update changelog, remove unused inputs from cutadapt

CHANGELOG.md

@@ -11,6 +11,10 @@ that users understand how the changes affect the new version.
 
 version 2.2.0-dev
 ---------------------------
++ Removed unused inputs (trimPrimer and format) for cutadapt.
++ Various minor command tweaks to increase stability.
++ Fixed unused inputs in bedtools sort (inputs are now used).
++ Added miniwdl check to linting.
 + Update TALON default image to version 4.4.1.
 
 version 2.1.0

cutadapt.wdl

@@ -6,7 +6,6 @@ task Cutadapt {
         File? read2
         String read1output = "cut_r1.fq.gz"
         String? read2output
-        String? format
         Array[String] adapter = []
         Array[String] front = []
         Array[String] anywhere = []
@@ -49,7 +48,6 @@ task Cutadapt {
         String? untrimmedPairedOutputPath
         Boolean? colorspace
         Boolean? doubleEncode
-        Boolean? trimPrimer
         Boolean? stripF3
         Boolean? maq
         Boolean? bwa
@@ -169,10 +167,6 @@ task Cutadapt {
             description: "The name of the resulting second end fastq file.",
             category: "common"
         }
-        format: {
-            description: "Equivalent to cutadapt's --format option.",
-            category: "advanced"
-        }
         adapter: {
             description: "A list of 3' ligated adapter sequences to be cut from the given first or single end fastq file.",
             category: "common"
@@ -341,10 +335,6 @@ task Cutadapt {
             description: "Equivalent to cutadapt's --double-encode flag.",
             category: "advanced"
         }
-        trimPrimer: {
-            description: "Equivalent to cutadapt's --trim-primer flag.",
-            category: "advanced"
-        }
         stripF3: {
             description: "Equivalent to cutadapt's --strip-f3 flag.",
             category: "advanced"