diff --git a/CHANGELOG.md b/CHANGELOG.md index 9bf5701d8ab9edd98d64f60d6df07d46e906e923..ad9ea5f05072c653dadcd971820d94104468bfc5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,4 +11,6 @@ that users understand how the changes affect the new version. version 1.0.0-dev --------------------------- ++ Add feature type, idattr and additional attributes to htseq-count. + Added allow-contain option to bowtie. ++ Added a changelog to keep track of changes. diff --git a/htseq.wdl b/htseq.wdl index ed13167cc800627a8370634d667f96022c3bfe5a..ef9c0ed2f2bb115d3053ea7b821d30c2ff584a86 100644 --- a/htseq.wdl +++ b/htseq.wdl @@ -9,6 +9,9 @@ task HTSeqCount { String format = "bam" String order = "pos" String stranded = "no" + String? featureType + String? idattr + Array[String] additionalAttributes = [] Int memory = 40 String dockerImage = "quay.io/biocontainers/htseq:0.9.1--py36h7eb728f_2" @@ -21,6 +24,9 @@ task HTSeqCount { -f ~{format} \ -r ~{order} \ -s ~{stranded} \ + ~{"--type " + featureType} \ + ~{"--idattr " + idattr} \ + ~{true="--additional-attr " false="" length(additionalAttributes) > 0 }~{sep=" --additional-attr " additionalAttributes} \ ~{sep=" " inputBams} \ ~{gtfFile} \ > ~{outputTable}