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CHANGELOG
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Changelog
==========
<!--
Newest changes should be on top.
This document is user facing. Please word the changes in such a way
that users understand how the changes affect the new version.
-->
version 4.0.0
---------------------------
+ Workflow was adjusted to conform with Hartwig Medical Foundation's
pipeline5 version 5.31.
+ Updated tool were versions:
+ TODO
+ TODO
+ Adjusted structure of output directory.
+ Added support for target regions (experimental).
+ Many inputs were added, adjusted or removed:
+ `referenceImg`: removed
+ `somaticCodingPanel`: replaced by `codingPanel`
+ `viralReference`, `viralReferenceFai`, `viralReferenceDict` and
`viralReferenceImg`: replaced by `viralReferenceBwaIndex`
+ `PON` and `PONindex`: removed
+ `repeatMaskerDb`: added
+ `ponFile`: added
+ `ponArtefactFile`: added
+ `mappabilityHdr`: removed
+ `germlineCoveragePanel`: replaced by `coverageCodingPanel`
+ `germlineCodingPanel`: removed
+ `gnomadFreqFiles`: added (defaults to an empty list)
+ `hlaRegions`: added
+ `germlineDelFreqFile`: added
+ `svPrepBlacklistBed`: added
+ `signaturesFile`: added
+ `roseActionabilityDatabaseTsv`: added
+ `filterFastq` is now set to `false` by default.
+ `fastpCorrection` is now set to `false` by default.
+ `targetRegionsBed`: added (optional)
+ `targetRegionsNormalisationTsv`: added (optional)
+ `targetRegionsRatios`: added (optional)
+ `targetRegionsMsiIndels`: added (optional)
+ Fixed an issue where fastp's metrics for the tumor fastq files
were not being included in the multiQC report.
version 3.2.0
---------------------------
+ Added the `shallow` input to enable shallow mode. Defaults to false.
+ Added the `runPolyGTrimming` input to control whether or not poly-
G-tail trimming should be performed by fastp. By default fastp's
default behaviour will be used, ie. enabled for NextSeq/NovaSeq data
as determined from the FastQ headers.
+ Added the `mappingThreads` input to control the number of threads
used per BWA mem job. Defaults to 8.
+ Added the `splitFastq` input to control whether fastq files should
get split into chunks or not. Defaults to true.
+ Added the `filterFastq` input to control whether fastq files should
get filtered on quality and read length prior to mapping. Default to
true.
+ Added the `fastpCorrection` input to control whether fastp's
correction should be enabled. DEfaults to true.
version 3.1.1
---------------------------
+ Fixed an error in sortReportedVcf caused by an incomplete VCF header.
version 3.1.0
---------------------------
+ Added a task to call genotypes for specific sites.
version 3.0.3
---------------------------
+ `runAdapterClipping` is now set to true by default.
version 3.0.2
---------------------------
+ Limit the number of chunks per fastq file to 16. Fastp will run into
issues if the number of chunks is not divisible by the number of
threads it uses, which is limited to 16 theads.
+ Runtime attributes for Amber were adjusted:
+ memory increased from `70GiB` (javaXmx: `64G`) to `85GiB`
(javaXmx: `80G`).
+ timeMinutes increased from `240` to `480`.
version 3.0.1
---------------------------
+ Fixed an issue where fastp errors if the number of splits for
a fastq file is set to 1.
+ Fixed a bug that caused the header of the reportedVAR.vcf output to
be malformed. (see v2.1.1)
+ Memory requested for mark duplicate tasks increased from 25000 Mb to
50000 Mb.
version 3.0.0
---------------------------
(Does not include changes from 2.1.1)
+ Use fastp for adapter clipping and initial QC metrics collection
instead of the biowdl QC workflow (which uses cutadapt and fastqc).
Also replaces fastqsplitter for chunking of the fastq files.
+ Added picard CollectInsertSizeMetrics.
+ Added MultiQC.
+ Increased the number of threads used for duplicate marking to 8 (was 3).
version 2.1.1
---------------------------
+ Fixed a bug that caused the header of the reportedVAR.vcf output to
be malformed.
version 2.1.0
---------------------------
+ Added a task that generates a table of VAFs (as determined by Purple)
for somatic variants.
+ Added an output stating the pipeline version.
+ Removed unused `breakpointHotspot` input.
+ Removed unused `peachTranscriptTsv` input.
+ Removed unused import of snpEff task.
+ Chunk numbers per input fastq are now calculated based on size.
The total number of chunks can be set using the
`totalMappingChunks` inputs, which defaults to 25.
+ For various jobs the default runtime attributes have been adjusted
to be more efficient.
version 2.0.0
---------------------------
+ Tool versions were upgraded:
+ Cuppa: 1.4 -> 1.6
+ Gripss: 1.11 -> 2.0
+ Linx: 1.16 -> 1.18
+ Protect: 1.4 -> 2.0
+ Purple: 3.1 -> 3.2
+ virus-interpreter: 1.0 -> 1.2
+ Peach: 1.0 -> 1.5
+ snpEff was replaced with Pave.
+ LinxVisualization was added.
+ CupGenerateReport was added.
+ Orange was added.
+ Added a job to create a VCF of reported variants.
version 1.0.1
---------------------------
+ Fixed a bug causing health-checker to finish with return code 1
despite finishing successfully.