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.dockstore.yml
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.dockstore.yml
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version: 1.2
workflows:
- name: Dipcall
subclass: WDL
primaryDescriptorPath: /QC/wdl/tasks/dipcall.wdl
- name: BUSCO
subclass: WDL
primaryDescriptorPath: /QC/wdl/tasks/busco.wdl
- name: Quast
subclass: WDL
primaryDescriptorPath: /QC/wdl/tasks/quast.wdl
testParameterFiles:
- /QC/test/s3_quast.json
- name: Meryl
subclass: WDL
primaryDescriptorPath: /QC/wdl/tasks/meryl.wdl
- name: Merqury
subclass: WDL
primaryDescriptorPath: /QC/wdl/tasks/merqury.wdl
- name: Asmgene
subclass: WDL
primaryDescriptorPath: /QC/wdl/tasks/asmgene.wdl
- name: YakAsmStats
subclass: WDL
primaryDescriptorPath: /QC/wdl/tasks/yak.wdl
- name: YakAsmStatsnoQV
subclass: WDL
primaryDescriptorPath: /QC/wdl/tasks/yak_no_qv.wdl
- name: asmChrCompleteness
subclass: WDL
primaryDescriptorPath: /QC/wdl/tasks/asm_chr_completeness.wdl
- name: Mash
subclass: WDL
primaryDescriptorPath: /QC/wdl/tasks/mash.wdl
- name: NTSM
subclass: WDL
primaryDescriptorPath: /data_processing/wdl/tasks/ntsm.wdl
- name: MaskAssembly
subclass: WDL
primaryDescriptorPath: /QC/wdl/tasks/mask_assembly.wdl
- name: renameContigsAddMT
subclass: WDL
primaryDescriptorPath: /assembly/wdl/tasks/renameContigsAddMT.wdl
- name: finalizeGenbankAssembly
subclass: WDL
primaryDescriptorPath: /assembly/wdl/tasks/finalizeGenbankAssembly.wdl
- name: findMitoContigs
subclass: WDL
primaryDescriptorPath: /QC/wdl/tasks/findMitoContigs.wdl
- name: ReadStats
subclass: WDL
primaryDescriptorPath: /data_processing/wdl/tasks/read_stats.wdl
testParameterFiles:
- /QC/test/s3_read_stats.json
- name: FullQC
subclass: WDL
primaryDescriptorPath: /QC/wdl/workflows/full_qc.wdl
- name: StandardQC
subclass: WDL
primaryDescriptorPath: /QC/wdl/workflows/standard_qc.wdl
- name: StandardQCnoQV
subclass: WDL
primaryDescriptorPath: /QC/wdl/workflows/standard_qc_no_qv.wdl
- name: StandardQCnonTrio
subclass: WDL
primaryDescriptorPath: /QC/wdl/workflows/standard_qc_nontrio.wdl
- name: FilterHiFiAdapter
subclass: WDL
primaryDescriptorPath: /assembly/wdl/tasks/filter_hifi_adapter.wdl
- name: ExtractMitoContigs
subclass: WDL
primaryDescriptorPath: /QC/wdl/tasks/extractMitoContigs.wdl
- name: dropFastaContigs
subclass: WDL
primaryDescriptorPath: /QC/wdl/tasks/dropFastaContigs.wdl
- name: writeUnmappedReads
subclass: WDL
primaryDescriptorPath: /QC/wdl/tasks/writeUnmappedReads.wdl
- name: fastqReadCounts
subclass: WDL
primaryDescriptorPath: /data_processing/wdl/tasks/fastqReadCounts.wdl
testParameterFiles:
- /QC/test/s3_fastqReadCounts.json
- name: fastqReadCoverage
subclass: WDL
primaryDescriptorPath: /QC/wdl/tasks/fastqReadCoverage.wdl
- name: TrioHifiasmAssembly
subclass: WDL
primaryDescriptorPath: /assembly/wdl/workflows/trio_hifiasm_assembly.wdl
- name: TrioHifiasmAssemblyYakInput
subclass: WDL
primaryDescriptorPath: /assembly/wdl/workflows/trio_hifiasm_assembly_yak_input.wdl
- name: TrioHifiasmAssemblyYakInputCutadapt
subclass: WDL
primaryDescriptorPath: /assembly/wdl/workflows/trio_hifiasm_assembly_yak_input_cutadapt.wdl
- name: TrioHifiasmAssemblyYakInputCutadaptMultiStep
subclass: WDL
primaryDescriptorPath: /assembly/wdl/workflows/trio_hifiasm_assembly_yak_input_cutadapt_multistep.wdl
- name: TrioHifiasmAssemblyStep3
subclass: WDL
primaryDescriptorPath: /assembly/wdl/tasks/hifiasm_cutadapt_trio_step3.wdl
- name: HiCHifiasmAssemblyStep2
subclass: WDL
primaryDescriptorPath: /assembly/wdl/tasks/hifiasm_cutadapt_hic_step2.wdl
- name: HiCHifiasmAssemblyStep3
subclass: WDL
primaryDescriptorPath: /assembly/wdl/tasks/hifiasm_cutadapt_hic_step3.wdl
- name: TrioVerkkoAssembly
subclass: WDL
primaryDescriptorPath: /assembly/wdl/workflows/trio_verkko_assembly.wdl
- name: TrioVerkkoAssemblyScatter
