A rule to generate bam files with duplicates removed: rules/qc/remove_duplicates
A rule to generate coverage reports from bams with duplicates removed: rules/qc/calculate_coverage
A rule to copy the report to MinIO: rules/cre/snvreport/minio
An input function to check whether only variant reports should be copied to MinIO, or variant reports, coverage reports, and multiqc report: rules/cre/snvreport/check_qual
A checkpoint that is evaluated by check_qual so that Snakemake knows whether or not to generate coverage reports
A parameter config["run"]["minio"] that specifies base path to MinIO directory. If empty, reports won't be copied anywhere.
Tested on family 2086 (dup percentage >20% in at least one sample) with MinIO path arbitrarily set to /hpf/largeprojects/ccmbio/mcouse/C4R/development/2086. Test run is in /hpf/largeprojects/ccmbio/mcouse/C4R/development/test_coverage_report_2086.
Also tested on family 2638 (dup percentage all below 20%). Test run is in /hpf/largeprojects/ccmbio/mcouse/C4R/development/test_coverage_report_2638.
Noting that I had to make changes to peddy so that the input file (created by function peddy_ped) does not get recreated each time the workflow is evaluated, and to the wrapper so that it does not re-index the input VCF file, which results in all rules downstream being re-run when the checkpoint is evaluated at the minio rule.
After pushing to master and pulling to cre-snakemake-slurm:
revise exome_setup_stager.py to add minio path to config.yaml
copy properly sorted /hpf/largeprojects/ccm_dccforge/dccdipg/Common/annotation/exons/hg19_UCSC_exons_canonical_placeholder.bed to CHEO-RI space
This PR adds the following:
Tested on family 2086 (dup percentage >20% in at least one sample) with MinIO path arbitrarily set to /hpf/largeprojects/ccmbio/mcouse/C4R/development/2086. Test run is in /hpf/largeprojects/ccmbio/mcouse/C4R/development/test_coverage_report_2086.
Also tested on family 2638 (dup percentage all below 20%). Test run is in /hpf/largeprojects/ccmbio/mcouse/C4R/development/test_coverage_report_2638.
Noting that I had to make changes to peddy so that the input file (created by function peddy_ped) does not get recreated each time the workflow is evaluated, and to the wrapper so that it does not re-index the input VCF file, which results in all rules downstream being re-run when the checkpoint is evaluated at the minio rule.
After pushing to master and pulling to cre-snakemake-slurm: