diff --git a/gatk.wdl b/gatk.wdl index 160849ad00e3d849bfb26a44ce717b73e2c4918f..d4613d9c93d7cbf8df2c69f66d4f6cf2862f28d4 100644 --- a/gatk.wdl +++ b/gatk.wdl @@ -271,7 +271,7 @@ task SplitNCigarReads { SplitNCigarReads \ -I ${input_bam} \ -R ${ref_fasta} \ - -O ${output_bam} # might have to be -o depending on GATK version \ + -O ${output_bam} \ -L ${sep=' -L ' intervals} } diff --git a/star.wdl b/star.wdl index d7d3b7b595953704ab0de936b82e1ba7405fe279..32dd0565dc2511c7c3073531c5f8e28c9ba707bf 100644 --- a/star.wdl +++ b/star.wdl @@ -12,6 +12,7 @@ task Star { String? outStd String? twopassMode Array[String]? outSAMattrRGline + Int? limitBAMsortRAM Int? memory @@ -34,6 +35,7 @@ task Star { ${"--runThreadN " + runThreadN} \ ${"--outStd " + outStd} \ ${"--twopassMode " + twopassMode} \ + ${"--limitBAMsortRAM " + limitBAMsortRAM} \ ${true="--outSAMattrRGline " false="" defined(outSAMattrRGline)} ${sep=" , " outSAMattrRGline} }