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Fix importFile documentation

Status: Open.

#480 In BD2KGenomics/toil-scripts;

· cket opened on Feb 18, 2017

Pass job to germline docker call fuctions

in progress

Status: Open.

#478 In BD2KGenomics/toil-scripts;

· jpfeil opened on Nov 24, 2016

Fix ADAM/GATK pipeline input errors

Status: Open.

#471 In BD2KGenomics/toil-scripts;

· jpfeil opened on Oct 12, 2016

GATK Pipeline Validation Testing

Status: Open.

#470 In BD2KGenomics/toil-scripts;

· alex-hancock opened on Oct 11, 2016

Make sure stdout and stderr from tools are not suppressed in worker log

Status: Open.

#466 In BD2KGenomics/toil-scripts;

· hannes-ucsc opened on Sep 17, 2016

Request: Accept cram input to toil-exome

enhancement

Status: Open.

#444 In BD2KGenomics/toil-scripts;

· Jeltje opened on Sep 8, 2016

Wrap ADAM pipeline calls in logged timers

spark/adam

Status: Open.

#435 In BD2KGenomics/toil-scripts;

· fnothaft opened on Sep 6, 2016

change STAR outSAMunmapped argument

Status: Open.

#433 In BD2KGenomics/toil-scripts;

· hbeale opened on Sep 6, 2016

S3 tests should be skipped if bucket can't be accessed

bug

Status: Open.

#429 In BD2KGenomics/toil-scripts;

· fnothaft opened on Aug 31, 2016

Eliminate config options for approximate input file size

enhancement

Status: Open.

#427 In BD2KGenomics/toil-scripts;

· hannes-ucsc opened on Aug 24, 2016

Support germline joint genotyping and hard filtering

Status: Open.

#426 In BD2KGenomics/toil-scripts;

· jpfeil opened on Aug 24, 2016

Refactor germline shared files download

Status: Open.

#425 In BD2KGenomics/toil-scripts;

· jpfeil opened on Aug 24, 2016