Fix test and add in singularity.

workflow/main.nf

@@ -6,7 +6,7 @@
 // Define Input variables
 params.reads = "$baseDir/../test_data/*.fastq.gz"
 params.pairedEnd = false
-params.designFile = "$baseDir/../test_data/design_ENCSR238SGC_SE.txt"
+params.designFile = "$baseDir/../test_data/design_ENCSR265ZXX_SE.txt"
 params.genome = 'GRCm38'
 params.genomes = []
 params.bwaIndex = params.genome ? params.genomes[ params.genome ].bwa ?: false : false
@@ -241,7 +241,8 @@ process tssEnrich {
 
   input:
 
-  set sampleId, deduped, bai, experimentId, biosample, factor, treatment, replicate from tssEnrich:
+  set sampleId, deduped, bai, experimentId, biosample, factor, treatment, replicate from tssEnrich
+
 
   output:
 
@@ -250,7 +251,7 @@ process tssEnrich {
   script:
 
   """
-  singularity run metaseq.simg $baseDir/scripts/atac_qc.py -b $deduped -p $sampleId
+  singularity run metaseq.simg $baseDir/scripts/atac_qc.py -b $deduped -p $sampleId -t $tssFile -c $chromSizes
   """
 
 }