Test tool without localization.

bam2fastx.wdl

@@ -103,31 +103,16 @@ task Bam2Fastq {
         String dockerImage = "quay.io/biocontainers/bam2fastx:1.3.1--hf05d43a_1"
     }
 
-    command <<<
+    command {
         set -e
         mkdir -p "$(dirname ~{outputPrefix})"
-
-        # Localise the bam and pbi files so they are next to each other in the
-        # current folder.
-        bamFiles=""
-        for bamFile in ~{sep=" " bam}
-        do
-            ln -s ${bamFile} ./
-            bamFiles=${bamFiles}" ./$(basename ${bamFile})"
-        done
-
-        for indexFile in ~{sep=" " bamIndex}
-        do
-            ln -s ${indexFile} ./
-        done
-
         bam2fastq \
         --output ~{outputPrefix} \
         -c ~{compressionLevel} \
         ~{true="--split-barcodes" false="" splitByBarcode} \
         ~{"--seqid-prefix " + seqIdPrefix} \
-        ${bamFiles}
-    >>>
+        ~{bam}
+    }
 
     output {
         File fastqFile = outputPrefix + ".fastq.gz"