4.20. demux_deplete¶
Picard-based demultiplexing and basecalling from a tarball of a raw BCL directory, followed by QC metrics, depletion, and SRA submission prep.
4.20.1. Inputs¶
4.20.1.1. Required inputs¶
demux_deplete.flowcell_tgz
File — Default: None
Illumina BCL directory compressed as tarball. Must contain RunInfo.xml, SampleSheet.csv, RTAComplete.txt, and Data/Intensities/BaseCalls/*
demux_deplete.samplesheets
Array[File]+ — Default: None
Custom formatted 'extended' format tsv samplesheets that will override any SampleSheet.csv in the illumina BCL directory. Must supply one file per lane of the flowcell, and must provide them in lane order. Required tsv column headings are: sample, library_id_per_sample, barcode_1, barcode_2 (if paired reads, omit if single-end), library_strategy, library_source, library_selection, design_description. 'sample' must correspond to a biological sample. 'sample' x 'library_id_per_sample' must be unique within a samplesheet and correspond to independent libraries from the same original sample. barcode_1 and barcode_2 must correspond to the actual index sequence. Remaining columns must follow strict ontology: see 3rd tab of https://www.ncbi.nlm.nih.gov/core/assets/sra/files/SRA_metadata_acc_example.xlsx for controlled vocabulary and term definitions.
demux_deplete.spikein_db
File — Default: None
???
4.20.1.2. Other inputs¶
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demux_deplete.biosample_map
File? — Default: None
A two-column tsv that contains at least the following columns: sample_name, accession. sample_name refers to the external sample id, accession is the NCBI BioSample accession number (SAMNxxx). If this file is omitted, SRA submission prep will be skipped.
demux_deplete.blastDbs
Array[File]? — Default: None
???
demux_deplete.bmtaggerDbs
Array[File]? — Default: None
???
demux_deplete.bwaDbs
Array[File]? — Default: None
???
demux_deplete.default_filename_keys
Array[String] — Default: ["spike_in"]
???
demux_deplete.default_sample_keys
Array[String] — Default: ["amplicon_set", "control"]
???
demux_deplete.deplete.clear_tags
Boolean? — Default: false
???
demux_deplete.deplete.cpu
Int? — Default: 8
???
demux_deplete.deplete.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.1.16.0"
???
demux_deplete.deplete.machine_mem_gb
Int? — Default: None
???
demux_deplete.deplete.query_chunk_size
Int? — Default: None
???
demux_deplete.deplete.tags_to_clear_space_separated
String? — Default: "XT X0 X1 XA AM SM BQ CT XN OC OP"
???
demux_deplete.illumina_demux.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???
demux_deplete.illumina_demux.flowcell
String? — Default: None
???
demux_deplete.illumina_demux.forceGC
Boolean? — Default: true
???
demux_deplete.illumina_demux.machine_mem_gb
Int? — Default: None
???
demux_deplete.illumina_demux.maxMismatches
Int? — Default: 0
???
demux_deplete.illumina_demux.maxNoCalls
Int? — Default: None
???
demux_deplete.illumina_demux.maxReadsInRamPerTile
Int? — Default: None
???
demux_deplete.illumina_demux.maxRecordsInRam
Int? — Default: None
???
demux_deplete.illumina_demux.minimumBaseQuality
Int? — Default: 10
???
demux_deplete.illumina_demux.minimumQuality
Int? — Default: None
???
demux_deplete.illumina_demux.minMismatchDelta
Int? — Default: None
???
demux_deplete.illumina_demux.readStructure
String? — Default: None
???
demux_deplete.illumina_demux.runinfo
File? — Default: None
???
demux_deplete.illumina_demux.runStartDate
String? — Default: None
???
demux_deplete.illumina_demux.sequencingCenter
String? — Default: None
???
demux_deplete.illumina_demux.threads
Int? — Default: None
???
demux_deplete.instrument_model
String? — Default: None
???
demux_deplete.min_reads_per_bam
Int — Default: 100
???
demux_deplete.multiqc_cleaned.comment
String? — Default: None
???
demux_deplete.multiqc_cleaned.config
File? — Default: None
???
demux_deplete.multiqc_cleaned.config_yaml
String? — Default: None
???
demux_deplete.multiqc_cleaned.data_dir
Boolean — Default: false
???
demux_deplete.multiqc_cleaned.docker
String — Default: "quay.io/biocontainers/multiqc:1.8--py_2"
???
demux_deplete.multiqc_cleaned.exclude_modules
Array[String]? — Default: None
???
demux_deplete.multiqc_cleaned.export
Boolean — Default: false
???
