diff --git a/bam2fastx.wdl b/bam2fastx.wdl index a8f1342ccd8266325af0ec72de6712c5fac9d23b..42240cd4da789985ca1d84ec86973f833f15672b 100644 --- a/bam2fastx.wdl +++ b/bam2fastx.wdl @@ -22,7 +22,7 @@ version 1.0 task Bam2Fasta { input { - Array[File]+ inputFile + Array[File]+ bam Array[File]+ bamIndex String outputPrefix Int compressionLevel = 1 @@ -43,7 +43,7 @@ task Bam2Fasta { -c ~{compressionLevel} \ ~{true="--split-barcodes" false="" splitByBarcode} \ ~{"--seqid-prefix " + seqIdPrefix} \ - ~{sep=" " inputFile} + ~{sep=" " bam} } output { @@ -58,7 +58,7 @@ task Bam2Fasta { parameter_meta { # inputs - inputFile: {description: "The input pacbio bam file(s).", category: "required"} + bam: {description: "The input pacbio bam file(s).", category: "required"} bamIndex: {description: "The .pbi index for the input file(s).", category: "required"} outputPrefix: {description: "Output directory path + output file prefix.", category: "required"} compressionLevel: {description: "Gzip compression level [1-9]", category: "advanced"} @@ -75,7 +75,7 @@ task Bam2Fasta { task Bam2Fastq { input { - Array[File]+ inputFile + Array[File]+ bam Array[File]+ bamIndex String outputPrefix Int compressionLevel = 1 @@ -96,7 +96,7 @@ task Bam2Fastq { -c ~{compressionLevel} \ ~{true="--split-barcodes" false="" splitByBarcode} \ ~{"--seqid-prefix " + seqIdPrefix} \ - ~{sep=" " inputFile} + ~{sep=" " bam} } output { @@ -111,7 +111,7 @@ task Bam2Fastq { parameter_meta { # inputs - inputFile: {description: "The input pacbio bam file(s).", category: "required"} + bam: {description: "The input pacbio bam file(s).", category: "required"} bamIndex: {description: "The .pbi index for the input file(s).", category: "required"} outputPrefix: {description: "Output directory path + output file prefix.", category: "required"} compressionLevel: {description: "Gzip compression level [1-9]", category: "advanced"}