v1.3.2

Added a module to perform covreport to panelCapture.wdl

v1.3.0

This version adds several features:

• the new script metaAutoDLML.sh allows the parallel treatment of the samples (they were treated sequentially until now), with a huge decrease of the treatment time (-30 to -80% depending on the panel size). This script is coupled with a new workflow file (metaPanelcapture.wdl) which uses the classical panelCapture.wdl as subworflow.
• water samples are excluded base on fastq size (< 2Ko)
• new file generated to track SNPs from a predefined list
• added possibility to add caseAB and caseDepth for achab files

Main limitation: all samples must be analysed with the same genome version (but ROI files can still be mixed up).

Dev and validation of metaPanelcapture, water sample management and the SNP feature: @tetedange13
Dev and validation of the achab options: @JC-Delmas

fixed ghost executions errors

• bug fix: if anything a task fails, an error is thrown up
• added new tests

v1.2.2

bug fix: a module (samtools sort) had not been upgraded to WDL1.0, causing alignment post processing to be basically ignored.

v1.2.1

• modified computeCoverage module to consider 5-columns bed files (and others)
• fixed computePoorCoverage module with WDL 1.0 syntax
• fixed variable reported by autoDLML when the json template is not found

v1.2

• added HC option --disable-spanning-event-genotyping, thanks @Char-Al
• deparallelized GATK ApplyBQSR and LeftAlignIndels (see discussion here), thanks @tetedange13
• added a workflow for amplicon analysis (warning does not consider per-amplicon analysis, to be used with caution)
• each module now uses conda
• code upgraded to WDL 1.0

v1.1.1

• several minor additions:
  • HC parameter '--max-mnp-distance' set to 2 by default
  • toolVersion bug fix when running in debug mode

v1.1

Improvements in panelCapture Workflow:

• Includes DeepVariant as a second variant caller
• Outputs Crumbled CRAM alignment files

v1.0

Initial release of mobiDL with 2 workflows:
-panelCapture for secondary analysis of NGS gene panel experiments
-captainAchab for tertiary analysis