update test

Author: Juke34

.github/workflows/main.yml

@@ -80,10 +80,12 @@ jobs:
         run: bash build_containers.sh --docker --github_action
 
       # Run test(s)
-      - name: test short single
-        run: nextflow run rain.nf -profile docker,test
+      - name: test short single list
+        run: nextflow run rain.nf -profile docker,test_short_single_list
 
-      - name: test short paired
-        run: nextflow run rain.nf -profile docker,test2
+      - name: test short paired folder
+        run: nextflow run rain.nf -profile docker,test_short_paired_folder
 
+      - name: test csv mix
+        run: nextflow run rain.nf -profile docker,test_mix_csv
 

nextflow.config

@@ -58,22 +58,34 @@ profiles {
     local {
         includeConfig "$baseDir/config/resources/local.config"
     }
-    test {
+    test_short_single_list {
         params.aligner        = "STAR" 
         params.reads          = "${baseDir}/data/chr21/chr21_small_R1.fastq.gz,${baseDir}/data/chr21/chr21_small_R2.fastq.gz"
         params.genome         = "${baseDir}/data/chr21/chr21_small.fasta.gz"
         params.annotation     = "${baseDir}/data/chr21/chr21_small_filtered.gff3.gz"
         params.strandedness   = "ISR" 
         params.read_type      = "short_single"
     }
-    test2 {
+    test_short_paired_folder {
         params.aligner        = "STAR" 
         params.reads          = "${baseDir}/data/chr21/"
         params.genome         = "${baseDir}/data/chr21/chr21_small.fasta.gz" 
         params.annotation     = "${baseDir}/data/chr21/chr21_small_filtered.gff3.gz"
         params.strandedness   = "ISR" 
         params.read_type      = "short_paired"
     }
+    test_short_single_csv {
+        params.aligner        = "STAR" 
+        params.reads          = "${baseDir}/data/chr21/chr21_small_single.csv"
+        params.genome         = "${baseDir}/data/chr21/chr21_small.fasta.gz" 
+        params.annotation     = "${baseDir}/data/chr21/chr21_small_filtered.gff3.gz"
+    }
+     test_mix_csv {
+        params.aligner        = "STAR" 
+        params.reads          = "${baseDir}/data/chr21/chr21_small_mix.csv"
+        params.genome         = "${baseDir}/data/chr21/chr21_small.fasta.gz" 
+        params.annotation     = "${baseDir}/data/chr21/chr21_small_filtered.gff3.gz"
+    }
 }
 
 resume = true