diff --git a/cutadapt.wdl b/cutadapt.wdl index f6b8211e259d886ea6d1dd0780d02c8444891e9b..19e4ef0e45b32d473cb77603045750bafd76d98b 100644 --- a/cutadapt.wdl +++ b/cutadapt.wdl @@ -74,13 +74,10 @@ task Cutadapt { Boolean? zeroCap Boolean? noZeroCap String reportPath = "cutadapt_report.txt" - #Int compressionLevel = 1 # This only affects outputs with the .gz suffix. - # --compression-level has a bug in 2.4 https://github.com/marcelm/cutadapt/pull/388 - #~{"--compression-level=" + compressionLevel} \ - Boolean Z = true # equal to compressionLevel=1 # Fixme: replace once upstream is fixed. - Int cores = 1 + Int compressionLevel = 1 # This only affects outputs with the .gz suffix. + Int cores = 4 String memory = "4G" - String dockerImage = "quay.io/biocontainers/cutadapt:2.4--py37h14c3975_0" + String dockerImage = "quay.io/biocontainers/cutadapt:2.8--py37h516909a_0" } String realRead2output = select_first([read2output, "cut_r2.fq.gz"]) @@ -95,7 +92,6 @@ task Cutadapt { ~{read2outputArg} cutadapt \ ~{"--cores=" + cores} \ - ~{true="-Z" false="" Z} \ ~{true="-a" false="" length(adapter) > 0} ~{sep=" -a " adapter} \ ~{true="-A" false="" length(adapterRead2) > 0} ~{sep=" -A " adapterRead2} \ ~{true="-g" false="" length(front) > 0} ~{sep=" -g " front} \ @@ -103,6 +99,7 @@ task Cutadapt { ~{true="-b" false="" length(anywhere) > 0} ~{sep=" -b " anywhere} \ ~{true="-B" false="" length(anywhereRead2) > 0} ~{sep=" -B " anywhereRead2} \ --output ~{read1output} ~{if defined(read2) then "-p " + realRead2output else ""} \ + --compression-level ~{compressionLevel} \ ~{"--to-short-output " + tooShortOutputPath} \ ~{"--to-short-paired-output " + tooShortPairedOutputPath} \ ~{"--to-long-output " + tooLongOutputPath} \