Rename skip_short_read_qc to skip_shortread_qc for consistency

Author: erikrikarddaniel

nextflow.config

@@ -28,7 +28,7 @@ params {
     adapterremoval_adapter2              = 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT'
     adapterremoval_trim_quality_stretch  = false
     keep_phix                            = false
-    skip_short_read_qc                   = false
+    skip_shortread_qc                    = false
     // long read preprocessing options
     longread_adaptertrimming_tool        = "porechop_abi"
     longread_filtering_tool              = "filtlong"

nextflow_schema.json

@@ -376,7 +376,7 @@
                     "type": "boolean",
                     "description": "Skip read preprocessing using fastp or adapterremoval."
                 },
-                "skip_short_read_qc": {
+                "skip_shortread_qc": {
                     "type": "boolean",
                     "description": "Skip all QC steps for short reads.",
                     "help": "Skips clipping and removal of phiX sequences as well as the second FastQC run. Does not affect host sequence removal."

workflows/mag.nf

@@ -136,7 +136,7 @@ workflow MAG {
             ch_host_fasta,
             ch_host_bowtie2index,
             ch_phix_db_file,
-            params.skip_short_read_qc,
+            params.skip_shortread_qc,
         )
 
         ch_versions = ch_versions.mix(SHORTREAD_PREPROCESSING.out.versions)