change jgi_summarize_bam_contig_depths --percentidentity default from…

… 97 to 90 when dealing with longreads
nf-core · Nov 28, 2024 · 18ae00d · 18ae00d
1 parent c7a5cdf
commit 18ae00d
Show file tree

Hide file tree

Showing 3 changed files with 7 additions and 5 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -620,6 +620,7 @@ process {
     }
 
     withName: METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS {
+        ext.args = { meta.assembler in ['FLYE', 'METAMDBG'] ? "--percentIdentity ${params.longred_percentidentity}" : '' }
         publishDir = [path: { "${params.outdir}/GenomeBinning/depths/contigs" }, mode: params.publish_dir_mode, pattern: '*-depth.txt.gz']
         ext.prefix = { "${meta.assembler}-${meta.id}-depth" }
     }

diff --git a/nextflow.config b/nextflow.config
@@ -53,6 +53,7 @@ params {
     min_length_unbinned_contigs          = 1000000
     max_unbinned_contigs                 = 100
     skip_prokka                          = false
+    longread_percentidentity             = 90
 
     // assembly options
     coassemble_group                     = false

diff --git a/subworkflows/local/binning.nf b/subworkflows/local/binning.nf
@@ -2,11 +2,11 @@
  * Binning with MetaBAT2 and MaxBin2
  */
 
-include { METABAT2_METABAT2                                            } from '../../modules/nf-core/metabat2/metabat2/main'
-include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS                         } from '../../modules/nf-core/metabat2/jgisummarizebamcontigdepths/main'
-include { MAXBIN2                                                      } from '../../modules/nf-core/maxbin2/main'
-include { GUNZIP as GUNZIP_BINS                                        } from '../../modules/nf-core/gunzip/main'
-include { GUNZIP as GUNZIP_UNBINS                                      } from '../../modules/nf-core/gunzip/main'
+include { METABAT2_METABAT2                                                                      } from '../../modules/nf-core/metabat2/metabat2/main'
+include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS                                                   } from '../../modules/nf-core/metabat2/jgisummarizebamcontigdepths/main'
+include { MAXBIN2                                                                                } from '../../modules/nf-core/maxbin2/main'
+include { GUNZIP as GUNZIP_BINS                                                                  } from '../../modules/nf-core/gunzip/main'
+include { GUNZIP as GUNZIP_UNBINS                                                                } from '../../modules/nf-core/gunzip/main'
 
 include { CONVERT_DEPTHS                        } from '../../modules/local/convert_depths'
 include { ADJUST_MAXBIN2_EXT                    } from '../../modules/local/adjust_maxbin2_ext'