There is a newer version of the record available.

Published August 7, 2020 | Version v4.0.0
Software Open

biowdl/RNA-seq: Release 4.0.0

Creators

  • 1. @LUMC
  • 2. Leiden University Medical Center
  • 3. LUMC

Description

  • Default docker images for various tools have been updated.
  • Changes in Cromwell 48 made it impossible to use the wide array of inputs in our documentation (such as RNAseq.sampleJobs.qc.Cutadapt.minimumLength). Fixes have been made upstream and in the pipeline. From Cromwell 52 onwards these options will be available again.
  • Bam files are no longer indexed after alignment, saving compute time.
  • WDL files and imports zip packages are now provided each release to make running pipelines easier.
  • The output directory was simplified. All files related to a sample are now in the samples/<sample_id> directory.
  • Use the scatter-regions tool to replace biopet-scatterregions.
  • The pipeline was renamed from "pipeline" to "RNAseq".
  • Tasks were updated to contain the time_minutes runtime attribute and associated timeMinutes input, describing the maximum time the task will take to run.
  • Added a step to generate the STAR index, if neither a STAR nor a Hisat2 index is provided.
  • Document the use of cromwell's final_workflow_outputs_dir feature which makes the RNA-seq pipeline usable on all of Cromwell's supported backends. Users are encouraged to use this feature. outputDir references are removed from the documentation.
  • Make the MultiQC task suitable for use with a final_workflow_outputs_dir so it can be used on all of Cromwell's supported backends.
  • Added a picard markduplicates step after UMI deduplication.
  • Move common optional inputs to top-level workflow, so nested inputs are not required anymore for the majority of configurations.
  • The pipeline has been altered so it starts the variant calling jobs in a more efficient way.
  • Major bug fix: The --dont-use-soft-clipped-reads is now used on HaplotypeCaller in concordance with GATK best practices.

Files

biowdl/RNA-seq-v4.0.0.zip

Files (4.6 MB)

Name Size Download all
md5:55da7b89a339011c34cd0bc9a1fbaf60
4.6 MB Preview Download

Additional details

Related works

Is supplement to
https://github.com/biowdl/RNA-seq/tree/v4.0.0 (URL)