Revert "Changed bambu installation"

This reverts commit 00cbe6e.
IGDRion · Dec 4, 2024 · ceca0f3 · ceca0f3
1 parent 5219142
commit ceca0f3
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Showing 2 changed files with 4 additions and 6 deletions.
diff --git a/environment.yml b/environment.yml
@@ -17,10 +17,6 @@ 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
 

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