v0.1.0

Release v0.1.0

This release is the first and represents the baseline use case for quilt-nf. The workflows support JAX Genome Technologies Low-Coverage WGS service. Some of the supporting modules are similar to or shared with JAX cs-nf-pipelines in order to match organizational standards where possible.

Workflows:

• make_quilt_reference_data: Uses the mouse reference genome (GRCm39) and Sanger Mouse Genomes Project SNPs to construct IMPUTE2 haplotype files, phased founder genotypes, and genetic maps for any set of strains included in the Sanger SNP set.
• quilt: Processes .fastq files and aligns them to the reference genome, imputes genotypes, and performs haplotype reconstructions required for QTL mapping.

Modules:

• concatenate_reads_PE.nf
• concatenate_reads_SE.nf
• fastqc.nf
• multiqc.nf
• fastp.nf
• clone_filter.nf
• read_group.nf
• bwa_mem.nf
• picard_sortsam.nf
• picard_markduplicates.nf
• picard_collectalignmentsummarymetrics.nf
• picard_collectwgsmetrics.nf
• calc_pileups.nf
• downsample_bam.nf
• create_bamlist.nf
• run_quilt.nf
• quilt_to_qtl2.nf
• genoprobs.nf
• concatenate_genoprobs.nf