Change lima outputs.

CHANGELOG.md

@@ -11,8 +11,7 @@ that users understand how the changes affect the new version.
 
 version 4.1.0-dev
 ---------------------------
-+ Add copy command to bam2fastx tasks to make sure bam file and its index are
-  always in the same directory.
++ Remove globs from lima outputs.
 + Added a task for GRIDSS.
 + Add wdl file for pacbio's bam2fastx tool.
 

bam2fastx.wdl

@@ -24,7 +24,6 @@ task Bam2Fasta {
     input {
         File inputFile
         File bamIndex
-        String basenameInputFile = basename(inputFile)
         String outputPrefix
         Int compressionLevel = 1
         Boolean splitByBarcode = false
@@ -39,16 +38,12 @@ task Bam2Fasta {
     command {
         set -e
         mkdir -p "$(dirname ~{outputPrefix})"
-        # The bam file and its index need to be in the same directory.
-        # Cromwell will put them in separate iputs folders.
-        cp ~{inputFile} ./
-        cp ~{bamIndex} ./
         bam2fasta \
         --output ~{outputPrefix} \
         -c ~{compressionLevel} \
         ~{true="--split-barcodes" false="" splitByBarcode} \
         ~{"--seqid-prefix " + seqIdPrefix} \
-        ./~{basenameInputFile}
+        ~{inputFile}
     }
 
     output {
@@ -81,7 +76,6 @@ task Bam2Fasta {
 task Bam2Fastq {
     input {
         File inputFile
-        String basenameInputFile = basename(inputFile)
         File bamIndex
         String outputPrefix
         Int compressionLevel = 1
@@ -97,16 +91,12 @@ task Bam2Fastq {
     command {
         set -e
         mkdir -p "$(dirname ~{outputPrefix})"
-        # The bam file and its index need to be in the same directory.
-        # Cromwell will put them in separate iputs folders.
-        cp ~{inputFile} ./
-        cp ~{bamIndex} ./
         bam2fastq \
         --output ~{outputPrefix} \
         -c ~{compressionLevel} \
         ~{true="--split-barcodes" false="" splitByBarcode} \
         ~{"--seqid-prefix " + seqIdPrefix} \
-        ./~{basenameInputFile}
+        ~{inputFile}
     }
 
     output {

lima.wdl

@@ -95,12 +95,15 @@ task Lima {
         cp "~{basename(outputPrefix)}.fl.lima.counts" "~{outputPrefix}.fl.lima.counts"
         cp "~{basename(outputPrefix)}.fl.lima.report" "~{outputPrefix}.fl.lima.report"
         cp "~{basename(outputPrefix)}.fl.lima.summary" "~{outputPrefix}.fl.lima.summary"
+        find . -path "*.bam" > bamFiles.txt
+        find . -path "*.bam.pbi" > bamIndexes.txt
+        find . -path "*.subreadset.xml" > subreadsets.txt
     }
 
     output {
-        Array[File] limaBam = glob("*.bam")
-        Array[File] limaBamIndex = glob("*.bam.pbi")
-        Array[File] limaXml = glob("*.subreadset.xml")
+        Array[File] limaBam = read_lines("bamFiles.txt")
+        Array[File] limaBamIndex = read_lines("bamIndexes.txt")
+        Array[File] limaXml = read_lines("subreadsets.txt")
         File limaStderr = outputPrefix + ".fl.stderr.log"
         File limaJson = outputPrefix + ".fl.json"
         File limaCounts = outputPrefix + ".fl.lima.counts"