Merge pull request #517 from nf-core/test-gpu-profile

create separate test_gpu profile

Author: sateeshperi

assets/samplesheet_single_gpu.csv

@@ -0,0 +1,2 @@
+sample,fastq_1,fastq_2,genome
+SRR7961150_GSM3415714_MShef4_bulk,s3://ngi-igenomes/test-data/methylseq/SRR7961150_GSM3415714_MShef4_bulk_BSseq_Homo_sapiens_Bisulfite-Seq_1.fastq.gz,s3://ngi-igenomes/test-data/methylseq/SRR7961150_GSM3415714_MShef4_bulk_BSseq_Homo_sapiens_Bisulfite-Seq_2.fastq.gz,

conf/test_gpu.config

@@ -0,0 +1,32 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/methylseq -profile test,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Test GPU profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function'
+
+    // Input data
+    input = "${projectDir}/assets/samplesheet_gpu.csv"
+
+    // Genome references
+    fasta       = "${params.pipelines_testdata_base_path}/reference/genome.fa.gz"
+    fasta_index = "${params.pipelines_testdata_base_path}/reference/genome.fa.fai"
+}
+
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
+}
+

conf/test_single_gpu.config

@@ -0,0 +1,20 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/methylseq -profile test,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Test GPU profile with one single full size sample'
+    config_profile_description = 'Test dataset to check pipeline GPU function'
+
+    // Input data
+    input  = "${projectDir}/assets/samplesheet_single_gpu.csv"
+    genome = 'GRCh38'
+}

nextflow.config

@@ -225,8 +225,10 @@ profiles {
         apptainer.runOptions    = '--nv'
         singularity.runOptions  = '--nv'
     }
-    test        { includeConfig 'conf/test.config'      }
-    test_full   { includeConfig 'conf/test_full.config' }
+    test            { includeConfig 'conf/test.config'            }
+    test_gpu        { includeConfig 'conf/test_gpu.config'        }
+    test_single_gpu { includeConfig 'conf/test_single_gpu.config' }
+    test_full       { includeConfig 'conf/test_full.config'       }
 }
 
 // Load nf-core custom profiles from different Institutions