filter_vcf_depth.cwl problems handling DNPs?

Hey Guys,

I'm seeing the following error for a somatic_wgs run:

2022-11-20 11:58:36,779 cromwell-system-akka.dispatchers.engine-dispatcher-5918 INFO  - WorkflowManagerActor Workflow e1ad4b27-9f38-403d-adc6-a5ddd6112f9a failed (during ExecutingWorkflowState): Job filter_vcf_depth:NA:1 e
xited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
Check the content of stderr for potential additional information: /storage1/fs1/christophermaher/Active/maherlab/tmp/1360_PA_A/cwlruns/cromwell-executions/somatic_wgs.cwl/e1ad4b27-9f38-403d-adc6-a5ddd6112f9a/call-detect_va
riants/detect_variants_wgs.cwl/c5e1d716-8028-4fb4-b2e8-9c3ec6b8b7cc/call-filter_vcf/filter_vcf.cwl/bd37d80f-cd19-4717-845a-8b7df39e9378/call-filter_vcf_depth/execution/stderr.
 [First 300 bytes]:Traceback (most recent call last):
  File "/usr/bin/depth_filter.py", line 105, in <module>
    main()
  File "/usr/bin/depth_filter.py", line 93, in main
    elif(depth < args.minimum_depth):
TypeError: '<' not supported between instances of 'NoneType' and 'int'
Traceback (most recent call last):

2022-11-20 11:58:36,821 cromwell-system-akka.dispatchers.engine-dispatcher-5918 INFO  - WorkflowManagerActor WorkflowActor-e1ad4b27-9f38-403d-adc6-a5ddd6112f9a is in a terminal state: WorkflowFailedState

