Error: "TMP_DIR is not a recognized option" from CreateRecalibrationTable

[alneberg]

Describe the bug
I just saw this error:
A USER ERROR has occurred: TMP_DIR is not a recognized option
when running CreateRecalibrationTable.

I'm guessing it could be due to the recent update of GATK, but the tests on travis were fine. Is it not using the most recent version of the docker image?

To Reproduce
Steps to reproduce the behavior:

nextflow run germlineVC.nf -profile awsbatch --awsqueue Sarek_pricing_benchmark_10 --awsqueue_tiny Sarek_pricing_benchmark_10_tiny -work-dir s3://sarek-work-benchmark/work-tiny_2018_12_13 --outDir s3://sarek-result-benchmark
/results_tiny_20181213 --verbose -resume --local-report-dir Reports_tiny --sample s3://sarek-result-benchmark/results_tiny_20181213/Preprocessing/Recalibrated/recalibrated.tsv --genome smallGRCh37 --genome_base s3://sarek-references/small
/ --tools HaplotypeCaller,Manta,Strelka

ERROR ~ Error executing process > 'CreateRecalibrationTable (1234-1234N)'                                                                                                                                                           [640/1960]

Caused by:
  Process `CreateRecalibrationTable (1234-1234N)` terminated with an error exit status (1)

Command executed:

  gatk --java-options -Xmx60g   BaseRecalibrator   --input 1234N_0.md.bam   --output 1234N.recal.table  --TMP_DIR /tmp   -R human_g1k_v37_decoy.small.fasta   -L small.intervals   --known-sites dbsnp_138.b37.small.vcf   --known-sites 1000G
_phase1.indels.b37.small.vcf --known-sites Mills_and_1000G_gold_standard.indels.b37.small.vcf   --verbosity INFO

Command exit status:
  1

Command output:
  (empty)

Command error:
  --maximum-mapping-quality:Integer
                                Maximum mapping quality to keep (inclusive)  Default value: null.

  --minimum-mapping-quality:Integer
                                Minimum mapping quality to keep (inclusive)  Default value: 10.

  Valid only if "OverclippedReadFilter" is specified:
  --dont-require-soft-clips-both-ends:Boolean
                                Allow a read to be filtered out based on having only 1 soft-clipped block. By default,
                                both ends must have a soft-clipped block, setting this flag requires only 1 soft-clipped
                                block  Default value: false. Possible values: {true, false}

  --filter-too-short:Integer    Minimum number of aligned bases  Default value: 30.

  Valid only if "PlatformReadFilter" is specified:
  --platform-filter-name:String Platform attribute (PL) to match  This argument must be specified at least once. Required.

  Valid only if "PlatformUnitReadFilter" is specified:
  --black-listed-lanes:String   Platform unit (PU) to filter out  This argument must be specified at least once. Required.

  Valid only if "ReadGroupBlackListReadFilter" is specified:
  --read-group-black-list:StringThe name of the read group to filter out  This argument must be specified at least once.
                                Required.

  Valid only if "ReadGroupReadFilter" is specified:
  --keep-read-group:String      The name of the read group to keep  Required.

  Valid only if "ReadLengthReadFilter" is specified:
  --max-read-length:Integer     Keep only reads with length at most equal to the specified value  Required.

  --min-read-length:Integer     Keep only reads with length at least equal to the specified value  Default value: 1.

  Valid only if "ReadNameReadFilter" is specified:
  --read-name:String            Keep only reads with this read name  Required.

  Valid only if "ReadStrandFilter" is specified:
  --keep-reverse-strand-only:Boolean
                                Keep only reads on the reverse strand  Required. Possible values: {true, false}

  Valid only if "SampleReadFilter" is specified:
  --sample,-sample:String       The name of the sample(s) to keep, filtering out all others  This argument must be
                                specified at least once. Required.



  ***********************************************************************

  A USER ERROR has occurred: TMP_DIR is not a recognized option

  ***********************************************************************
  Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.

Work dir:
  s3://sarek-work-benchmark/work-tiny_2018_12_13/56/3f46bbb097cf8644bbf0f0d14423fc

Tip: when you have fixed the problem you can continue the execution appending to the nextflow command line the option `-resume`

 -- Check '.nextflow.log' file for details
N E X T F L O W  ~  version 18.10.1 5003
Sarek - Workflow For Somatic And Germline Variations ~ 2.2.1 - 32e8613c3b

[maxulysse]

it's now --tmp-dir:
https://software.broadinstitute.org/gatk/documentation/tooldocs/4.0.9.0/org_broadinstitute_hellbender_tools_walkers_bqsr_BaseRecalibrator.php#--tmp-dir