diff --git a/biopet/bamstats.wdl b/biopet/bamstats.wdl index df919ef82352df4c73b4ec6efe290c2d5b34784b..d48e55f6893b1b8ce44a6309a91bca8e5d368811 100644 --- a/biopet/bamstats.wdl +++ b/biopet/bamstats.wdl @@ -15,7 +15,7 @@ task Generate { Boolean tsvOutputs = false String outputDir Reference? reference - Int memory = 4 + Int memory = 8 Float memoryMultiplier = 2.0 } diff --git a/fastqc.wdl b/fastqc.wdl index f1d23885f210e73b2452be62b499ca6ab553ed85..3a3b1110f6836104e9960a019ec241bac056326e 100644 --- a/fastqc.wdl +++ b/fastqc.wdl @@ -21,10 +21,10 @@ task Fastqc { } # Chops of the .gz extension if present. - String name = sub(seqFile, "\.gz$","") + String name = basename(sub(seqFile, "\.gz$","")) # The Basename needs to be taken here. Otherwise paths might differ between similar jobs. # This regex chops of the extension and replaces it with _fastqc for the reportdir. # Just as fastqc does it. - String reportDir = outdirPath + "/" + sub(basename(name), "\.[^\.]*$", "_fastqc") + String reportDir = outdirPath + "/" + sub(name, "\.[^\.]*$", "_fastqc") command { set -e -o pipefail