Changed bambu installation

environment.yml

@@ -6,7 +6,7 @@ dependencies:
   - pytorch::pytorch=1.12.0
   - pytorch::cpuonly
 
-  - conda-forge::r-base=4.1
+  - conda-forge::r-base=4.4
   - conda-forge::r-rcolorbrewer
   - conda-forge::r-tidyverse=1.3.2
   - conda-forge::r-dplyr=1.0.10
@@ -17,6 +17,10 @@ dependencies:
   - conda-forge::r-ggpattern
   - bioconda::bioconductor-rtracklayer
 
+  - bioconda::bioconductor-bambu=3.4.0
+  - conda-forge::r-xgboost=1.7.6=cpu_r43had0c348_6
+  - bioconda::bioconductor-bsgenome
+
   - conda-forge::procps-ng
   - conda-forge::mkl<=2024.0
 

modules/bambu/bambu.nf

@@ -1,8 +1,6 @@
 process BAMBU {
-  conda (params.enable_conda ? "bioconda::bioconductor-bambu=3.0.8" : null)
-  container "${ workflow.containerEngine == 'singularity' ? 
-                'https://depot.galaxyproject.org/singularity/bioconductor-bambu:3.4.0--r43hf17093f_1' :
-                'quay.io/biocontainers/bioconductor-bambu:3.4.0--r43hf17093f_1 ' }"
+  conda (params.enable_conda ? "$baseDir/environment.yml" : null)
+  container "ghcr.io/igdrion/annexa:${workflow.revision? workflow.revision: "main"}"
   publishDir "$params.outdir/bambu", mode: 'copy'
   cpus params.maxCpu
   memory params.maxMemory