subclass: WDL
primaryDescriptorPath: /assembly/wdl/workflows/trio_verkko_assembly_scatter.wdl
- name: VerkkoAssemblyScatter
subclass: WDL
primaryDescriptorPath: /assembly/wdl/workflows/verkko_assembly_scatter.wdl
- name: VerkkoCreateUnphasedGFA
subclass: WDL
primaryDescriptorPath: /assembly/wdl/tasks/verkko_create_unphased_gfa.wdl
- name: VerkkoConsensusFromGFAse
subclass: WDL
primaryDescriptorPath: /assembly/wdl/tasks/verkko_consensus_from_gfase.wdl
- name: VerkkoHiCPhasing
subclass: WDL
primaryDescriptorPath: /assembly/wdl/tasks/verkko_hic.wdl
- name: VerkkoExtractPhasedAsms
subclass: WDL
primaryDescriptorPath: /assembly/wdl/tasks/verkko_extract_run_folder.wdl
- name: VerkkoRephaseRukki
subclass: WDL
primaryDescriptorPath: /assembly/wdl/tasks/verkko_rerun_rukki.wdl
- name: YakNoStats
subclass: WDL
primaryDescriptorPath: /assembly/wdl/tasks/yak_no_stats.wdl
- name: YakNoStatsHiFi
subclass: WDL
primaryDescriptorPath: /assembly/wdl/tasks/yak_no_stats_hifi.wdl
- name: PhasedGFAs2Fasta
subclass: WDL
primaryDescriptorPath: /assembly/wdl/tasks/gfatools.wdl
- name: StandardQCHaploid
subclass: WDL
primaryDescriptorPath: /QC/wdl/workflows/standard_qc_haploid.wdl
- name: Primrose
subclass: WDL
primaryDescriptorPath: /data_processing/wdl/tasks/primrose.wdl
- name: Contamination
subclass: WDL
primaryDescriptorPath: /QC/wdl/tasks/contamination.wdl
- name: MinigraphMap
subclass: WDL
primaryDescriptorPath: /QC/wdl/tasks/minigraph.wdl
- name: MisjoinCheck
subclass: WDL
primaryDescriptorPath: /QC/wdl/tasks/misjoinCheck.wdl
- name: snvInDelAssembly
subclass: WDL
primaryDescriptorPath: /QC/wdl/workflows/snv_indel_assembly.wdl
- name: svAssembly
subclass: WDL
primaryDescriptorPath: /QC/wdl/workflows/SV_assembly.wdl
- name: Guppy
subclass: WDL
primaryDescriptorPath: /data_processing/wdl/workflows/scatterGuppy.wdl
- name: BreakIntoContigs
subclass: WDL
primaryDescriptorPath: /assembly/wdl/tasks/break_into_contigs.wdl
- name: LengthFilterFasta
subclass: WDL
primaryDescriptorPath: /assembly/wdl/tasks/len_filter_fasta.wdl
- name: DownSampling
subclass: WDL
primaryDescriptorPath: /assembly/wdl/tasks/down_sampling.wdl
- name: FilterShortReads
subclass: WDL
primaryDescriptorPath: /assembly/wdl/tasks/filter_short_reads.wdl
- name: chopperFilter
subclass: WDL
primaryDescriptorPath: /data_processing/wdl/tasks/chopper.wdl
- name: LiftOff
subclass: WDL
primaryDescriptorPath: /QC/wdl/tasks/liftoff.wdl
- name: ShortQC
subclass: WDL
primaryDescriptorPath: /QC/wdl/workflows/short_qc.wdl
- name: asmComparisonQC
subclass: WDL
primaryDescriptorPath: /QC/wdl/workflows/comparison_qc.wdl
- name: asmComparisonQCdiploid
subclass: WDL
primaryDescriptorPath: /QC/wdl/workflows/comparison_qc_diploid.wdl
- name: s5cmd_download
subclass: WDL
primaryDescriptorPath: /data_processing/wdl/tasks/s5cmd_download.wdl
- name: AssemblyCleanUp
subclass: WDL
primaryDescriptorPath: /assembly/wdl/tasks/assembly_clean_up.wdl
- name: ShortDiploidQC
subclass: WDL
primaryDescriptorPath: /QC/wdl/workflows/short_diploid_qc.wdl
- name: Readsbam4DC
subclass: WDL
primaryDescriptorPath: /data_processing/wdl/tasks/readsbam4dc.wdl
- name: ontSummaryStats
subclass: WDL
primaryDescriptorPath: /data_processing/wdl/tasks/calc_ont_summary_stats.wdl
- name: compleasmRun
subclass: WDL
primaryDescriptorPath: /QC/wdl/tasks/compleasm.wdl
- name: hifiQC
subclass: WDL
primaryDescriptorPath: /data_processing/wdl/workflows/hifi_qc_workflow.wdl
- name: ontQC
subclass: WDL
primaryDescriptorPath: /data_processing/wdl/workflows/ont_qc_workflow.wdl
- name: NucFreq
subclass: WDL
primaryDescriptorPath: /QC/wdl/tasks/nucfreq.wdl
- name: bedToBigBed
subclass: WDL
primaryDescriptorPath: /annotation/wdl/tasks/bed_to_bigbed.wdl
- name: repeatMasker
subclass: WDL
primaryDescriptorPath: /annotation/wdl/workflows/repeat_masker.wdl