Changes Added an initial step of read trimming with FASTP. This also provides a QC report in HTML and JSON format. To skip read trimming use --skip_trimming Automated tests migrated to Github Pipeline migrated to DSL 2 The definition of the conda dependencies is now granular at the process leve
Changes: Add an optional step to get metrics from the BAM file using Picard's CollectMultipleMetric...
Changes Add optional step SplitNCigarReads to support RNA data Change Picard's MarkDuplicates by sa...
Changes Bugfix on the sort before MarkDuplicates using default temp folder which eventually lead to...
Major changes Add read trimming with fastp Output QC results in JSON format Integrate 4 variant...
Changes Amend documentation for non optional --reference Add tag with sample name to fastp process...
Non functional changes Migrate workflow to DSL 2 Automated tests on GitHub Make conda dependencies ...
Changes: Add support for single samples using --input_fastq1 and --input_fastq
Non functional changes Migrate workflow to DSL 2 Make conda dependencies more granular Improve test
Major changes: Add coverage analysis for FASTQ pipeline Add Pfam domain annotations in the outpu...
Changes Upgraded GATK version to 4.2.5.0 (see release notes https://github.com/broadinstitute/gatk/...
Changes: Memory and CPUs are now parametrised more granularily Analysis intervals are now optional ...
Major changes Support DNA assemblies in FASTA format as input instead of raw reads. Variant calli...
Changes Adds an optional step to trim primers when a bed with primer regions is provided with --pri...
We have removed FASTQC and Cutadapt, and replaced them with FastP, which trims and assesses quality ...
Changes: Number of required parametrised on --cpus, default 8 Memory required parametrised on --...
Changes: Add an optional step to get metrics from the BAM file using Picard's CollectMultipleMetric...
Changes Add optional step SplitNCigarReads to support RNA data Change Picard's MarkDuplicates by sa...
Changes Bugfix on the sort before MarkDuplicates using default temp folder which eventually lead to...
Major changes Add read trimming with fastp Output QC results in JSON format Integrate 4 variant...
Changes Amend documentation for non optional --reference Add tag with sample name to fastp process...
Non functional changes Migrate workflow to DSL 2 Automated tests on GitHub Make conda dependencies ...
Changes: Add support for single samples using --input_fastq1 and --input_fastq
Non functional changes Migrate workflow to DSL 2 Make conda dependencies more granular Improve test
Major changes: Add coverage analysis for FASTQ pipeline Add Pfam domain annotations in the outpu...
Changes Upgraded GATK version to 4.2.5.0 (see release notes https://github.com/broadinstitute/gatk/...
Changes: Memory and CPUs are now parametrised more granularily Analysis intervals are now optional ...
Major changes Support DNA assemblies in FASTA format as input instead of raw reads. Variant calli...
Changes Adds an optional step to trim primers when a bed with primer regions is provided with --pri...
We have removed FASTQC and Cutadapt, and replaced them with FastP, which trims and assesses quality ...
Changes: Number of required parametrised on --cpus, default 8 Memory required parametrised on --...
Changes: Add an optional step to get metrics from the BAM file using Picard's CollectMultipleMetric...
Changes Add optional step SplitNCigarReads to support RNA data Change Picard's MarkDuplicates by sa...
Changes Bugfix on the sort before MarkDuplicates using default temp folder which eventually lead to...
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