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CHANGES

2.6.2

  • update regex expression to restrict files returned in search

2.6.1

  • updated CWL files metadata schema IRI
  • updated container version that CWL tools will pull
  • being more flexible on tophatpost index files

2.6.0

  • Added 2 new params to allow direct pathing to work around assumed paths that don't allow multiple builds in a reference area

2.5.0

  • Added run-cgprna subcommands: tophat-fusion, start-fusion and defuse to run infuse pipeline.
  • Re-organized expected file structure in Star reference bundle. Previous Star reference bundle on the FTP server will not work for this version.
  • Added CWL files to run Infuse pipeline in cgpRna and example JSON files for using them with Dockstore.
  • Uploaded new set of reference bundle files for GRCh38 and GRCh37d5 to the FTP server.
  • Updated setup.sh to install Python3 RSeQC and HTSeq.

2.4.1

  • added a patched topaht-fusion-post script, in which the contig name bug #37 is fixed

2.4.0

  • Revised Dockerfile so that the builder stage is properly used and the image size is reduced. Resolved #28.
  • Added a CLI, so that user can complete a step in RNA-seq data workflow with just one command, which also eases the development of CWL files.
    • CLI is written in Python
    • currently 4 subcommands are implemented:
      • map: uses star_mapping.pl to map and marks duplicates after mapping.
      • stats: generates mapping stats using bam_stats and RSeQC.
      • bigwig: generates bigwig file using bamToBw.pl
      • counts: counts reads using htseq-count.
  • Built a new set of reference files for CLI to use. They're available on ftp://ftp.sanger.ac.uk/pub/cancer/support-files/cgpRna_container/.
  • Added CWL files:
    • added a workflow to map sample by lanes, generate mapping stats for lanes, merge lane bams, generate bigwig file and count reads.
    • added CWL tools/workflows for the workflow above to use.
    • added example JSON for most of the CWL files.

2.3.4

  • RG tags are converted to shell safe strings before passing to Star. partially resolve #30.

2.3.3

  • fixed verison numbers

2.3.2

  • fixed blatSrc url in setup.sh

2.3.1

  • fixed blatSrc url in Docker container build script

2.3.0

  • dockerised cgpRna. Within the docker container, version of some dependent tools have been changed:

    1. Python3(3.7.X) is used in the container, thus:

      • RSeQC is updated from version 2.6.4 to 3.0.0.
      • However, version of HTSeq is not changed.

    2. Defuse is updated from v0.7.0 to v0.8.2 due to "Possible precedence issue with control flow operator" warning with the version of Perl installed in the container. The fix is here. However it is not merged in any v0.7.x versions (also because there's only ONE v0.7.x version --v0.7.0), hence v0.8.2, which is the latest version at the time, was chosen.

    3. To utilise apt packages for the ease of their installations, the following tool version changes were made:

      • BedTools: 2.21.0 to 2.25.0-1 in apt,
      • bowtie1: 1.1.1 to 1.1.2-3 in apt,
      • bowtie2: 2.2.3 to 2.2.6-2 in apt,
      • blast: 2.2.30 to 2.2.31-4 in apt,
      • gmap: 2015-09-10 to 2015-12-31.v7-1 in apt.

  • added an extra option "-updateconfig" to defuse_fusion.pl. It takes a file as input, which content is used to update defuse-config.txt. It'll search defuse.ini to find its default value. This addition shouldn't break any existing usage.

  • defuse_fusion.pl will always create a defuse-config.txt file in its temp folder and use it to run defuse.pl. In the temp file, dataset_directory is corrected using related command line input values. If "-updateconfig" presents, values in the file will be used to overwrite corresponding values in the temp file. Note: if dataset_directory key presents in the "-updateconfig" file, this will be the final value in the temp config file.

  • tophat-fusion-post now skips read dist step, which our infuse pipeline does not care and the tophat-fusion-post.py does not insert generated read distributions in final html report anyway neither.

2.2.2

  • Change tabix query call to query_full

2.2.1

  • Handle files not being written by tophat-fusion-post when no events generated.

2.2.0

  • RSeqQC - Updated to 2.6.4, fixes known issues with low levels of mapped data.
    • Also resolves 2.6.3 that is no longer available from central repos.
  • HTSeq - updated to 0.7.2 to ensure compatilbility with current pysam.

2.1.9

  • Fix missed compilation failure

2.1.8

  • Fix issues with empty output from tophatpost when running tophat_filter

2.1.6-2.1.7

  • Fixing issues with data exhibiting no fusions.

2.1.5

  • updating cpanm source url

2.1.4

  • Fixing installation of tophat. Since we no longer use a compiled repository. Bug introduced in 2.1.2.

2.1.3

  • Correct name from sample.bas to sample.bam.bas

2.1.2

  • Fixed tophat-fusion-post issue in local tophat fork added tophat v2.1.0a to setup.sh

2.1.1

  • Added HTseq installer for read counting