2.5.0 Can run Infuse pipeline through CLI and CWL

• 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.

2.4.0 Added run-cgprna command line tool and CWL workflows

• Reduced Docker image size
• Added run-cgprna command line tool, which can be used to complete a step in RNA-seq data workflow with just one command. 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 run-cgprna to use. They're available on ftp://ftp.sanger.ac.uk/pub/cancer/support-files/cgpRna_container/.
• CWL tools and workflows:
  • 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.

2.3.3 - Corrected blatSrc urls and version numbers

Minor changes from 2.3.0:

• updated blatSrc URL when building the container/installing cgpRna
• corrected version numbers in its Perl build and Docker container.

Backport - dependency url fix

Corrects blatSrc35 download location.

This is for legacy use only please see the 2.3+ for new deployments.

2.3.0 - Dockerised

• 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, the 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

2.2.2

• Change tabix query call to query_full

2.2.0 - installation and versions

• 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 compilation error

• Fixed compilation error

2.1.8 - Fix empty files from tophat_post

• Fix issues with empty output from tophatpost when running tophat_filter

2.1.7 - fix for downstream files when quiet data.

Essentially a continuation of 2.1.6.