demux_deplete.multiqc_cleaned.flat
Boolean — Default: false
???
demux_deplete.multiqc_cleaned.force
Boolean — Default: false
???
demux_deplete.multiqc_cleaned.full_names
Boolean — Default: false
???
demux_deplete.multiqc_cleaned.ignore_analysis_files
String? — Default: None
???
demux_deplete.multiqc_cleaned.ignore_sample_names
String? — Default: None
???
demux_deplete.multiqc_cleaned.interactive
Boolean — Default: true
???
demux_deplete.multiqc_cleaned.lint
Boolean — Default: false
???
demux_deplete.multiqc_cleaned.megaQC_upload
Boolean — Default: false
???
demux_deplete.multiqc_cleaned.module_to_use
Array[String]? — Default: None
???
demux_deplete.multiqc_cleaned.no_data_dir
Boolean — Default: false
???
demux_deplete.multiqc_cleaned.out_dir
String — Default: "./multiqc-output"
???
demux_deplete.multiqc_cleaned.output_data_format
String? — Default: None
[tsv|yaml|json] default:tsv
demux_deplete.multiqc_cleaned.pdf
Boolean — Default: false
???
demux_deplete.multiqc_cleaned.sample_names
File? — Default: None
???
demux_deplete.multiqc_cleaned.tag
String? — Default: None
???
demux_deplete.multiqc_cleaned.template
String? — Default: None
???
demux_deplete.multiqc_cleaned.title
String? — Default: None
???
demux_deplete.multiqc_cleaned.zip_data_dir
Boolean — Default: false
???
demux_deplete.multiqc_raw.comment
String? — Default: None
???
demux_deplete.multiqc_raw.config
File? — Default: None
???
demux_deplete.multiqc_raw.config_yaml
String? — Default: None
???
demux_deplete.multiqc_raw.data_dir
Boolean — Default: false
???
demux_deplete.multiqc_raw.docker
String — Default: "quay.io/biocontainers/multiqc:1.8--py_2"
???
demux_deplete.multiqc_raw.exclude_modules
Array[String]? — Default: None
???
demux_deplete.multiqc_raw.export
Boolean — Default: false
???
demux_deplete.multiqc_raw.flat
Boolean — Default: false
???
demux_deplete.multiqc_raw.force
Boolean — Default: false
???
demux_deplete.multiqc_raw.full_names
Boolean — Default: false
???
demux_deplete.multiqc_raw.ignore_analysis_files
String? — Default: None
???
demux_deplete.multiqc_raw.ignore_sample_names
String? — Default: None
???
demux_deplete.multiqc_raw.interactive
Boolean — Default: true
???
demux_deplete.multiqc_raw.lint
Boolean — Default: false
???
demux_deplete.multiqc_raw.megaQC_upload
Boolean — Default: false
???
demux_deplete.multiqc_raw.module_to_use
Array[String]? — Default: None
???
demux_deplete.multiqc_raw.no_data_dir
Boolean — Default: false
???
demux_deplete.multiqc_raw.out_dir
String — Default: "./multiqc-output"
???
demux_deplete.multiqc_raw.output_data_format
String? — Default: None
[tsv|yaml|json] default:tsv
demux_deplete.multiqc_raw.pdf
Boolean — Default: false
???
demux_deplete.multiqc_raw.sample_names
File? — Default: None
???
demux_deplete.multiqc_raw.tag
String? — Default: None
???
demux_deplete.multiqc_raw.template
String? — Default: None
???
demux_deplete.multiqc_raw.title
String? — Default: None
???
demux_deplete.multiqc_raw.zip_data_dir
Boolean — Default: false
???
demux_deplete.sample_rename_map
File? — Default: None
If 'samples' need to be renamed, provide a two-column tsv that contains at least the following columns: internal_id, external_id. All samples will be renamed prior to analysis. Any samples described in the samplesheets that are not present in sample_rename_map will be unaltered. If this is omitted, no samples will be renamed.
demux_deplete.samplesheet_rename_ids.new_id_col
String — Default: 'external_id'
???
demux_deplete.samplesheet_rename_ids.old_id_col
String — Default: 'internal_id'
???
demux_deplete.spike_summary.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???
demux_deplete.spike_summary.output_prefix
String — Default: "count_summary"
???
demux_deplete.spikein.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???
demux_deplete.spikein.machine_mem_gb
Int? — Default: None
???
demux_deplete.spikein.topNHits
Int — Default: 3
???
demux_deplete.sra_meta_prep.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???
demux_deplete.sra_title
String? — Default: None
???
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