2023 10:56:07 +0100
Subject: [PATCH 04/10] add dragonflye hybrid-mode to readme

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 7cd33be0..43595176 100644
--- a/README.md
+++ b/README.md
@@ -36,7 +36,7 @@ The pipeline can then perform long read assembly utilizing [Unicycler](https://g
 
 ### Hybrid Assembly
 
-For users specifying both short read and long read (NanoPore) data, the pipeline can perform a hybrid assembly approach utilizing [Unicycler](https://github.com/rrwick/Unicycler), taking the full set of information from short reads and long reads into account.
+For users specifying both short read and long read (NanoPore) data, the pipeline can perform a hybrid assembly approach utilizing [Unicycler](https://github.com/rrwick/Unicycler) or [Dragonflye](https://github.com/rpetit3/dragonflye) (polishing of the assembled genome with short reads), taking the full set of information from short reads and long reads into account.
 
 ### Assembly QC and annotation
 

From 43d5aedec35fb68e2fd61ec6abdbe84fbb9028d5 Mon Sep 17 00:00:00 2001
From: Daniel-VM <danielvmillares@gmail.com>
Date: Fri, 3 Nov 2023 17:34:08 +0100
Subject: [PATCH 05/10] temp fix of dragonflye modules.config

---
 conf/modules.config | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 4f39a538..39f2566b 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -96,7 +96,7 @@ process {
 
     withName: 'DRAGONFLYE' {
         ext.args = {
-            if ( !$meta.gsize?.equals('NA') ){
+            if ( !(${meta.gsize}.equals('NA')) && ${meta.gsize} != null ){
                 if ( !params.dragonflye_args.contains("--gsize") ) {
                     "--gsize ${meta.gsize} ${params.dragonflye_args}"
                 } else {
@@ -106,7 +106,6 @@ process {
                 params.dragonflye_args ?: ''
             }
         }
-
         publishDir = [
             path: { "${params.outdir}/Dragonflye" },
             mode: params.publish_dir_mode,
@@ -114,8 +113,10 @@ process {
             saveAs: { filename ->
                 if (filename.equals('versions.yml')) {
                     null
-                } else {
+                } else if (filename.endsWith('.log')) {
                     "${meta.id}.${filename}"
+                } else {
+                    filename
                 }
             }
         ]

From 01df1d2d457c6e7915034dc5fc1d2e100056a7ea Mon Sep 17 00:00:00 2001
From: Dani VM <da.valle@isciii.es>
Date: Mon, 6 Nov 2023 09:10:59 +0100
Subject: [PATCH 06/10] complete fix of dragonflye module config

---
 conf/modules.config | 2 +-
 workflows/bacass.nf | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 39f2566b..8c3f11cf 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -96,7 +96,7 @@ process {
 
     withName: 'DRAGONFLYE' {
         ext.args = {
-            if ( !(${meta.gsize}.equals('NA')) && ${meta.gsize} != null ){
+            if ( meta.gsize && !meta.gsize.equals('NA') ){
                 if ( !params.dragonflye_args.contains("--gsize") ) {
                     "--gsize ${meta.gsize} ${params.dragonflye_args}"
                 } else {
diff --git a/workflows/bacass.nf b/workflows/bacass.nf
index aba591c5..7a2ce5cc 100644
--- a/workflows/bacass.nf
+++ b/workflows/bacass.nf
@@ -295,7 +295,7 @@ workflow BACASS {
     }
 
     //
-    // MODULE: Dragonflye, genome assembly of long reads. Short reads polishing of the draft genome is available, when both short and long reads are present.
+    // MODULE: Dragonflye, genome assembly of long reads. Moreover, it provides the option for polishing the draft genome using short reads when both short and long reads are available.
     //
     if( params.assembler == 'dragonflye' ){
         DRAGONFLYE(

From 7eb99318ec7b754696af900a3cf7c148316001b1 Mon Sep 17 00:00:00 2001
From: Daniel-VM <danielvmillares@gmail.com>
Date: Tue, 7 Nov 2023 10:48:16 +0100
Subject: [PATCH 07/10] update CHANGELOG #106

---
 CHANGELOG.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1889c243..a76fd9e8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,7 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
-- [#104](https://github.com/nf-core/bacass/pull/104) - Added dragonflye module for long-reads assembly
+- [#104](https://github.com/nf-core/bacass/pull/104) - Added dragonflye module for long-reads assembly.
+- [#106](https://github.com/nf-core/bacass/pull/106) - Added patch to dragonflye module enbling draft genome polishing with short-reads.
 
