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nf-cmgg/preprocessing: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

3.0.0

  • Add MultiQC-SAV module for Illumina Run QC reports
  • Migrate readgroup parsing from preprocessing.nf to a local subworkflow
  • Update pipeline to use topic channels only, deprecation versions channels
  • Drop bcl_demultiplex subworkflow in favour of bcl-convert module
  • Update the output handling to use the new workflow output definitions.
  • Bump all modules to latest versions.
  • The workflow now outputs data in a subdirectory per library, including a library specific MultiQC report
  • Drop support for unaligned cram outputs in favor of untrimmed fastq outputs, which are more widely supported and can be used for a wider range of downstream analyses.
  • Add support for untrimmed fastq outputs for unsupported genomes or when aligner is set to false.
  • Drop support for global aligner parameter. The aligner must now be specified per sample in the sample sheet or sample info.
  • Drop support for global markdup and umi_aware parameters. Marking duplicates must now be specified per sample in the sample sheet or sample info.
  • Drop support for global run_coverage and disable_picard_metrics parameters. Running coverage analysis must now be specified per sample in the sample sheet or sample info.
  • Drop support for global skip_trimming, trim_front, trim_tail, adapter_R1 and adapter_R2 parameters. Trimming must now be specified per sample in the sample sheet or sample info.
  • Drop support for global roi parameter. Regions of interest must now be specified per sample in the sample sheet or sample info.
  • Simplify fastq sharding and make it user configurable via the split_fastq parameter.
  • Added splice junctions and junctions outputs for RNA-seq alignments using STAR.

v2.0.6

  • Update bash options for nextflow version 25.04.2
  • Update bcl-convert module to 4.3.13
  • Update bowtie2 module to 2.5.4
  • Update multiqc module to 1.29

v2.0.5

  • Panel coverage will now run all genelists' coverage analysis in one process per sample
  • Fix readgroup sample names for snp_ prefixed samples
  • Edit WGS profile to include samtools/sormadup and enable UMI aware duplicate marking

v2.0.4

  • Add flag to snap to allow for more expansion of compressed data
  • Parse readgroup samplenames for snp_ prefixed samples
  • Replace GRCh39 by mm10 as default genome for Mus musculus

v2.0.3

  • Update modules
  • Fix bugs where samples with unequal number of files were not processed correctly
  • Update to nf-core template v3.1.1
  • Fix all tests

v2.0.2

  • Drop unused params
  • Set aligner to star for RNA-seq
  • Finetune resources
  • Fix some bugs for different input tags
  • Update modules

v2.0.1

  • Fix syntax according to new rules
  • Drop usage of check_max function in favour of resourceLimits
  • Bump nf-schema to v2.1.0
  • Add configuration profiles for several datatypes
  • Fix usage of --run_coverage parameter
  • Update modules

v2.0.0

  • Move repo to nf-cmgg organisation
  • Overhaul reference data handling. All data is now sourced from the igenomes config file and dynamically loaded based on the organism metadata field.
  • Drop support for bam/cram inputs
  • Update to nf-core template v2.13.1
  • Drop fgbio/fastqtosam in favour of samtools/import
  • Add samtools/coverage for coverage analysis
  • Add testing with nf-test
  • Overhaul panel coverage analysis
  • Add support for STAR aligner for RNA-seq
  • Replace CSV sampleinfo definition with validated JSON/YAML
  • Update modules

v1.2.0

  • Add fix for sample replicates with different split sizes
  • Add option to use samtools for duplicate marking
  • Updated modules
  • Updated to nf-core template v2.8
  • Fix issue where unaligned samples were not merged and fixed naming
  • Add minimal support for sample "tags" in sample sheet
  • Add panel coverage analysis
  • Limit panel coverage analyses to samples with WES/WGS tags
  • Make BAM_ARCHIVE accept channels with cram files
  • Drop ELPREP support
  • Add support for cram and index outputs in SAMTOOLS_SORMADUP
  • Add option to disable marking duplicates
  • Update to nf-core template v2.9
  • Start using nf-validation for input parsing
  • Drop support for generating aligner indices

v1.1.2

  • Support for bamprocessing with ELPREP
  • Improved sample grouping
  • Meta value clean up
  • bump modules
  • fix multiqc report to include all results
  • fix duplicate marking with bamsormadup
  • drop post alignment sorting, doesn't make sense as we do sort/markdup afterwards
  • Add option to use elprep for alignment postprocessing

v1.0.2dev

  • Add unaligned denominator to unaligned samples

v1.0.1

  • Updated modules

Fixed

  • Bug with fgbio/fastqtosam where having multiple files per read requires a read structure

v1.0dev - [06/09/2022]

Initial release of CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing, created with the nf-core template.