1.2.4

Add option to output pBAM and use that for quantification and signal tracks.
Cromwell 59 or newer is needed to run this version.

1.2.3

No functional changes. Improve WDL metadata, run tests with caper instead of directly with Cromwell.

v1.2.2

In some cases (most likely due alignment task running low on disk space) bam files get truncated. To detect this samtools quickcheck step was added causing the pipeline to fail when a flawed bam has been created.

v1.2.1

Docker image hosting moved to Docker Hub from quay.io.

v1.2.0

Kallisto parameters kallisto_fragment_length and kallisto_sd_of_fragment_length are now of types Array[Int] and Array[Float] enabling user to define different values for replicates.

v1.1.4

Add Boolean workflow parameter run_kallisto that makes running Kallisto optional. This parameter is true by default, so to retain the same behavior as before, no changes to inputs are needed.

v1.1.3

Freeze bedSort and bedGraphToBigWig versions to 385.

v1.1.2

Minor release, adding automatic USCS genome browser track generation to croo output_definition.json.

v1.1.1

Minor release that changes the signal track outputs into type File from Array[File].

v1.1

• Output all the QC metrics in .json format in addition to the originals.
• Each replicate can now consist of multiple fastqs. Note that the input format for fastqs has changed, see documentation.