Sarek 2.3.FIX1

• Fix output directories

Sarek 2.3 - Äpar

• mapping step can now map BAM files too
• Improve ASCAT
• Improve AWS Batch configuration
• Improve bamQC
• Improve VEP
• Run Sarek with conda
• Use SnpEff and VEP cache
• Improve usage of targetBED params
• Improve targeted for Manta
• Multiple patients TSV file
• Update VEP from 95.1 to 95.2
• Strelka Best Practices output is now prefixed with StrelkaBP_
• VCFs and Annotated VCFs are now ordered by Patient, then tools

Sarek 2.2.2

CHANGELOG

• Update GATK 4.0.6.0 -> 4.0.9.0
• Update FastQC 0.11.7 -> 0.11.8
• Update VEP 90.6 -> 92
• Enhance QC
• Improved AWS Batch usage
• Add AWS iGenomes possibilities
• New publishDirMode param

Sarek 2.2.1

CHANGELOG

• Update pathfindr submodule
• Update Nextflow 0.31.1 -> 0.32.0
• Update docs
• Fix RunMultiQC.nf bug

Sarek 2.2.0 - Skårki

Sarek 2.2.0 - Skårki

CHANGELOG

• Process targeted sequencing with a target BED
• Refactor documentation
• Use correct .simg extension for Singularity images
• Container updated:
  • MultiQC 1.5 -> 1.6
  • Qualimap 2.2.2a -> 2.2.2b
  • VCFanno 0.2.8 -> 0.3.0
  • VCFtools 0.1.15 -> 0.1.16
• Simplify tests

Ruotes

Main changes:

• Realignment removed
• No Mutect1
• Sarek container contains most of the tools

Sarek 2.0.0

CAW is dead, long live Sarek!!
With this new version, a change of name.
The main script is now separated into five different scripts.
So there is obviously some minor changes for executing the workflow.
But apart from that, it's the same pipeline it was before.

[2.0.0] - 2018-03-23

Added

• basic wrapper script
• Abstract, posters and figures
• ROI selector and FreeBayes sanitizer scripts
• New logo and icon for the project
• check for existing tumor/normal channel
• lib/SarekUtils.groovy with checkParams, checkParameterList, checkParameterExistence and isAllowedParams functions
• some runOptions for docker (prevent some user right problem)
• This CHANGELOG

Changed

• CAW is now Sarek
• Dissect Workflow in 5 new scripts: annotate.nf, main.nf, germlineVC.nf, runMultiQC.nf and somaticVC.nf
• report.html, timeline.html and trace.html are generated in Reports/
• --version is now used to define the workflow version
• most params are now defined in the base.config file instead of in the scripts
• update RELEASE_CHECKLIST.md
• checkParams, checkParameterList, checkParameterExistence and isAllowedParams in script functions are now called within SarekUtils
• nf_required_version is now params.nfRequiredVersion
• in buildReferences.nf script, channels now begin by ch_, and files by f_
• use PublishDir mode: 'link'`` instead of copy`
• directoryMap now contains params.outDir
• use Nextflow support of scratch (close #539)
• reordered Travis CI tests
• update documentation
• MultiQC version in container from v1.4 to v1.5
• vepgrch37 container base image from release_90.6 to release_92
• vepgrch38 container base image from release_90.6 to release_92
• VEP version in containers from v90 to v91
• nucleotidesPerSecond is now params.nucleotidesPerSecond
• default params.tag is now latest instead of current version, so --tag needs to be specified with the right version to be sure of using the containers corresponding

Deprecated

• standard profile
• uppmax-localhost.config file

Removed

• scripts/skeleton_batch.sh
• old data and tsv files
• UPPMAX directories from containers
• --step in annotate.nf, germlineVC.nf and somatic.nf
• some runOptions for Singularity (binding not needed anymore on UPPMAX)
• download profile

Fixed

• Replace VEP --pick option by --per_gene (fix #533)
• use $PWD for default outDir (fix #530)

CAW 1.2.5

• Fixed version of COSMIC GRCh37 v83
• Add delivery README
• Write an error message when --sampleDir does not find any FASTQ files
• Document use of the --sampleDir option
• Add CAW Contributing Guidelines
• Add Issue Templates
• Add Release Checklist
• Update Nextflow to 0.26.0 (new fancy report + AWS Batch)
• Add extra time on Travis CI testing
• Replace bundleDir by params.genome_base
• Update MultiQC to 1.3 (MEGAQC FTW)
• Add --outDir
• Add base.config for ConcatVCF process
• Add awsbatch profile
• Add aws-batch.config config file
• Move and rename some test files
• Add new --noBAMQC params (failing in AWS Batch, and sometimes on Bianca)
• Fix file specification for recalibrationReport in RecalibrateBam process (got error on AWS Batch)

CAW 1.2.4

Bug fixes:

• #488 Better CPU requirements for ConcatVCF
• #489 Add exception handling for ASCAT
• #490 Add CPU requirements for runSingleStrelka and runSingleManta

CAW 1.2.3

Merging PR:

• #476 to resolve #475 (16 cpu for local executor)
• #485 to resolve #357 (ASCAT works for GRCh38)
• #483 to resolve #471 (Running singularity on /scratch), #480 (no tsv for step annotate) and to prepare for NGI deployment