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Add GATK/Picard tasks for generating WGS qc metrics #110

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6 tasks done
mark-welsh opened this issue Sep 12, 2019 · 1 comment
Open
6 tasks done

Add GATK/Picard tasks for generating WGS qc metrics #110

mark-welsh opened this issue Sep 12, 2019 · 1 comment
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mark-welsh commented Sep 12, 2019 •
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For UI issues

  • Tool: Picard
  • Version: 2.19.0

Description

WGS pipelines are long and therefore can have a high degree of variability across runs. Picard has many commands for generating QC metrics and md5s that will help maintain integrity/traceability.

What I Did

add task wrappers for:

  • CalculateReadGroupChecksum
  • CollectMultipleMetrics
  • CollectQualityYieldMetrics
  • CollectVariantCallingMetrics
  • CollectWgsMetrics
  • ValidateSamFile
@mark-welsh mark-welsh self-assigned this Sep 12, 2019
mark-welsh added a commit that referenced this issue Sep 12, 2019
@mark-welsh
[refs #110] Init commit for Picard tasks
574b6a2
mark-welsh added a commit that referenced this issue Sep 13, 2019
@mark-welsh
[refs #110] Adds Picard ValidateSamFile
08c950f
@mark-welsh mark-welsh changed the title Add Picard tasks for generating WGS qc metrics Add GATK/Picard tasks for generating WGS qc metrics Sep 13, 2019
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also going to add GATK ValidateVariants as a part of this

mark-welsh added a commit that referenced this issue Sep 13, 2019
@mark-welsh
[refs #110] Adds GATK ValidateVariants
f20eafe 
this tool is a little weird... it doesn't output any files for WDL to
check as a "success" condition. instead, it either exits with $? == 0 or
it displays and error

to signal success back to the Cromwell engine, I echo "true" if the
preceding GATK command finishes, which is read as a boolean from stdout
mark-welsh added a commit that referenced this issue Sep 13, 2019
@mark-welsh
[refs #110] Adds input_idx_bam everywhere
2b309fa 
and changes previous name to this for cohesion (and no invalids on my
PRs 😃)
mark-welsh added a commit that referenced this issue Sep 13, 2019
@mark-welsh
[refs #110] Removes false statement from param. meta
a514c18
mark-welsh added a commit that referenced this issue Sep 19, 2019
@mark-welsh
[refs #110] Init commit for Picard tasks
43f4b18
mark-welsh added a commit that referenced this issue Sep 19, 2019
@mark-welsh
[refs #110] Adds Picard ValidateSamFile
e25ae06
mark-welsh added a commit that referenced this issue Sep 19, 2019
@mark-welsh
[refs #110] Adds GATK ValidateVariants
a49c80e 
this tool is a little weird... it doesn't output any files for WDL to
check as a "success" condition. instead, it either exits with $? == 0 or
it displays and error

to signal success back to the Cromwell engine, I echo "true" if the
preceding GATK command finishes, which is read as a boolean from stdout
mark-welsh added a commit that referenced this issue Sep 19, 2019
@mark-welsh
[refs #110] Adds input_idx_bam everywhere
133807f 
and changes previous name to this for cohesion (and no invalids on my
PRs 😃)
mark-welsh added a commit that referenced this issue Sep 19, 2019
@mark-welsh
[refs #110] Removes false statement from param. meta
d8b21be
mark-welsh added a commit that referenced this issue Sep 19, 2019
@mark-welsh
[refs #110] ValidateSamFile new userString
fbb48df 
also enabled verbosity by default
mark-welsh added a commit that referenced this issue Sep 19, 2019
@mark-welsh
[refs #110] Change Validation Stringency
8e785c0 
(d3b doesn't have it at all)
mark-welsh added a commit that referenced this issue Sep 20, 2019
@mark-welsh
[refs #110] ValidateSamFile needs continueOnReturnCode
0d87468 
if a BAM fails Validation (i.e. rc file has code 1), we still want to
finish the workflow
mark-welsh added a commit that referenced this issue Sep 20, 2019
@mark-welsh
[refs #110] Fixes bug in WgsMetrics for intervals
f7c6405 
command only takes one interval list, not multiple. it has been changed
to be optional since the interval for WGS is, well, the whole genome...
mark-welsh added a commit that referenced this issue Sep 23, 2019
@mark-welsh
[refs #110] Removes intervals var
e192573
mark-welsh added a commit that referenced this issue Sep 23, 2019
@mark-welsh
[refs #110] Removes intervals from param_meta
5f60d2e
mark-welsh added a commit that referenced this issue Sep 24, 2019
@mark-welsh
[refs #110] Removes "sort_order"; valid parameter
748796a
mark-welsh added a commit that referenced this issue Oct 2, 2019
@mark-welsh
[refs #110] Removes some default MultipleMetrics cmds
3e64287
mark-welsh added a commit that referenced this issue Oct 4, 2019
@mark-welsh
[refs #110] Updates to correct CVC output filenames
70a56a2
mark-welsh added a commit that referenced this issue Nov 8, 2019
@mark-welsh
[refs #110] Doubles CVCM memory
2659b3f 
seeing an error with large BAMs (>100 GB) running out of memory.
hopefully this fixes that issue
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