DSL2: nf-test conversion test_full

conf/test_full.config

@@ -10,15 +10,68 @@
 ----------------------------------------------------------------------------------------
 */
 
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
+
+    withName: FASTQC {
+        cpus   = { 1                    }
+        memory = { 15.GB * task.attempt }
+    }
+    withName: ADAPTER_REMOVAL {
+        cpus   = { 8                    }
+        memory = { 15.GB * task.attempt }
+        time   = { 2.h   * task.attempt }
+    }
+    withName: PICARD_CREATESEQUENCEDICTIONARY {
+        cpus   = { 12                   }
+        memory = { 15.GB * task.attempt }
+        time   = { 8.h   * task.attempt }
+    }
+    withName: PICARD_MARKDUPLICATES {
+        memory = { 15.GB                }
+    }
+    withName: BWA_ALN {
+        cpus   = { 8                    }
+        memory = { 15.GB * task.attempt }
+        time   = { 8.h   * task.attempt }
+    }
+    withName: DEDUP {
+        cpus   = { 8                    }
+        memory = { 15.GB * task.attempt }
+        time   = { 4.h   * task.attempt }
+    }
+    withName: GENOTYPING_HC {
+        cpus   = { 8                    }
+        memory = { 15.GB * task.attempt }
+        time   = { 8.h   * task.attempt }
+    }
+}
+
 params {
-    config_profile_name        = 'Full test profile'
-    config_profile_description = 'Full test dataset to check pipeline function'
+    config_profile_name           = 'Full test profile'
+    config_profile_description    = 'Full test dataset to check pipeline function'
+    pipelines_testdata_base_path  = 'https://raw.githubusercontent.com/TCLamnidis/test-datasets/'
 
     // Input data for full size test
-    // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
-    // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv'
+    input                         = params.pipelines_testdata_base_path + 'eager/testdata/Benchmarking/eager3_benchmarking_vikingfish.tsv'
 
     // Genome references
-    genome = 'R64-1-1'
+    // Genome reference
+    fasta                         = 'https://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_other/Gadus_morhua/reference/GCF_902167405.1_gadMor3.0/GCF_902167405.1_gadMor3.0_rna.fna.gz'
+
+    bwaalnn                       = 0.04
+    bwaalnl                       = 1024
+
+    run_bam_filtering             = true
+    bam_unmapped_type             = 'discard'
+    bam_mapping_quality_threshold = 25
+
+    run_genotyping                = true
+    genotyping_tool               = 'hc'
+    genotyping_source             = 'raw'
+    gatk_ploidy                   = 2
 }