Merge branch 'update_binette' into 'devel'

Update binette

See merge request !35

conf/base.config

@@ -104,6 +104,7 @@ process {
         cpus = 20
     }
     withName: BINETTE {
+        container = 'quay.io/biocontainers/binette:1.1.0--pyh7e72e81_0'
         memory = { 128.GB * task.attempt }
         cpus = 10
     }

conf/test.config

@@ -107,6 +107,7 @@ process {
         executor = "local"
     }
     withName: BINETTE {
+        container = 'quay.io/biocontainers/binette:1.1.0--pyh7e72e81_0'
         memory = { 12.GB * task.attempt }
         cpus = 8
     }

env/Singularity_recipe_binning

@@ -17,13 +17,6 @@ micromamba env create -f /binning.yml  && micromamba clean -a
 
 export PATH=/opt/conda/envs/binning/bin:$PATH
 
-# install Binette
-wget  https://github.com/genotoul-bioinfo/Binette/archive/refs/tags/v0.1.5.tar.gz 
-tar -xf v0.1.5.tar.gz 
-rm v0.1.5.tar.gz
-
-pip install Binette-0.1.5/
-
 %environment
 export PATH=/opt/conda/envs/binning/bin/:/checkm2/bin/:$PATH
 

modules/binning.nf

@@ -135,7 +135,7 @@ process BINETTE {
     sed -i 's/size/Size/' bin_refinement/final_bins_quality_reports.tsv 
     sed -i 's/^/${meta.id}_bin_/' bin_refinement/final_bins_quality_reports.tsv 
     sed -i 's/^${meta.id}_bin_bin_id/genome/' bin_refinement/final_bins_quality_reports.tsv 
-    cut -f 2,3 --complement bin_refinement/final_bins_quality_reports.tsv > bins_stats.tsv 
+    cut -f 1,4- bin_refinement/final_bins_quality_reports.tsv > bins_stats.tsv 
 
     cd bin_refinement/final_bins