add podman [ci skip]

TORCH-Consortium · Jul 31, 2023 · 451e7c5 · 451e7c5
1 parent 1cb0cb2
commit 451e7c5
Show file tree

Hide file tree

Showing 2 changed files with 23 additions and 0 deletions.
diff --git a/conf/podman.config b/conf/podman.config
@@ -0,0 +1,22 @@
+process {
+
+    //----------------------------------------------
+    // Custom containers for all deps.
+    //----------------------------------------------
+
+    withName:
+    'GATK.*|LOFREQ.*|DELLY.*|TBPROFILER.*|MULTIQC.*|FASTQC.*|UTILS.*|FASTQ.*|SAMPLESHEET.*' {
+        container = "ghcr.io/torch-consortium/magma/magma-container-1:1.1.0"
+    }
+
+    withName:
+    'BWA.*|IQTREE.*|SNPDISTS.*|SNPSITES.*|BCFTOOLS.*|BGZIP.*|SAMTOOLS.*|SNPEFF.*|CLUSTERPICKER.*' {
+        container = "ghcr.io/torch-consortium/magma/magma-container-2:1.1.0"
+    }
+
+}
+
+
+podman {
+    enabled = true
+}
diff --git a/nextflow.config b/nextflow.config
@@ -57,6 +57,7 @@ profiles {
     // Package management specific settings
     conda_local { includeConfig 'conf/conda_local.config' }
     docker { includeConfig 'conf/docker.config' }
+    podman { includeConfig 'conf/podman.config' }
 
     // Executor specific settings
     pbs { includeConfig 'conf/pbs.config' }