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Change Log

This change log only lists the major changes between releases. For a full list of changes refer to the commit log.

2017-10

New pipelines:

  • chromatin-profiling/atacseq: runs Bowtie2 and MACS2 to call ATAC-Seq peaks
  • rnaseq/wafergen-scrna: analyses WaferGen's single cell sequencing data, using umis and scRNApipe for the core analysis.

Changes to pipelines and framework:

  • Major pipelines now produce benchmarking logs
  • STAR-RSEM now supports --estimate-rspd and new strandedness option
  • Shotgun-metagenomics: Added SRST2, read counting and coverage threshold for decontamination
  • GATK: support for joint variant calling (--joint-calls) and added a new option (--gvcf-only). Also added a new optional references config for agressive splitting
  • Added --restarts option to control number of automatic restarts in case of failure
  • Minor additions to SG10K and many under the hood changes to bc2lfastq

2017-06

New pipelines:

  • metagenomics/shotgun-metagenomics: runs several metagenomics profilers and pathway analysis
  • germs/vipr3: Assembles viral NGS data and analyses low frequency variants

Changes to pipelines and framework

  • Reduced number of submitted jobs in all pipelines (bundling of jobs e.g. in GATK and use of master slot through local rules)
  • Reduced cluster memory footprint in all pipelines
  • bcl2fastq now also creates index reads by default
  • Workflows are restarted automatically once after failure
  • S3 suport for FastQ files listed on config files
  • Support for injection of processed BAM into GATK and Lacer-LoFreq
  • Now using environment modules instead of dotkit

Software Upgrades:

  • GATK 3.7
  • BWA 0.7.15
  • Lacer 0.424
  • Snakemake-3.11.2

2017-01

  • New pipelines:
    • chromatin-profiling/chipseq running dfilter and macs2, followed by meme-chip
  • Added default SNPeff annotation to all variant callers
  • Fasta and bed compatibility now checked before running
  • Added option to skip variant calling in GATK pipeline (--bam-only)
  • Added option to use precomputed BAM into GATK pipeline (--raw-bam)
  • Several fixes for fluidigm-ht-c1-rnaseq to be able to better deal with the typically huge number of files and jobs
  • Cluster limit adjustments for all pipelines to reflect move from vmem to RSS in GIS
  • Log files are now automatically bundled on success
  • Job completion emails can now be send to other users
  • Version upgrades:
    • snakemake 3.8.2
    • sambamba 0.6.5

2016-10:

  • New pipelines:
    • somatic/lofreq-somatic
    • somatic/mutect
  • Update of variant-calling/gatk to GATK 3.6 incl. adoption of new best practices (also fixes use of changes known sites according to https://software.broadinstitute.org/gatk/guide/article?id=1247)
    • Addition of padding parameter for non-WGS samples
  • PCR duplicates are now marked after merging using sambamba (previously we used samblaster streaming per fastq pair) in all pipelines
  • New configuration options: the previously monolithic conf.default.yaml was split into references.yaml, modules.yaml and params.yaml. These are user changeable via newly added parameters. This way one can for example change reference bundles etc.
  • Multisample support was implemented for most pipelines, with lots of internal changes. However, this can lead to surprisingly high memory consumption by snakemake itself. See notes in README.md
  • Many optimizations (thread settings, cluster settings) and bug-fixes
  • Added several of auxiliary tools, e.g. create_mux_cfg.py and whereismux.py
  • Added convenience wrapper run
  • Substantially extended documentation (main README, README per pipeline and added example workflow visualizations)
  • Reduced all threads to maximum of 16 (NSCC limit 24)
  • Refer to git commit messages for more details and changes under the hood

2016-07:

  • newly production ready pipelines
    • BWA-MEM
    • [essential-genes]
    • fluidigm-ht-c1-rnaseq
    • rnaseq
    • variant-calling-gatk
    • variant-calling-lofreq
  • new web service: bcl2fastq_record.py
  • now using drmaa by default
  • simplified wrappers with class PipelineHandler()
  • new tools: whatapps and production warnings helper

2016-06:

bcl2fastq:

  • new no_archive option
  • mail to ngsp and requestor (send_email_status.py)
  • new tool: bcl2fastq_dbrecords.py
  • many bug fixes

2016-05

  • first ever used deployment
  • only bcl2fastq