Execution appeared to stop at this variant

chr2    160016665       .       AA      TT      .       PASS    AC=1;AF=0.25;AN=4;AS_FilterStatus=SITE;AS_SB_TABLE=158%2C166|2%2C1;DP=338;ECNT=1;GERMQ=93;MBQ=20,20;MFRL=198,118;MMQ=60,60;MPOS=43;NALOD=2.0;NLOD=29.19;POPAF=6.0;TLOD=5.74;set=mutect;CSQ=TT|missense_variant|MODERATE|PLA2R1|ENSG00000153246|Transcript|ENST00000283243.12|protein_coding|9/30||ENST00000283243.12:c.1499_1500inv|ENSP00000283243.7:p.Ile500Lys|1706-1707|1499-1500|500|I/K|aTT/aAA|||-1||1|substitution|HGNC|HGNC:9042|YES||1|P3|CCDS33309.1|ENSP00000283243|Q13018||UPI00001AEA9D|||deleterious(0)|possibly_damaging(0.851)|Gene3D:3.10.100.10&Pfam_domain:PF00059&PROSITE_profiles:PS50041&hmmpanther:PTHR22803&hmmpanther:PTHR22803:SF74&SMART_domains:SM00034&Superfamily_domains:SSF56436&Conserved_Domains:cd00037|||||||||||||||||||||||||||||||||MLLSPSLLLLLLLGAPRGCAEGVAAALTPERLLEWQDKGIFVIQSESLKKCIQAGKSVLTLENCKQANKHMLWKWVSNHGLFNIGGSGCLGLNFSAPEQPLSLYECDSTLVSLRWRCNRKMITGPLQYSVQVAHDNTVVASRKYIHKWISYGSGGGDICEYLHKDLHTIKGNTHGMPCMFPFQYNHQWHHECTREGREDDLLWCATTSRYERDEKWGFCPDPTSAEVGCDTIWEKDLNSHICYQFNLLSSLSWSEAHSSCQMQGGTLLSITDETEENFIREHMSSKTVEVWMGLNQLDEHAGWQWSDGTPLNYLNWSPEVNFEPFVEDHCGTFSSFMPSAWRSRDCESTLPYICKKYLNHIDHEIVEKDAWKYYATHCEPGWNPYNRNCYKLQKEEKTWHEALRSCQADNSALIDITSLAEVEFLVTLLGDENASETWIGLSSNKIPVSFEWSNDSSVIFTNWHTLEPHIFPNRSQLCVSAEQSEGHWKVKNCEERLFYICKKAGHVLSDAESGCQEGWERHGGFCYKIDTVLRSFDQASSGYYCPPALVTITNRFEQAFITSLISSVVKMKDSYFWIALQDQNDTGEYTWKPVGQKPEPVQYTHWNTHQPRYSGGCVAMRGRHPLGRWEVKHCRHFKAMSLCKQPVENQEKAEYEERWPFHPCYLDWESEPGLASCFKVFHSEKVLMKRTWREAEAFCEEFGAHLASFAHIEEENFVNELLHSKFNWTEERQFWIGFNKRNPLNAGSWEWSDRTPVVSSFLDNTYFGEDARNCAVYKANKTLLPLHCGSKREWICKIPRDVKPKIPFWYQYDVPWLFYQDAEYLFHTFASEWLNFEFVCSWLHSDLLTIHSAHEQEFIHSKIKALSKYGASWWIGLQEERANDEFRWRDGTPVIYQNWDTGRERTVNNQSQRCGFISSITGLWGSEECSVSMPSICKRKKVWLIEKKKDTPKQHGTCPKGWLYFNYKCLLLNIPKDPSSWKNWTHAQHFCAEEGGTLVAIESEVEQAFITMNLFGQTTSVWIGLQNDDYETWLNGKPVVYSNWSPFDIINIPSHNTTEVQKHIPLCALLSSNPNFHFTGKWYFEDCGKEGYGFVCEKMQDTSGHGVNTSDMYPMPNTLEYGNRTYKIINANMTWYAAIKTCLMHKAQLVSITDQYHQSFLTVVLNRLGYAHWIGLFTTDNGLNFDWSDGTKSSFTFWKDEESSLLGDCVFADSNGRWHSTACESFLQGAICHVPPETRQSEHPELCSETSIPWIKFKSNCYSFSTVLDSMSFEAAHEFCKKEGSNLLTIKDEAENAFLLEELFAFGSSVQMVWLNAQFDGNNETIKWFDGTPTDQSNWGIRKPDTDYFKPHHCVALRIPEGLWQLSPCQEKKGFICKMEADIHTAEALPEKGPSHSIIPLAVVLTLIVIVAICTLSFCIYKHNGGFFRRLAGFRNPYYPATNFSTVYLEENILISDLEKSDQ||||||||||,TT|missense_variant|MODERATE|PLA2R1|ENSG00000153246|Transcript|ENST00000392771.1|protein_coding|9/27||ENST00000392771.1:c.1499_1500inv|ENSP00000376524.1:p.Ile500Lys|1706-1707|1499-1500|500|I/K|aTT/aAA|||-1|||substitution|HGNC|HGNC:9042|||1|A2|CCDS42767.1|ENSP00000376524|Q13018||UPI0000208F9D|||deleterious(0)|possibly_damaging(0.587)|Gene3D:3.10.100.10&Pfam_domain:PF00059&PROSITE_profiles:PS50041&hmmpanther:PTHR22803&hmmpanther:PTHR22803:SF74&SMART_domains:SM00034&Superfamily_domains:SSF56436&Conserved_Domains:cd00037|||||||||||||||||||||||||||||||||MLLSPSLLLLLLLGAPRGCAEGVAAALTPERLLEWQDKGIFVIQSESLKKCIQAGKSVLTLENCKQANKHMLWKWVSNHGLFNIGGSGCLGLNFSAPEQPLSLYECDSTLVSLRWRCNRKMITGPLQYSVQVAHDNTVVASRKYIHKWISYGSGGGDICEYLHKDLHTIKGNTHGMPCMFPFQYNHQWHHECTREGREDDLLWCATTSRYERDEKWGFCPDPTSAEVGCDTIWEKDLNSHICYQFNLLSSLSWSEAHSSCQMQGGTLLSITDETEENFIREHMSSKTVEVWMGLNQLDEHAGWQWSDGTPLNYLNWSPEVNFEPFVEDHCGTFSSFMPSAWRSRDCESTLPYICKKYLNHIDHEIVEKDAWKYYATHCEPGWNPYNRNCYKLQKEEKTWHEALRSCQADNSALIDITSLAEVEFLVTLLGDENASETWIGLSSNKIPVSFEWSNDSSVIFTNWHTLEPHIFPNRSQLCVSAEQSEGHWKVKNCEERLFYICKKAGHVLSDAESGCQEGWERHGGFCYKIDTVLRSFDQASSGYYCPPALVTITNRFEQAFITSLISSVVKMKDSYFWIALQDQNDTGEYTWKPVGQKPEPVQYTHWNTHQPRYSGGCVAMRGRHPLGRWEVKHCRHFKAMSLCKQPVENQEKAEYEERWPFHPCYLDWESEPGLASCFKVFHSEKVLMKRTWREAEAFCEEFGAHLASFAHIEEENFVNELLHSKFNWTEERQFWIGFNKRNPLNAGSWEWSDRTPVVSSFLDNTYFGEDARNCAVYKANKTLLPLHCGSKREWICKIPRDVKPKIPFWYQYDVPWLFYQDAEYLFHTFASEWLNFEFVCSWLHSDLLTIHSAHEQEFIHSKIKALSKYGASWWIGLQEERANDEFRWRDGTPVIYQNWDTGRERTVNNQSQRCGFISSITGLWGSEECSVSMPSICKRKKVWLIEKKKDTPKQHGTCPKGWLYFNYKCLLLNIPKDPSSWKNWTHAQHFCAEEGGTLVAIESEVEQAFITMNLFGQTTSVWIGLQNDDYETWLNGKPVVYSNWSPFDIINIPSHNTTEVQKHIPLCALLSSNPNFHFTGKWYFEDCGKEGYGFVCEKMQDTSGHGVNTSDMYPMPNTLEYGNRTYKIINANMTWYAAIKTCLMHKAQLVSITDQYHQSFLTVVLNRLGYAHWIGLFTTDNGLNFDWSDGTKSSFTFWKDEESSLLGDCVFADSNGRWHSTACESFLQGAICHVPPETRQSEHPELCSETSIPWIKFKSNCYSFSTVLDSMSFEAAHEFCKKEGSNLLTIKDEAENAFLLEELFAFGSSVQMVWLNAQFDGNSK|||||||||| GT:AD:AF:DP:F1R2:F2R1:FAD:SB:MQ0:MQ0FRAC
        0/1:187,3:0.029:190:74,2:54,0:133,3:92,95,2,1:0:0.0     0/0:137,0:0.009932:137:50,0:38,0:97,0:66,71,0,0:.:.     ./.:.:.:.:.:.:.:.:.:.

I see the Depth field does have a depth with an integer, so i'm a bit confused why execution would stop here, do you guys see something i'm not?

tagging @chrisamiller and @johnegarza

genome / analysis-workflows

filter_vcf_depth.cwl problems handling DNPs? #1081