v1.3.3

new features:

• a basic module isExome discards covreport if the bed files contains 'Exome' or 'exome' in its name
• bams and crams files are deleted during the process of the workflow, when they're not useful anymore, instead of being cleaned at the very end, in order to save some disk space during analysis
• covreport is optional for panels
• updated unit tests

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