diff --git a/spades.wdl b/spades.wdl index 724285d4a4b0e3ee119359faf03278a15e826b34..ce9de29cecb0b48d20faff177fc1a007e0e7c312 100644 --- a/spades.wdl +++ b/spades.wdl @@ -49,7 +49,7 @@ task spades { ${"--nanopore " + nanoporeReads } \ ${"--tslr " + tslrContigs } \ ${"--trusted-contigs " + trustedContigs } \ - ${"--untrusted-contigs" + untrustedContigs } \ + ${"--untrusted-contigs " + untrustedContigs } \ ${true="--only-error-correction" false="" onlyErrorCorrection } \ ${true="--only-assembler" false="" onlyAssembler } \ ${true="--careful" false="" careful } \ diff --git a/unicycler.wdl b/unicycler.wdl index dac048a1a8a1d21390aa79378b86c2103df27acf..f7aa36a48067bcd2f880a843d1a4aa401c7f5078 100644 --- a/unicycler.wdl +++ b/unicycler.wdl @@ -9,8 +9,10 @@ task unicycler { Int? minFastaLength Int? keep Boolean? vcf - Int threads - Int memory + Int? threads + Int? memory + Int finalThreads = select_first(threads, 1) + Int finalMemory = select_first(memory, 4) String? mode Float? minBridgeQual Int? linearSeqs @@ -55,7 +57,7 @@ task unicycler { ${"--min_fasta_length " + minFastaLength} \ ${"--keep " + keep } \ ${true="--vcf" false="" vcf } \ - ${"--threads " + threads } \ + ${"--threads " + finalThreads } \ ${"--mode " + mode } \ ${"--min_bridge_qual " + minBridgeQual } \ ${"--linear_seqs " + linearSeqs } \ @@ -94,7 +96,7 @@ task unicycler { File log = out + "/unicycler.log" } runtime { - cpu: threads - memory: memory + cpu: finalThreads + memory: finalMemory } } \ No newline at end of file