vardict not giving variants

[ionox0]

most likely this was introduced since 1.3.26

possible culprits are:

  EnvVarRequirement:
    envDef:
      JAVA_HOME: /dmp/resources/prod/tools/system/java/jdk1.8.0_121

and

self.__ENV_VARS.append("JAVA_HOME")

or something to do with ShellCommandRequirement
b/c this works

/opt/common/CentOS_6-dev/vardict/v1.5.1/bin/VarDict \                                                                                                    ░▒▓ ✔ | miniconda3 Py | with accessbot at juno | at 16:19:09
-E \
3 \
-G \
/juno/work/access/production/resources/reference/versions/hg19/Homo_sapiens_assembly19.fasta \
-N \
C-2AVE7W-L003-d \
-c \
1 \
-b \
'/juno/work/access/production/runs/Project_10619_B/bam_qc/Project_10619_B_1.3.26/10619_B_group_2-1.3.26/C-2AVE7W-L003-d/C-2AVE7W-L003-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam|/work/access/production/resources/msk-access/current/novaseq_unmatched_normal_plasma_duplex_bams_dmp/current/DONOR22-TP_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam' \
-g \
4 \
-f \
0.0005 \
-S \
2 \
-r \
1 \
/juno/work/access/production/resources/msk-access/v1.0/regions_of_interest/versions/v1.0/MSK-ACCESS-v1_0panelA_canonicaltargets_500buffer.bed \
| \
/opt/common/CentOS_6-dev/vardict/v1.5.1/vardict_328e00a/testsomatic.R \
| \
/opt/common/CentOS_6-dev/vardict/v1.5.1/vardict_328e00a/var2vcf_paired.pl \
-A \
-N \
'C-2AVE7W-L003-d|DONOR22-TP' \
-f \
0.0005 > C-2AVE7W-L003-d.DONOR22-TP.vardict.vcf

but this doesn't

/bin/sh -c '/opt/common/CentOS_6-dev/vardict/v1.5.1/bin/VarDict' '-E' '3' '-G' '/juno/work/access/production/resources/reference/versions/hg19/Homo_sapiens_assembly19.fasta' '-N' 'C-2AVE7W-L003-d' '-c' '1' '-b' '/juno/work/access/production/runs/Project_10619_B/bam_qc/Project_10619_B_1.3.26/10619_B_group_2-1.3.26/C-2AVE7W-L003-d/C-2AVE7W-L003-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam|/work/access/production/resources/msk-access/current/novaseq_unmatched_normal_plasma_duplex_bams_dmp/current/DONOR22-TP_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam' '-g' '4' '-f' '0.0005' '-S' '2' '-r' '1' '/juno/work/access/production/resources/msk-access/v1.0/regions_of_interest/versions/v1.0/MSK-ACCESS-v1_0panelA_canonicaltargets_500buffer.bed' | '/opt/common/CentOS_6-dev/vardict/v1.5.1/vardict_328e00a/testsomatic.R' | '/opt/common/CentOS_6-dev/vardict/v1.5.1/vardict_328e00a/var2vcf_paired.pl' '-A' '-N' 'C-2AVE7W-L003-d|DONOR22-TP' '-f' '0.0005' > 'C-2AVE7W-L003-d.DONOR22-TP.vardict.vcf'