MUSIC: add tests.sh file to run the tests

src/nf_modules/MUSIC/peak_calling_paired.config

-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $compute_mappability {
-        container = "music:6613c53"
-      }
-      $music_preprocessing {
-        container = "music:6613c53"
-      }
-      $music_computation {
-        container = "music:6613c53"
-      }
-    }
-  }
-  sge {
-    process{
-      $compute_mappability {
-        beforeScript = "module purge; module load MUSIC/6613c53"
-      }
-      $music_preprocessing {
-        beforeScript = "module purge; module load MUSIC/6613c53"
-      }
-      $music_computation {
-        beforeScript = "module purge; module load MUSIC/6613c53"
-      }
-    }
-  }
-}

src/nf_modules/MUSIC/tests.sh

+cp results/training/bams/sBNLN18.bam results/training/bams/sBNLN18_control.bam
+./nextflow src/nf_modules/MUSIC/peak_calling_single.nf \
+  -c src/nf_modules/MUSIC/peak_calling_single.config \
+  -profile docker \
+  --fasta "results/training/fasta/*.fasta" \
+  --bam "results/training/bams/s*.bam" \
+  --index "results/training/mapping/index/*" \
+  --read_size 50 --frag_size 300

src/training_dataset.nf

@@ -147,7 +147,7 @@ if ( params.fastq_paired != "" ) {
       set file_id, "*.fastq" into fastq_files_extracted
     script:
   """
-  samtools fastq -1 s${file_id}_R1.fastq -2 s${file_id}_R2.fastq -f 0x2 ${bam}
+  samtools fastq -1 s${file_id}_R1.fastq -2 s${file_id}_R2.fastq -F 0x4 ${bam}
   """
   }
 
@@ -163,7 +163,7 @@ if ( params.fastq_paired != "" ) {
       set file_id, "*.bam" into filtered_bam_files_paired
     script:
   """
-  samtools view -@ ${task.cpus} -hb ${bam} -f 0x2 > f${file_id}.bam
+  samtools view -@ ${task.cpus} -hb ${bam} -F 0x4 > f${file_id}.bam
   """
   }