diff --git a/cutadapt.wdl b/cutadapt.wdl index bb04e337c4227329b687df02c0710b4800eac29e..5f51e9caeb39e93291355bc5c32c9d60bf3bc2a6 100644 --- a/cutadapt.wdl +++ b/cutadapt.wdl @@ -80,10 +80,10 @@ task Cutadapt { Int compressionLevel = 1 # This only affects outputs with the .gz suffix. Int cores = 4 String? memory - Int? runtimeMinutes + Int? timeMinutes String dockerImage = "quay.io/biocontainers/cutadapt:2.8--py37h516909a_0" } - Int estimatedRuntimeMin = 1 + ceil(size([read1, read2], "G") * 12.0 / cores) + Int estimatedTimeMinutes = 1 + ceil(size([read1, read2], "G") * 12.0 / cores) String estimatedMemory = "~{300 + 100 * cores}M" String realRead2output = select_first([read2output, "cut_r2.fq.gz"]) @@ -170,7 +170,7 @@ task Cutadapt { runtime { cpu: cores memory: select_first([memory, estimatedMemory]) - runtime_minutes: select_first([runtimeMinutes, estimatedRuntimeMin]) + time_minutes: select_first([timeMinutes, estimatedTimeMinutes]) docker: dockerImage } diff --git a/fastqc.wdl b/fastqc.wdl index adc103e8213c1d19152526dc747f3d6cd33623b9..fc9358904faf67ea73f7f35b55f469aa2879d338 100644 --- a/fastqc.wdl +++ b/fastqc.wdl @@ -39,13 +39,13 @@ task Fastqc { Int threads = 1 String? memory - Int? runtimeMinutes + Int? timeMinutes String dockerImage = "quay.io/biocontainers/fastqc:0.11.9--0" Array[File]? NoneArray File? NoneFile } String estimatedMemory = "~{250 + 250 * threads}M" - Int estimatedRuntimeMin = 1 + ceil(size(seqFile, "G")) * 4 + Int estimatedTimeMinutes = 1 + ceil(size(seqFile, "G")) * 4 # Chops of the .gz extension if present. # The Basename needs to be taken here. Otherwise paths might differ between similar jobs. @@ -87,7 +87,7 @@ task Fastqc { cpu: threads memory: select_first([memory, estimatedMemory]) docker: dockerImage - runtime_minutes: select_first([runtimeMinutes, estimatedRuntimeMin]) + time_minutes: select_first([timeMinutes, estimatedTimeMinutes]) } parameter_meta {