grenepipe v0.10.0

This is the release version accompanying the grenepipe publication:

grenepipe: A flexible, scalable, and reproducible pipeline
to automate variant calling from sequence reads.
Lucas Czech and Moises Exposito-Alonso. Bioinformatics. 2022.
doi:10.1093/bioinformatics/btac600 [pdf]

Notable Changes

• Add HAF-pipe rules for computing haplotype-based allele frequencies
• Add proper 1001g-based known-variants file as an example and for testing
• Add copy samples script

Bug Fixes

• Fix hard filter name duplication in filtered VCF
• Fix bcftools sample sorting order issue
• Ungroup GATK HaplotypeCaller merging
• Ungroup filter merge step
• Add progressbar and termcolor python dependencies to grenepipe env

grenepipe v0.9.0

Notable Changes

• Properly implement GATK Variant Quality Score Recalibration (VQSR)
• Add bcftools call for individual samples instead of combined calling
• Add read clipping with BamUtil
• Add SeqKit for reporting statistics of the reference genome
• Add bcftools stats reporting on the final vcf
• Add settings for keeping/removing intermediate files, to save disk storage

Bug Fixes

• Fix all issues related to samtool sort needing a temporary directory to properly run
• Fix using optional mapping steps in combination with DeDup
• Fix fastqc log output, which was not properly reported

grenepipe v0.8.0

Notable Changes

• Change main grenepipe environment to Snakemake 6.0.5 (for now)
• Add platform info to bam read group tags #20
• Add support for local snpEff database #13
• Remove shadow rules, as they create too many intermediate files

Bug Fixes

• Fix snpEff download directory to work without trailing slash #12
• Fix R1 matching in generate table script
• Switch from pandas append to concat to avoid deprecation

grenepipe v0.7.0

Notable Changes

• Add SeqPrep for trimming
• Remove write-protection from intermediate called files, as this caused more trouble than benefits

Bug Fixes

• Fix general incompatibility issues caused by conflicting versions of python/pandas/numpy in rule-specific conda environments

grenepipe v0.6.1

Bug Fixes

• Fix an issue where the requested wall time in the cluster profile was ignored for some mapping tools.

grenepipe v0.6.0

Notable Changes

• Add bwa mem2 for mapping
• Add better support for genomes with small contigs / scaffolds to avoid submitting individual compute jobs for each of them
• Refactor FastQC rules to use both files of paired end reads, or merge trimmed reads
• Declare the restrict-regions setting experimental

Bug Fixes

• Fix picard CollectMultipleMetrics missing dependency
• Fix missing fasta dict dependency in filtering rule
• Fix incompatibility issue with python 3.8 and pandas under snakemake > 6
• Fix incompatibility between samtools 1.9 and python 3.7

grenepipe v0.5.1

Bug Fixes

• Fix the order of mpileup columns in merged pilup files to fit with the order of the input samples table.

grenepipe v0.5.0

This release adds better support for bam files, adds support for (m)pileup files, and provides fixes for conda dependency issues on clusters where conda and python are not well set up.

Notable Changes

• Add targets and rules to create bam files only, see here
• Add targes and rules to create (m)pileup files
• Allow changing the bcftools call calling method

Bug Fixes

• Fix conda dependency specifications for Bowtie2, Cutadapt, Picard, Trimmomatic, bwa, freebayes, MultiQC, VEP, snpeff, and all GATK tools
• Fix generate table script to work with symlinks
• Fix prepare step issue with gz-compressed reference genomes on CentOS
• Fix incompatibility between bcftools and Picard by switching to vcflib for merging
• Fix issue with bcftools calls containing IUPAC ambiguity codes
• Fix issue with freebayes not sorting large vcf files properly

grenepipe v0.4.0

Grenepipe is now a single-command tool. The prep step is no longer needed!

Notable Changes

• Refactor to remove prep step requirement
• Add VEP annotation tool
• Change SnpEff config setup, moving the database name to the params section
• Change SnpEff stats output directory to annotated

Bug Fixes

• Fix yet more missing dependency issues in the MultiQC and bwa wrappers

grenepipe v0.3.0

Notable Changes

• Add bwa aln mapping tool
• Add extra parameters config settings for tools that did not have them yet
• Remove vqsr filtering / GATK VariantRecalibrator
• Add testing setup and test cases for all tools

Bug Fixes

• Fix issue with Picard CollectMultipleMetrics omitting empty files
• Fix bowtie2 conda environment issues due to changed dependency
• Disable incompatibility between bowtie2 and picard
• Disable recalibrate-base-qualities usage wihtout known-variants