Publication date
February 2022
DOIAbstract
Changes Amend documentation for non optional --reference Add tag with sample name to fastp processes Output BAM index created with samtools inde
Changes Amend documentation for non optional --reference Add tag with sample name to fastp processes Output BAM index created with samtools inde
Changes Bugfix on the sort before MarkDuplicates using default temp folder which eventually lead to...
Bugfix on swapped tumor and normal BAMs in the nextflow workflow. The Python package version remains...
Non functional changes Migrate workflow to DSL 2 Make conda dependencies more granular Improve test
Changes: Add support for single samples using --input_fastq1 and --input_fastq
Changes: Add an optional step to get metrics from the BAM file using Picard's CollectMultipleMetric...
Non functional changes Migrate workflow to DSL 2 Automated tests on GitHub Make conda dependencies ...
Changes Add an initial sort step to avoid GATK strange behaviour with unsorted BAMs Record software...
Changes: add support for a single input BAM file fix realignment step when no known indels are p...
Changes Support for single sample through CLI parameters --input_name, --input_tumor_bam and --inpu...
Changes: Number of required parametrised on --cpus, default 8 Memory required parametrised on --...
Changes Added an initial step of read trimming with FASTP. This also provides a QC report in HTML a...
Changes Add support for STAR for RNA-seq alignment Record software versions in the samples outpu
Changes Add optional step SplitNCigarReads to support RNA data Change Picard's MarkDuplicates by sa...
Release equivalent to v0.3.0, this one should come out with a DOI for referencing this software
Changes Upgraded GATK version to 4.2.5.0 (see release notes https://github.com/broadinstitute/gatk/...
Changes Bugfix on the sort before MarkDuplicates using default temp folder which eventually lead to...
Bugfix on swapped tumor and normal BAMs in the nextflow workflow. The Python package version remains...
Non functional changes Migrate workflow to DSL 2 Make conda dependencies more granular Improve test
Changes: Add support for single samples using --input_fastq1 and --input_fastq
Changes: Add an optional step to get metrics from the BAM file using Picard's CollectMultipleMetric...
Non functional changes Migrate workflow to DSL 2 Automated tests on GitHub Make conda dependencies ...
Changes Add an initial sort step to avoid GATK strange behaviour with unsorted BAMs Record software...
Changes: add support for a single input BAM file fix realignment step when no known indels are p...
Changes Support for single sample through CLI parameters --input_name, --input_tumor_bam and --inpu...
Changes: Number of required parametrised on --cpus, default 8 Memory required parametrised on --...
Changes Added an initial step of read trimming with FASTP. This also provides a QC report in HTML a...
Changes Add support for STAR for RNA-seq alignment Record software versions in the samples outpu
Changes Add optional step SplitNCigarReads to support RNA data Change Picard's MarkDuplicates by sa...
Release equivalent to v0.3.0, this one should come out with a DOI for referencing this software
Changes Upgraded GATK version to 4.2.5.0 (see release notes https://github.com/broadinstitute/gatk/...
Changes Bugfix on the sort before MarkDuplicates using default temp folder which eventually lead to...
Bugfix on swapped tumor and normal BAMs in the nextflow workflow. The Python package version remains...
Non functional changes Migrate workflow to DSL 2 Make conda dependencies more granular Improve test
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