 ### `Fixed`
 

From ca59305c971acc6fdc167a42d33c9a621f4f4ff3 Mon Sep 17 00:00:00 2001
From: Daniel-VM <danielvmillares@gmail.com>
Date: Thu, 9 Nov 2023 09:58:07 +0100
Subject: [PATCH 08/10] add reviewer suggestions #106

---
 CHANGELOG.md                                  |  4 +--
 README.md                                     |  2 +-
 conf/modules.config                           |  1 +
 conf/test_hybrid_dragonflye.config            | 30 +++++++++++++++++++
 modules.json                                  |  3 +-
 modules/nf-core/porechop/porechop/main.nf     |  4 +--
 .../porechop/porechop/porechop-porechop.diff  | 23 --------------
 nextflow.config                               | 15 +++++-----
 8 files changed, 44 insertions(+), 38 deletions(-)
 create mode 100644 conf/test_hybrid_dragonflye.config
 delete mode 100644 modules/nf-core/porechop/porechop/porechop-porechop.diff

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a76fd9e8..b290d9a8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,9 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
-- [#104](https://github.com/nf-core/bacass/pull/104) - Added dragonflye module for long-reads assembly.
-- [#106](https://github.com/nf-core/bacass/pull/106) - Added patch to dragonflye module enbling draft genome polishing with short-reads.
-
+- [#104](https://github.com/nf-core/bacass/pull/104), [#106](https://github.com/nf-core/bacass/pull/106) - Added dragonflye module and enbled draft genome polishing with short-reads.
 ### `Fixed`
 
 ### `Dependencies`
diff --git a/README.md b/README.md
index 6ed64f2a..5f2a7120 100644
--- a/README.md
+++ b/README.md
@@ -36,7 +36,7 @@ The pipeline can then perform long read assembly utilizing [Unicycler](https://g
 
 ### Hybrid Assembly
 
-For users specifying both short read and long read (NanoPore) data, the pipeline can perform a hybrid assembly approach utilizing [Unicycler](https://github.com/rrwick/Unicycler) or [Dragonflye](https://github.com/rpetit3/dragonflye) (polishing of the assembled genome with short reads), taking the full set of information from short reads and long reads into account.
+For users specifying both short read and long read (NanoPore) data, the pipeline can perform a hybrid assembly approach utilizing [Unicycler](https://github.com/rrwick/Unicycler) (short read assembly followed by gap closing with long reads) or [Dragonflye](https://github.com/rpetit3/dragonflye) (long read assembly followed by polishing with short reads), taking the full set of information from short reads and long reads into account.
 
 ### Assembly QC and annotation
 
diff --git a/conf/modules.config b/conf/modules.config
index 8c3f11cf..03a35293 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -33,6 +33,7 @@ process {
 
     withName: 'PORECHOP_PORECHOP' {
         ext.args = ''
+        ext.prefix = { "${meta.id}.porechop" }
         publishDir = [
             path: { "${params.outdir}/trimming/longreads" },
             mode: params.publish_dir_mode,
diff --git a/conf/test_hybrid_dragonflye.config b/conf/test_hybrid_dragonflye.config
new file mode 100644
index 00000000..669514d3
--- /dev/null
+++ b/conf/test_hybrid_dragonflye.config
@@ -0,0 +1,30 @@
+/*
+========================================================================================
+    Nextflow config file for running minimal tests
+========================================================================================
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/bacass -profile test_hybrid_dragonflye,<docker/singularity>
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Test hybrid-dragonflye profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function'
+
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus   = 2
+    max_memory = 6.GB
+    max_time   = 6.h
+
+    // Input data
+    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/bacass/bacass_hybrid_dragonflye.tsv'
+
+    // some extra args to speed tests up
+    assembly_type='hybrid'
+    assembler='dragonflye'
+    prokka_args=" --fast"
+    skip_kraken2 = true
+}
diff --git a/modules.json b/modules.json
index 8a3cf78d..2c61af54 100644
--- a/modules.json
+++ b/modules.json
@@ -75,8 +75,7 @@
                     "porechop/porechop": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/porechop/porechop/porechop-porechop.diff"
+                        "installed_by": ["modules"]
                     },
                     "prokka": {
                         "branch": "master",
diff --git a/modules/nf-core/porechop/porechop/main.nf b/modules/nf-core/porechop/porechop/main.nf
index f4bfd21c..8fe0dd2e 100644
--- a/modules/nf-core/porechop/porechop/main.nf
+++ b/modules/nf-core/porechop/porechop/main.nf
@@ -11,7 +11,7 @@ process PORECHOP_PORECHOP {
     tuple val(meta), path(reads)
 
     output:
-    tuple val(meta), path("*.porechop.fastq.gz"), emit: reads
+    tuple val(meta), path("*.fastq.gz"), emit: reads
     tuple val(meta), path("*.log")     , emit: log
     path "versions.yml"                , emit: versions
 
