4.28. demux_metadata_only¶

Picard-based demultiplexing and basecalling from a tarball of a raw BCL directory, followed by QC metrics, depletion, and SRA submission prep.

4.28.1. Inputs¶

demux_metadata_only.biosample_map_tsvs
Array[File] — Default: None
???

demux_metadata_only.cleaned_reads_unaligned_bams
Array[File] — Default: None
???

demux_metadata_only.meta_by_filename_json
File — Default: None
???

demux_metadata_only.raw_reads_unaligned_bams
Array[File] — Default: None
???

demux_metadata_only.run_info
Map[String,String] — Default: None
???

demux_metadata_only.samplesheets
Array[File]+ — Default: None
???

demux_metadata_only.sra_title
String — Default: None
???

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demux_metadata_only.biosample_map_tsv_join.machine_mem_gb
Int — Default: 7
???

demux_metadata_only.biosample_map_tsv_join.prefer_first
Boolean — Default: true
???

demux_metadata_only.biosample_to_table.docker
String — Default: "python:slim"
???

demux_metadata_only.biosample_to_table.sample_table_name
String — Default: "sample"
???

demux_metadata_only.check_terra_env.docker
String — Default: "quay.io/broadinstitute/viral-core:2.5.10"
???

demux_metadata_only.create_or_update_sample_tables.docker
String — Default: "quay.io/broadinstitute/viral-core:2.5.10"
???

demux_metadata_only.create_or_update_sample_tables.library_table_name
String — Default: "library"
???

demux_metadata_only.create_or_update_sample_tables.read_counts_cleaned_json
File? — Default: None
???

demux_metadata_only.create_or_update_sample_tables.read_counts_raw_json
File? — Default: None
???

demux_metadata_only.create_or_update_sample_tables.sample_table_name
String — Default: "sample"
???

demux_metadata_only.insert_demux_outputs_into_terra_tables
Boolean — Default: false
???

demux_metadata_only.instrument_model_user_specified
String? — Default: None
???

demux_metadata_only.sample_rename_map
File? — Default: None
???

demux_metadata_only.samplesheet_rename_ids.new_id_col
String — Default: 'external_id'
???

demux_metadata_only.samplesheet_rename_ids.old_id_col
String — Default: 'internal_id'
???

demux_metadata_only.sra_meta_prep.docker
String — Default: "quay.io/broadinstitute/viral-core:2.5.10"
???

demux_metadata_only.terra_load_biosample_data.docker
String — Default: "schaluvadi/pathogen-genomic-surveillance:api-wdl"
???

demux_metadata_only.instrument_model_inferred
String
???

demux_metadata_only.sra_metadata
File?
???

demux_metadata_only.terra_library_table
File?
???

demux_metadata_only.terra_sample_library_map
File?
???

demux_metadata_only.terra_sample_metadata
File?
???

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