pgx-main from prod added

pgx-main/tests/config/nat2.config

@@ -0,0 +1,90 @@
+
+
+
+params {
+    gene = "nat2"
+}
+
+
+process {
+
+    // ALL PROCESSES
+    cache = true
+    stageInMode = 'symlink'
+    stageOutMode = 'rsync'
+   // scratch = "$HOME/tmp"  // clean this regularly
+
+    // Containers
+
+    // Singularity
+
+//    withLabel: phase {
+//    singularity.enabled	= false
+    //container = "$PWD/containers/whatshap.sif" // this can be generated from docker://pacificbiosciences/whatshap
+//    }
+
+    withName: call_snvs1 {
+    singularity.enabled = true
+    container = "$PWD/containers/stellarpgx-dev.sif"
+    }
+
+    withName: call_snvs2 {
+    singularity.enabled	= true
+    container = "$PWD/containers/stellarpgx-dev.sif"
+    }
+
+    withName: call_sv_del {
+    singularity.enabled	= true
+    container = "$PWD/containers/stellarpgx-dev.sif"
+    }
+
+    withName: call_sv_dup {
+    singularity.enabled	= true
+    container = "$PWD/containers/stellarpgx-dev.sif"
+    }
+
+    withName: get_depth {
+    singularity.enabled	= true
+    container = "$PWD/containers/stellarpgx-dev.sif"
+    }
+
+    withName: format_snvs {
+    singularity.enabled	= true
+    container = "$PWD/containers/stellarpgx-dev.sif"
+    }
+
+    withName: get_core_var {
+    singularity.enabled	= true
+    container = "$PWD/containers/stellarpgx-dev.sif"
+    }
+
+    withName: analyse_1 {
+    singularity.enabled = true
+    container = "$PWD/containers/stellarpgx-dev.sif"
+    }
+
+    withName: analyse_2 {
+    singularity.enabled = true
+    container = "$PWD/containers/stellarpgx-dev.sif"
+    }
+
+    withName: analyse_3 {
+    singularity.enabled = true
+    container = "$PWD/containers/stellarpgx-dev.sif"
+    }
+
+    withName: analyse_4 {
+    singularity.enabled = true
+    container = "$PWD/containers/stellarpgx-dev.sif"
+    }
+
+    withName: call_stars {
+    singularity.enabled = true
+    container = "$PWD/containers/stellarpgx-dev.sif"
+    }
+
+    
+    // Docker
+    // container = "twesigomwedavid/stellarpgx-dev:latest" // Note that this Docker build needs to be pulled from Do
+
+}

pgx-main/tests/config/test.config

@@ -0,0 +1,23 @@
+
+
+params {
+// User-defined parameters
+
+   // reference genome
+   ref_file = "$PWD/tests/reference/hg38/chr22_hg38.fasta"
+
+
+   // BAM/CRAM file(s) and respective indexes 
+   in_bam = "$PWD/tests/samples/hg38/HG03130*{bam,bai}" 
+
+
+   // Output directoy (Default is $PWD/results)
+   out_dir = "$PWD/results"
+
+
+   // DO NOT modify these lines  
+   gene = "cyp2d6"
+   res_init = "$PWD/tests/resources"
+
+}
+