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cnr-ibba/nf-resequencing-mem: Changelog

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

0.6.1 - [2024-04-11]

  • Calculate samtools/depth on each chromosomes (#73)

Fixed

  • Passing args to modules/local/freebayes_splitcram
  • Calculate samtools/depth without 0 coverage regions

0.6.0 - [2024-04-04]

  • Replace *.bam file format with *.cram (#9)
  • Add Read Groups during the alignment step (#57)
  • Annotate VCF file with SnpEff (#59)
  • Configure MultiQC analysis (#60)
  • Update modules (#64)

Added

  • Add samtools/depth process
  • Add freebayes_splitcram custom module to split genome in regions relying on total sample coverage
  • Add cram_markduplicates_picard custom local subworkflow by modifying bam_markduplicates_picard to work with *.cram files by default
  • Add cram_stats_samtools custom local subworkflow by modifying bam_stats_samtools to work with *.cram files by default
  • Add freebayes_splitcram local module to splice alignments regions relying on samtools/depth step
  • Add snpeff/download module
  • Add snpeff/snpeff module
  • Add snpeff_annotate local subworkflow

Fixed

  • freebayes_parallel subworkflow was moved to cram_freebayes_parallel local subworkflow and was modified to deal with total sample coverage and to work with *.cram files
  • picard/markduplicates now works with .*.cram files
  • bwa/mem was configured to write files as *.cram files
  • samtools/depth was patched to write results with headers, with 0 coverage position and to compress output with gzip
  • resequencing-mem workflow was modified in order to use local subworkflow, for example to deal with samtools and markduplicates
  • fixed a issue when providing the --genome_bwa_index parameter
  • snpeff_download was patched in order to remove the version parameter
  • snpeff/snpeff module was patched to support custom database annotations and to compress VCF output using a mulled image with tabix
  • the configuration file for MultiQC module was updated to simplify results, to order them and to support all the supported modules

Removed

  • Remove cnr-ibba/bamaddrg module
  • Remove cnr-ibba/freebayes/splitbam module

0.5.2 - [2023-12-21]

  • Use MultiQC with all supported tools (#53)
  • Update modules
  • Minor fixes

Added

  • Add samtools/stats module
  • Add samtools/idxstats module
  • Add bcftools/stats module

0.5.1 - [2023-11-15]

  • Updated pipeline to support the latest version of nf-core/tools (#46)

Added

  • Check that reads IDs are unique (using seqkit/rmdup - #47)

v0.5.0 - [2022-11-21]

  • Improved freebayes performances (#41)
  • Calling freebayes in different processes (#44)

Fixed

  • CAT_FASTQ result is not saved by default
  • split chromosome relying on BAM size while running freebayes
  • call freebayes in distinct process for each chromosome chunk

v0.4.3 - [2022-11-03]

  • Upgrade modules (#34)
  • Solve linting issues (#32)
  • Force check_samplesheet.py assuming header present (#31)
  • Normalize VCF file (#33)

Added

  • Add bcftools/norm module
  • Add tabix/tabix module

Fixed

  • Force samplesheet having header in INPUT_CHECK:SAMPLESHEET_CHECK workflow
  • Fix software dump version
  • Support for --help option
  • Fix resource limits

Removed

  • Freebayes result is not more published by default
  • Removed unused params

v0.4.2 - [2022-07-29]

  • Improved coverage step with samtools/coverage (#27)
  • Saving indexed files as outputs

Added

  • Add samtools/coverage module

Removed

  • Remove BEDTOOLS_GENOMECOV local process

v0.4.1 - [2022-07-28]

  • Calling freebayes on all samples (#11)
  • Deal with compressed genomes (#14)
  • Calculate sample coverage (#17)
  • Provide indexes as parameters and save them as results

Added

  • Add freebayes/multi process
  • Add BEDTOOLS_GENOMECOV local process

Removed

  • Remove freebayes/single module

v0.4.0 - [2022-07-27]

  • Updating modules (#20, #4)
  • Name samples within bam (#18)
  • Export BAM and trimmed fastq (#16)
  • Add module and base config files (#10)
  • Get input from samplesheet (#15)

Added

  • Add INPUT_CHECK:SAMPLESHEET_CHECK workflow
  • Add bamaddrg module

Removed

  • Remove samtools/sort module (now sorting is done in bwa/mem)

Fixed

  • Track sample names in .bam files

v0.3.0 - [2021-11-08]

  • Support AWS environment (#2)
  • Structure pipeline with the new nextflow template (#7)

v1.0dev - [2020-11-24]

Initial release of cnr-ibba/nf-resequencing-mem as nexflow implementation of resequencing-mem pipeline