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.dockstore.yml
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version: 1.2
workflows:
- name: align_and_count_multiple_report
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/align_and_count_multiple_report.wdl
- name: align_and_count
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/align_and_count.wdl
- name: align_and_plot
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/align_and_plot.wdl
testParameterFiles:
- /test/input/WDL/test_inputs-align_and_plot-local.json
- name: assemble_denovo
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/assemble_denovo.wdl
testParameterFiles:
- /test/input/WDL/test_inputs-assemble_denovo-local.json
- name: assemble_refbased
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/assemble_refbased.wdl
testParameterFiles:
- /test/input/WDL/test_inputs-assemble_refbased-local.json
- name: augur_export_only
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/augur_export_only.wdl
- name: augur_from_assemblies
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/augur_from_assemblies.wdl
testParameterFiles:
- /test/input/WDL/test_inputs-augur_from_assemblies-local.json
- name: augur_from_beast_mcc
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/augur_from_beast_mcc.wdl
testParameterFiles:
- /test/input/WDL/test_inputs-augur_from_beast_mcc-local.json
- name: augur_from_mltree
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/augur_from_mltree.wdl
- name: augur_from_msa
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/augur_from_msa.wdl
- name: augur_from_msa_with_subsampler
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/augur_from_msa_with_subsampler.wdl
- name: bams_multiqc
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/bams_multiqc.wdl
- name: beast_gpu
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/beast_gpu.wdl
- name: blastoff
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/blastoff.wdl
- name: chunk_blast
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/megablast_chunk.wdl
- name: classify_kaiju
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/classify_kaiju.wdl
- name: classify_kraken2
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/classify_kraken2.wdl
testParameterFiles:
- /test/input/WDL/test_inputs-classify_kraken2-local.json
- name: classify_krakenuniq
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/classify_krakenuniq.wdl
- name: classify_multi
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/classify_multi.wdl
- name: classify_single
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/classify_single.wdl
- name: contigs
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/contigs.wdl
- name: coverage_table
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/coverage_table.wdl
- name: create_enterics_qc_viz
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/create_enterics_qc_viz.wdl
- name: create_enterics_qc_viz_general
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/create_enterics_qc_viz_general.wdl
- name: demux_metag
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/demux_metag.wdl
- name: demux_only
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/demux_only.wdl
- name: demux_deplete
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/demux_deplete.wdl
- name: demux_metadata_only
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/demux_metadata_only.wdl
- name: demux_plus
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/demux_plus.wdl
- name: deplete_only
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/deplete_only.wdl
- name: detect_cross_contamination
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/detect_cross_contamination.wdl
testParameterFiles:
- name: detect_cross_contamination_precalled_vcfs
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/detect_cross_contamination_precalled_vcfs.wdl
- name: diff_genome_sets
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/diff_genome_sets.wdl
- name: downsample
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/downsample.wdl
- name: dump_gcloud_env_info
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/dump_gcloud_env_info.wdl
- name: fastq_to_ubam
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/fastq_to_ubam.wdl
testParameterFiles:
- /test/input/WDL/test_inputs-fastq_to_ubam-local.json
- name: fetch_annotations
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/fetch_annotations.wdl
- name: fetch_sra_to_bam
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/fetch_sra_to_bam.wdl
- name: filter_classified_bam_to_taxa
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/filter_classified_bam_to_taxa.wdl
- name: filter_sequences
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/filter_sequences.wdl
- name: genbank_gather
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/genbank_gather.wdl
- name: genbank_single
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/genbank_single.wdl
testParameterFiles:
- /test/input/WDL/test_inputs-genbank_single-local.json
- name: isnvs_merge_to_vcf
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/isnvs_merge_to_vcf.wdl
- name: isnvs_lofreq
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/isnvs_lofreq.wdl
- name: isnvs_one_sample
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/isnvs_one_sample.wdl
- name: kraken2_build
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/kraken2_build.wdl
- name: mafft_and_snp
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/mafft_and_snp.wdl
- name: mafft_and_snp_annotated
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/mafft_and_snp_annotated.wdl
- name: mafft_and_trim
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/mafft_and_trim.wdl
- name: mafft
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/mafft.wdl
- name: merge_bams
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/merge_bams.wdl
- name: merge_metagenomics
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/merge_metagenomics.wdl
- name: merge_tar_chunks
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/merge_tar_chunks.wdl
- name: merge_vcfs_and_annotate
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/merge_vcfs_and_annotate.wdl
- name: merge_vcfs
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/merge_vcfs.wdl
- name: metagenomic_denovo
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/metagenomic_denovo.wdl
- name: multiqc_only
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/multiqc_only.wdl
- name: nextclade_single
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/nextclade_single.wdl
- name: populate_library_and_sample_tables_from_flowcell
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/populate_library_and_sample_tables_from_flowcell.wdl
- name: reconstruct_from_alignments
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/reconstruct_from_alignments.wdl
- name: sarscov2_batch_relineage
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_batch_relineage.wdl
- name: sarscov2_biosample_load
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_biosample_load.wdl
- name: sarscov2_data_release
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_data_release.wdl
- name: sarscov2_genbank
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_genbank.wdl
- name: sarscov2_genbank_ingest
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_genbank_ingest.wdl
- name: sarscov2_illumina_full
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_illumina_full.wdl
- name: sarscov2_lineages
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_lineages.wdl
testParameterFiles:
- /test/input/WDL/test_inputs-sarscov2_lineages-local.json
- name: calc_bam_read_depths
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/calc_bam_read_depths.wdl
- name: sarscov2_gisaid_ingest
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_gisaid_ingest.wdl
- name: sarscov2_nextclade_multi
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_nextclade_multi.wdl
- name: sarscov2_nextstrain
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_nextstrain.wdl
- name: sarscov2_nextstrain_aligned_input
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_nextstrain_aligned_input.wdl
- name: sarscov2_sequencing_reports
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_sequencing_reports.wdl
- name: sarscov2_sra_to_genbank
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_sra_to_genbank.wdl
- name: scaffold_and_refine
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/scaffold_and_refine.wdl
- name: scaffold_and_refine_multitaxa
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/scaffold_and_refine_multitaxa.wdl
- name: subsample_by_casecounts
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/subsample_by_casecounts.wdl
- name: subsample_by_metadata
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/subsample_by_metadata.wdl
- name: subsample_by_metadata_with_focal
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/subsample_by_metadata_with_focal.wdl
- name: taxid_to_nextclade
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/taxid_to_nextclade.wdl
- name: terra_table_to_tsv
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/terra_table_to_tsv.wdl
- name: terra_tsv_to_table
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/terra_tsv_to_table.wdl
- name: terra_update_assemblies
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/terra_update_assemblies.wdl
- name: trimal
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/trimal.wdl
- name: classify_qiime2_multi
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/classify_qiime2_multi.wdl
- name: qiime_import_bam
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/bam_to_qiime.wdl
- name: unpack_archive_to_bucket
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/unpack_archive_to_bucket.wdl