nf-core lint fixes

environment.yaml

@@ -27,3 +27,4 @@ dependencies:
     - parallel
     - scikit-learn==1.0.2
     - natsort
+    - graphviz

nextflow.config

@@ -13,7 +13,7 @@
 params {
     help = false
     fastq = null
-    ref_genome = false
+    ref_genome = null
     ref_annotation = null
     threads = 4
      // Thresholds for viewing isoforms in report table

nextflow_schema.json

@@ -200,7 +200,7 @@
                     "default": 0.65
                 },
                 "aligned_threshold": {
-                    "tpye": "number",
+                    "type": "number",
                     "description": "Minimum aligned fraction of read to be included in cluster",
                     "default": 0.2
                 },

reference_assembly.nf

@@ -28,8 +28,8 @@ process map_reads{
 
     if [[ -s "internal_priming_fail.tsv" ]];
         then
-            tail -n +2 "internal_priming_fail.tsv" | awk '{{print ">" \$1 "\\n" \$4 }}' - > "context_internal_priming_fail_start.fasta"
-            tail -n +2 "internal_priming_fail.tsv" | awk '{{print ">" \$1 "\\n" \$6 }}' - > "context_internal_priming_fail_end.fasta"
+            tail -n +2 "internal_priming_fail.tsv" | awk '{print ">" \$1 "\\n" \$4 }' - > "context_internal_priming_fail_start.fasta"
+            tail -n +2 "internal_priming_fail.tsv" | awk '{print ">" \$1 "\\n" \$6 }' - > "context_internal_priming_fail_end.fasta"
     fi
     """
 }