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.dockstore.yml
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.dockstore.yml
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version: 1.2
workflows:
- name: TheiaEuk_Illumina_PE_PHB
subclass: WDL
primaryDescriptorPath: /workflows/theiaeuk/wf_theiaeuk_illumina_pe.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: Cauris_CladeTyper_PHB
subclass: WDL
primaryDescriptorPath: /workflows/theiaeuk/wf_cauris_cladetyper.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: Snippy_Variants_PHB
subclass: WDL
primaryDescriptorPath: /workflows/standalone_modules/wf_snippy_variants.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: Snippy_Tree_PHB
subclass: WDL
primaryDescriptorPath: /workflows/phylogenetics/wf_snippy_tree.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: Nullarbor_PHB
subclass: WDL
primaryDescriptorPath: /workflows/standalone_modules/wf_nullarbor.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: TheiaCoV_ClearLabs_PHB
subclass: WDL
primaryDescriptorPath: /workflows/theiacov/wf_theiacov_clearlabs.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: TheiaCoV_ONT_PHB
subclass: WDL
primaryDescriptorPath: /workflows/theiacov/wf_theiacov_ont.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: TheiaCoV_Illumina_PE_PHB
subclass: WDL
primaryDescriptorPath: /workflows/theiacov/wf_theiacov_illumina_pe.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: TheiaCoV_Illumina_SE_PHB
subclass: WDL
primaryDescriptorPath: /workflows/theiacov/wf_theiacov_illumina_se.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: TheiaCoV_FASTA_PHB
subclass: WDL
primaryDescriptorPath: /workflows/theiacov/wf_theiacov_fasta.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: TheiaCoV_FASTA_Batch_PHB
subclass: WDL
primaryDescriptorPath: /workflows/theiacov/wf_theiacov_fasta_batch.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: Mercury_Prep_N_Batch_PHB
subclass: WDL
primaryDescriptorPath: /workflows/submission/wf_mercury_prep_n_batch.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: Terra_2_NCBI_PHB
subclass: WDL
primaryDescriptorPath: /workflows/submission/wf_terra_2_ncbi.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: Augur_PHB
subclass: WDL
primaryDescriptorPath: /workflows/phylogenetics/wf_augur.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: Augur_Prep_PHB
subclass: WDL
primaryDescriptorPath: /workflows/phylogenetics/wf_augur_prep.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: Pangolin_Update_PHB
subclass: WDL
primaryDescriptorPath: /workflows/theiacov/updates/wf_pangolin_update.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: VADR_Update_PHB
subclass: WDL
primaryDescriptorPath: /workflows/theiacov/updates/wf_vadr_update.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: NCBI_Scrub_SE_PHB
subclass: WDL
primaryDescriptorPath: /workflows/theiacov/updates/wf_ncbi_scrub_se.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: NCBI_Scrub_PE_PHB
subclass: WDL
primaryDescriptorPath: /workflows/theiacov/updates/wf_ncbi_scrub_pe.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: Freyja_FASTQ_PHB
subclass: WDL
primaryDescriptorPath: /workflows/freyja/wf_freyja_fastq.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: Freyja_Plot_PHB
subclass: WDL
primaryDescriptorPath: /workflows/freyja/wf_freyja_plot.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: Freyja_Dashboard_PHB
subclass: WDL
primaryDescriptorPath: /workflows/freyja/wf_freyja_dashboard.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: Freyja_Update_PHB
subclass: WDL
primaryDescriptorPath: /workflows/freyja/wf_freyja_update.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: kSNP3_PHB
subclass: WDL
primaryDescriptorPath: /workflows/phylogenetics/wf_ksnp3.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: MashTree_FASTA_PHB
subclass: WDL
primaryDescriptorPath: /workflows/phylogenetics/wf_mashtree_fasta.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: Core_Gene_SNP_PHB
subclass: WDL
