sample.wdl: Remove postUmiDedupMarkDuplicates. dockerImages.yml: Update umitools (v1.1.1) image (include samtools for indexing). Replace travis with github CI. renamedVCFs was changed to modifiedVcfs. Add the dockerImages to the output section. Add bwa-mem2 capability
Update command section syntax Minimap2, Talon, TranscriptClean and Centrifuge. Add CCS workflow WDL ...
Replace the bam-to-gvcf and jointgenotyping pipelines with a gatk-variantcalling pipeline. This red...
We simulated five human gut metagenomic samples to assess the taxonomic quantification accuracy of t...
A BioWDL variantcalling pipeline for germline DNA data. Starting with FASTQ files to produce VCF fil...
Update default CPAT version to 3.0.4. Use gffcompare to merge stringtie assembly GTF files, rather t...
Allow using csv table format samplesheet as input format. Update tasks so they pass the correct memo...
Small changes were made to support miniwdl and miniwdl is now the recommended tool to run this pipel...
The bam-to-gvcf and jointgenotyping subworkflows were combined in a single gatk-variantcalling pipel...
Make intervals optional for GATK CombineGVCFs Updated biowdl-input-converter version. GATK CombineGV...
Updated the versions of the installed tools in the image Added metagenomics taxonomic classification...
A BioWDL workflow for preprocessing BAM files for variantcalling. Based on the GATK Best Practices. ...
A BioWDL workflow for preprocessing BAM files for variantcalling. Based on the GATK Best Practices. ...
Add options to disable joint genotyping and allow per sample variant calling. Make sure all importan...
VerifyBamID2 to measure DNA contamination https://github.com/UMCUGenetics/DxNextflowWES/pull/32 Nex...
A BioWDL workflow for preprocessing BAM files for variantcalling. Based on the GATK Best Practices. ...
Update command section syntax Minimap2, Talon, TranscriptClean and Centrifuge. Add CCS workflow WDL ...
Replace the bam-to-gvcf and jointgenotyping pipelines with a gatk-variantcalling pipeline. This red...
We simulated five human gut metagenomic samples to assess the taxonomic quantification accuracy of t...
A BioWDL variantcalling pipeline for germline DNA data. Starting with FASTQ files to produce VCF fil...
Update default CPAT version to 3.0.4. Use gffcompare to merge stringtie assembly GTF files, rather t...
Allow using csv table format samplesheet as input format. Update tasks so they pass the correct memo...
Small changes were made to support miniwdl and miniwdl is now the recommended tool to run this pipel...
The bam-to-gvcf and jointgenotyping subworkflows were combined in a single gatk-variantcalling pipel...
Make intervals optional for GATK CombineGVCFs Updated biowdl-input-converter version. GATK CombineGV...
Updated the versions of the installed tools in the image Added metagenomics taxonomic classification...
A BioWDL workflow for preprocessing BAM files for variantcalling. Based on the GATK Best Practices. ...
A BioWDL workflow for preprocessing BAM files for variantcalling. Based on the GATK Best Practices. ...
Add options to disable joint genotyping and allow per sample variant calling. Make sure all importan...
VerifyBamID2 to measure DNA contamination https://github.com/UMCUGenetics/DxNextflowWES/pull/32 Nex...
A BioWDL workflow for preprocessing BAM files for variantcalling. Based on the GATK Best Practices. ...
Update command section syntax Minimap2, Talon, TranscriptClean and Centrifuge. Add CCS workflow WDL ...
Replace the bam-to-gvcf and jointgenotyping pipelines with a gatk-variantcalling pipeline. This red...
We simulated five human gut metagenomic samples to assess the taxonomic quantification accuracy of t...
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