remove pipeline specific command from samtools.wdl

bwa.wdl

@@ -83,7 +83,7 @@ task mem {
         INPUT=/dev/stdin OUTPUT=${outputFile}
     }
     output {
-        File samFile = select_first([outputFile])
+        File alignedFile = select_first([outputFile])
     }
     runtime {
         cpu: select_first([threads])

samtools.wdl

-task getContigMostCoverage {
-    String? preCommand
-    File bamFile
-    String? outputFilePath = "mostCoveredContig.bam"
-    command <<<
-        set -e -o pipefail
-        ${preCommand}
-        samtools view -hb wgs1.bam $( \
-            samtools idxstats wgs1.bam \
-            | grep -ve "^\*" \
-            | awk '{ print $1"\t"($3/$2)}' \
-            | sort -rnk2 \
-            | head -n 1 \
-            | cut -f1) \
-        > ${outputFilePath}
-        samtools index ${outputFilePath}
-    >>>
-
-    output {
-        File contig = outputFilePath
-    }
-
-    parameter_meta {
-        preCommand: "This command is run before running the samtools command. Can be used to set up environments such as conda."
-        bamFile: "Must be a sorted BAM file with an index"
-        outputFilePath: "where the output file is stored"
-    }
-}
\ No newline at end of file