Merge branch 'main' into continuous-integration

Author: eascarrunz

nextflow.config

@@ -51,20 +51,21 @@ profiles {
         includeConfig "$baseDir/config/ressources/local.config"
     }
     test {
-        params.aligner      = "hisat2"
-        params.genome       = "${baseDir}/test/hpv16.fa" 
-        params.reads        = "${baseDir}/test/U2OS_A1_R1_sub100000.fastq"
-        params.read_type    = "short_single"
-        params.library_type = "U"
-    }
-    test2 {
         params.aline_profiles = "${baseDir}/config/ressources/custom_aline.config" 
         params.aligner        = "STAR" 
         params.reads          = "${baseDir}/data/chr21/chr21_small_R1.fastq.gz "
-        params.genome         = "${baseDir}/data/chr21/chr21_small.fasta" 
+        params.genome         = "${baseDir}/data/chr21/chr21_small.fasta.gz" 
         params.library_type   = "ISR" 
         params.read_type      = "short_single"
     }
+    test2 {
+        params.aline_profiles = "${baseDir}/config/ressources/custom_aline.config" 
+        params.aligner        = "STAR" 
+        params.reads          = "${baseDir}/data/chr21/"
+        params.genome         = "${baseDir}/data/chr21/chr21_small.fasta.gz" 
+        params.library_type   = "ISR" 
+        params.read_type      = "short_paired"
+    }
 }
 
 resume = true
@@ -86,5 +87,5 @@ trace {
 
 dag {
     enabled = true
-    file = "${params.pipeline_report}/pipeline_dag.svg"
+    file = "${params.pipeline_report}/pipeline_dag_${new Date().format('yyyyMMddHHmmss')}.svg"
 }