hastings_rd_wes v0.5.1

Bug Fixes

• fix paths to exomedepth refs (096845d)

hastings_rd_wes v0.5.0

Features

• add config for the old twist panel (5d01cef)
• re-instate male and female exomdepth references (cef44ae)
• remove extra symbols from figures in general stats table (51ade63)

hastings_rd_wes v0.4.0

Features

• update HS metrics in multiqc report (3a12cf8)
• update multiqc and add software versions (2d3f36e)

hastings_rd_wes v0.3.1

Bug Fixes

• handle incomplete trios in samples.tsv (05df9cd)
• point to vep container (63b8917)

hastings_rd_wes v0.3.0

Features

• add peddy results to results folder (4ad2ee1)
• handles cases with more than one trio with the same parents (c3888d0)
• remove crumble rule import (042ab47)
• update cnv_sv and prealigment modules (fe41960)
• update common container (6a62955)
• update hydra version (9c1a7a5)
• update module versions and remove deeptrio (5417b07)
• update spring version (6d4d6d5)

Bug Fixes

• correctly creat the sample order file from the fastq path (ade24a1)
• don't use the same column names (a1a184b)
• report depth from design bed file in multiqc (218fc91)

hastings_rd_wes v0.2.1

Bug Fixes

• add all the peddy files needed for full pedddy multiqc report (edfc961)
• remove extra source to hydra-env (95013f1)
• skip upd analysis for trios that don't have all three members (398bf00)

hastings_rd_wes v0.2.0

Features

• add logging to coverage script (f95c778)
• handle cases in the sample sheet where the sex is unknown (190d0e6)
• remove records with read.ratio = 1 for alissa compatability (8835595)
• Update coverage bed in config.yaml (3d081d3)

Bug Fixes

• add bai, get right column for trio, multiqc order (49f0b07)
• don't print index in the units.tsv file (d38006e)
• handle overlapping genes in create_excel.py (9d34581)
• multiqc: add all mosdepth files to allow running with --notemp (a6a6f0c)
• multiqc: specify all peddy files as input for notemp runs (eb23a63)
• revert coverage script to e81aa1d (770cbd4)
• Update multiqc_config_DNA.yaml (20ad40e)

Documentation

• Create requirements.txt (641c5b8)

hastings_rd_wes v0.1.0

Features

• add automap (92e414a)
• add fix_af (e948efb)
• add rule and script to export exomedepth results for alissa (f3d28ad)
• add rule graph (2a350c1)
• add scripts for sample info extraction and running the pipeline (3df7497)
• add set -euo pipefail to run_hastings.sh (cef3245)
• add slurm drmaa profile (b26156a)
• change to samtools cram file for the results (32c3192)
• extract trio, sex and barcode info from SampleSheet.csv (0c9b87c)
• update config (73f6f07)
• update config (a499cb0)
• update gres resources (bcf380f)
• update modules (db728ed)
• update parabricks ans snv_indels modules (c6f552f)
• update snakefile and common for latest exomdepth_call rule (d60dd90)
• update the reference genome path (510da6d)
• update to latest parabricks module release (ecdb27f)
• update to latest release of compression module (55fb84d)
• use bed file with bcftools view on SNV/Indels vcf (9b9619f)

Bug Fixes

• add bam index files to deeptrio mk input (9ef1d07)
• create_cov_excel: list all inputs to script in rule (8fb9ae6)
• handle overlapping genes by sorting by gene name (c849fe3)
• import json and remove unused function (06d7f04)
• set familyid to sample id for non-trio samples (3b27f8a)
• set familyid to sample id for non-trio samples (a5ba81b)
• Snakefile: add gvcf_records as output (cee3730)