add reviewer suggestions #106

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`

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
 

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,

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
+}

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",

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