v1.2 Expecto Patronum - [05/11/2022]

Added

• Changed minimum time requirements in base.config for process_low, process_medium, process_high to 72.h and process_long to 120.h.
• SNP distance matrix addition as output.
• Updated qc_report.txt to include coverage mean depth and reads mapped.
• Positions masked (N) based on DP & Added functionality to use min_depth (Default 50).
• Change test profile to include min_depth = 2 so it will run to completion.

Fixed

• Bug fix for downsample mismatch.
• Change configuration variable name from vcftools_filter to gatkgenotypes_filter.
• Changed samplesheet creation to accept multiple directories as arguments and to recursively search for sequences.
• Set full vcf consensus file to debug output
• Remove part nf-core branding

Dependencies

Deprecated

TODO

• Update logo

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Issues closed:

• Reference genome inherited at positions with zero read support #45
• Read count for the same sample varies in the qc_report #47
• update configuration file for vcftools_filter clarity #51
• Updating QC_REPORT with mean depth and % mapped reads #53
• #58

What's Changed

• Remove extra tabs in qc_report and replace += on list by @rpetit3 in #46
• bug fix for downsample mismatch by @mciprianoCDC in #54
• Dev qcfiltervar by @mciprianoCDC in #55
• Dev mycosnp samplesheet by @mciprianoCDC in #57
• mask positions based on DP by @rpetit3 in #59
• Dev usedp by @mciprianoCDC in #62
• Dev optionsdebug by @mciprianoCDC in #64
• Changed time requirements in base.config by @jforstedt in #65
• Issue #53: Updating QC report by @cjjossart in #61
• v1.2 by @sateeshperi in #66

New Contributors

• @jforstedt made their first contribution in #65

Full Changelog: v1.1...v1.2