@@ -26,7 +26,7 @@ process PORECHOP_PORECHOP {
         -i $reads \\
         -t $task.cpus \\
         $args \\
-        -o ${prefix}.porechop.fastq.gz \\
+        -o ${prefix}.fastq.gz \\
         > ${prefix}.log
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/porechop/porechop/porechop-porechop.diff b/modules/nf-core/porechop/porechop/porechop-porechop.diff
deleted file mode 100644
index 528a4031..00000000
--- a/modules/nf-core/porechop/porechop/porechop-porechop.diff
+++ /dev/null
@@ -1,23 +0,0 @@
-Changes in module 'nf-core/porechop/porechop'
---- modules/nf-core/porechop/porechop/main.nf
-+++ modules/nf-core/porechop/porechop/main.nf
-@@ -11,7 +11,7 @@
-     tuple val(meta), path(reads)
- 
-     output:
--    tuple val(meta), path("*.fastq.gz"), emit: reads
-+    tuple val(meta), path("*.porechop.fastq.gz"), emit: reads
-     tuple val(meta), path("*.log")     , emit: log
-     path "versions.yml"                , emit: versions
- 
-@@ -26,7 +26,7 @@
-         -i $reads \\
-         -t $task.cpus \\
-         $args \\
--        -o ${prefix}.fastq.gz \\
-+        -o ${prefix}.porechop.fastq.gz \\
-         > ${prefix}.log
-     cat <<-END_VERSIONS > versions.yml
-     "${task.process}":
-
-************************************************************
diff --git a/nextflow.config b/nextflow.config
index fdf6d8c4..db36e044 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -196,13 +196,14 @@ profiles {
         executor.cpus          = 4
         executor.memory        = 8.GB
     }
-    test                { includeConfig 'conf/test.config'                  }
-    test_dfast          { includeConfig 'conf/test_dfast.config'            }
-    test_hybrid         { includeConfig 'conf/test_hybrid.config'           }
-    test_long           { includeConfig 'conf/test_long.config'             }
-    test_long_miniasm   { includeConfig 'conf/test_long_miniasm.config'     }
-    test_long_dragonflye{ includeConfig 'conf/test_long_dragonflye.config'  }
-    test_full           { includeConfig 'conf/test_full.config'             }
+    test                    { includeConfig 'conf/test.config'                  }
+    test_dfast              { includeConfig 'conf/test_dfast.config'            }
+    test_hybrid             { includeConfig 'conf/test_hybrid.config'           }
+    test_hybrid_dragonflye  { includeConfig 'conf/test_hybrid_dragonflye.config'}
+    test_long               { includeConfig 'conf/test_long.config'             }
+    test_long_miniasm       { includeConfig 'conf/test_long_miniasm.config'     }
+    test_long_dragonflye    { includeConfig 'conf/test_long_dragonflye.config'  }
+    test_full               { includeConfig 'conf/test_full.config'             }
 }
 
 // Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile

From 34d2f48c00621ee6861343fa5a693feaf6cf54af Mon Sep 17 00:00:00 2001
From: Daniel-VM <danielvmillares@gmail.com>
Date: Thu, 9 Nov 2023 10:07:32 +0100
Subject: [PATCH 09/10] fix prettier #106

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b290d9a8..4825c02f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Added`
 
 - [#104](https://github.com/nf-core/bacass/pull/104), [#106](https://github.com/nf-core/bacass/pull/106) - Added dragonflye module and enbled draft genome polishing with short-reads.
+
 ### `Fixed`
 
 ### `Dependencies`

From 544fbbb2643a63519af566f3dfb474b14d24c951 Mon Sep 17 00:00:00 2001
From: Daniel-VM <danielvmillares@gmail.com>
Date: Thu, 9 Nov 2023 11:02:30 +0100
Subject: [PATCH 10/10] add profile test_hybrid_dragonflye to github CI test

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index bf037552..f573725b 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -52,7 +52,7 @@ jobs:
     strategy:
       matrix:
         # Run remaining test profiles with minimum nextflow version
-        profile: [test_long_miniasm, test_hybrid, test_long, test_dfast]
+        profile: [test_long_miniasm, test_hybrid, test_long, test_dfast, test_hybrid_dragonflye]
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2