pgx-main from prod added

pgx-main/nextflow.config

@@ -0,0 +1,97 @@
+
+manifest {
+    author = 'David Twesigomwe'
+    description = 'Pipeline calls CYP450 star alleles from WGS BAM/CRAM files. Model gene: CYP2D6'
+    mainScript = 'main.nf'
+    version = '1.2.6'
+}
+
+
+
+params {
+// User-defined parameters
+
+   // reference genome
+   ref_file = "$PWD/hg38.fa"  // .fai index should be in the same folder
+
+
+   // BAM/CRAM file(s) and respective indexes 
+       // example1 (single sample): /path/to/data/GeT-RM/NA12878*{bam,bai}
+       // example2 (multiple samples): /path/to/data/GeT-RM/*{bam,bai}
+       // example3 (CRAM files): /path/to/data/GeT-RM/HG*{cram,crai}
+
+   in_bam = "$PWD/data/*{bam,bai}" 
+
+
+   // Output directoy (Default is $PWD/results). User-defined path should be an absolute path
+   out_dir = "$PWD/results"
+
+
+   // DO NOT modify these lines  
+   gene = "cyp2d6"
+   db_init = "$PWD/database"
+   res_init = "$PWD/resources"
+   caller_init = "$PWD/scripts"
+
+
+}
+
+
+singularity {
+    enabled = false // set to false when using Docker
+    autoMounts = true
+    cacheDir = "$PWD/containers"
+    runOptions = " --cleanenv"
+}
+
+// To use Docker, set "enabled" to "true" and do the opposite to the singularity config above. Also remember to change the container path in the process config below to point to the Docker container rather than Singularity. 
+
+docker {
+    enabled = true // change to true when using Docker
+    runOptions = '-u \$(id -u):\$(id -g)'
+}
+
+
+
+process {
+
+    // ALL PROCESSES
+    cache = true
+    stageInMode = 'symlink'
+    stageOutMode = 'rsync'
+   // scratch = "$HOME/tmp"  // clean this regularly
+
+    // Containers
+
+    // Singularity
+    // container = "$PWD/containers/stellarpgx-dev.sif"
+
+    // Docker
+    container = "twesigomwedavid/stellarpgx-dev:latest" // Note that this Docker build needs to be pulled from Docker Hub
+
+}
+
+
+profiles {
+
+
+    // Local machine (MacOS, Linux, cluster node etc)
+    standard { 
+        process.executor = 'local'
+    }
+
+    // SLURM scheduler
+    slurm { 
+        process.executor = 'slurm'
+        process.queue = 'batch'
+    } 
+
+    // Other scheduler
+    // sheduler_name {
+    //	process.executor = 'sheduler_name'
+    //	process.queue = 'batch'
+    //}
+
+    test { includeConfig "$PWD/tests/config/test.config" }
+
+}