Merge pull request #1 from Functional-Genomics-Lab/working-dreg

Change dREG container

bin/cuda_version.sh

@@ -0,0 +1,15 @@
+#!/bin/sh
+
+NVIDIA_SMI=$(which nvidia-smi)
+
+export LC_ALL=C
+export LANG=C
+
+if [ -x "$NVIDIA_SMI" ]; then
+    CUDA_VERSION=$($NVIDIA_SMI --version | grep "CUDA Version" | awk '{print $NF}')
+    echo "$CUDA_VERSION"
+    exit 0
+else
+    echo "CUDA is not available" >&2
+    exit 1
+fi

conf/cuda-container.config

@@ -0,0 +1 @@
+params.cuda = "${projectDir}/bin/cuda_version.sh".execute().text.trim()

modules/local/dreg/main.nf

@@ -1,7 +1,7 @@
 process DREG_RUN {
-    publishDir "${params.outdir}/dreg/", mode: 'copy', pattern: "*dREG*"
+    publishDir "${params.outdir}/dreg/", mode: 'copy', pattern: "dREG_output_*"
 
-    container "docker.io/biohpc/dreg"
+    container "docker.io/l1drm/dreg:cuda${params.cuda}"
 
     tag "$meta.id"
     memory '50 GB'
@@ -14,17 +14,17 @@ process DREG_RUN {
     path model
 
     output:
-    tuple val(meta), path("${prefix}.*"), emit: dREG
+    tuple val(meta), path("dREG_output_*"), emit: dREG
 
     script:
-    def prefix = "${meta.id}"
+    def prefix = "dREG_output_${meta.id}_"
     """
-    run_dREG.R \\
+    /dREG/run_dREG.R \\
         ${pos_bw} \\
         ${neg_bw} \\
         ${prefix} \\
         ${model} \\
         ${task.cpus} \\
-        ${task.accelerator.request}
+        0
     """
 }

nextflow.config

@@ -14,8 +14,10 @@ profiles {
         wave.enabled = true
         // wave.strategy = ['dockerfile','container']
         docker.enabled = true
+        docker.runOptions = "--rm --gpus all"
         includeConfig "conf/test.config"
-        params.input = "https://raw.githubusercontent.com/nf-core/nascent/master/assets/samplesheet.csv"
+        includeConfig "conf/cuda-container.config"
+        // params.input = "https://raw.githubusercontent.com/nf-core/nascent/master/assets/samplesheet.csv"
         // From a nascent test run
         // params.bwa_index = "~/src/nf-core/nascent/work/96/746b04f1c048d94194b86ab0704d97/bwa"
     }