primaryDescriptorPath: /workflows/phylogenetics/wf_core_gene_snp.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: TheiaProk_Illumina_PE_PHB
subclass: WDL
primaryDescriptorPath: /workflows/theiaprok/wf_theiaprok_illumina_pe.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: TheiaProk_Illumina_SE_PHB
subclass: WDL
primaryDescriptorPath: /workflows/theiaprok/wf_theiaprok_illumina_se.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: TheiaProk_FASTA_PHB
subclass: WDL
primaryDescriptorPath: /workflows/theiaprok/wf_theiaprok_fasta.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: TheiaProk_ONT_PHB
subclass: WDL
primaryDescriptorPath: /workflows/theiaprok/wf_theiaprok_ont.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: Gambit_Query_PHB
subclass: WDL
primaryDescriptorPath: /workflows/standalone_modules/wf_gambit_query.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: NCBI-AMRFinderPlus_PHB
subclass: WDL
primaryDescriptorPath: /workflows/standalone_modules/wf_amrfinderplus.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: Kraken2_PE_PHB
subclass: WDL
primaryDescriptorPath: /workflows/standalone_modules/wf_kraken2_pe.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: Kraken2_SE_PHB
subclass: WDL
primaryDescriptorPath: /workflows/standalone_modules/wf_kraken2_se.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: Kraken2_ONT_PHB
subclass: WDL
primaryDescriptorPath: /workflows/standalone_modules/wf_kraken2_ont.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: RASUSA_PHB
subclass: WDL
primaryDescriptorPath: /workflows/standalone_modules/wf_rasusa.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: BaseSpace_Fetch_PHB
subclass: WDL
primaryDescriptorPath: /workflows/utilities/data_import/wf_basespace_fetch.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: SRA_Fetch_PHB
subclass: WDL
primaryDescriptorPath: /workflows/utilities/data_import/wf_sra_fetch.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: Terra_2_BQ_PHB
subclass: WDL
primaryDescriptorPath: /workflows/utilities/data_import/wf_terra_2_bq.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: Concatenate_Column_Content_PHB
subclass: WDL
primaryDescriptorPath: /workflows/utilities/file_handling/wf_concatenate_column.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: Transfer_Column_Content_PHB
subclass: WDL
primaryDescriptorPath: /workflows/utilities/file_handling/wf_transfer_column.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: Zip_Column_Content_PHB
subclass: WDL
primaryDescriptorPath: /workflows/utilities/file_handling/wf_zip_column.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: Lyve_SET_PHB
subclass: WDL
primaryDescriptorPath: /workflows/phylogenetics/wf_lyveset.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: TheiaMeta_Illumina_PE_PHB
subclass: WDL
primaryDescriptorPath: /workflows/theiameta/wf_theiameta_illumina_pe.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: Snippy_Streamline_PHB
subclass: WDL
primaryDescriptorPath: /workflows/phylogenetics/wf_snippy_streamline.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: Assembly_Fetch_PHB
subclass: WDL
primaryDescriptorPath: /workflows/utilities/data_import/wf_assembly_fetch.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: TheiaValidate_PHB
subclass: WDL
primaryDescriptorPath: /workflows/utilities/wf_theiavalidate.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: Samples_to_Ref_Tree_PHB
subclass: WDL
primaryDescriptorPath: /workflows/phylogenetics/wf_nextclade_addToRefTree.wdl
- name: Terra_2_GISAID_PHB
subclass: WDL
primaryDescriptorPath: /workflows/submission/wf_terra_2_gisaid.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: Usher_PHB
subclass: WDL
primaryDescriptorPath: /workflows/phylogenetics/wf_usher.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: CZGenEpi_Prep_PHB
subclass: WDL
primaryDescriptorPath: /workflows/utilities/wf_czgenepi_prep.wdl
testParameterFiles:
- /tests/inputs/empty.json
- name: Rename_FASTQ_PHB
subclass: WDL
primaryDescriptorPath: /workflows/utilities/file_handling/wf_rename_fastq_files.wdl
testParameterFiles:
- /tests/inputs/empty.json