4.4. assemble_refbased

Reference-based microbial consensus calling. Aligns short reads to a singular reference genome, calls a new consensus sequence, and emits: new assembly, reads aligned to provided reference, reads aligned to new assembly, various figures of merit, plots, and QC metrics. The user may provide unaligned reads spread across multiple input files and this workflow will parallelize alignment per input file before merging results prior to consensus calling.

4.4.1. Inputs

4.4.1.1. Required inputs

assemble_refbased.reads_unmapped_bams
Array[File]+ — Default: None
Unaligned reads in BAM format

assemble_refbased.reference_fasta
File — Default: None
Reference genome to align reads to.

4.4.1.2. Other common inputs

assemble_refbased.sample_name
String — Default: basename(reads_unmapped_bams[0],'.bam')
Base name of output files. The 'SM' field in BAM read group headers are also rewritten to this value. Avoid spaces and other filename-unfriendly characters.

assemble_refbased.trim_coords_bed
File? — Default: None
optional primers to trim in reference coordinate space (0-based BED format)

4.4.1.3. Other inputs

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assemble_refbased.align_to_ref.aligner
String? — Default: "novoalign"
Short read aligner to use: novoalign or bwa. (Default: novoalign)

assemble_refbased.align_to_ref.docker
String — Default: "quay.io/broadinstitute/viral-core"
???

assemble_refbased.align_to_ref.sample_name
String — Default: basename(basename(basename(reads_unmapped_bam,".bam"),".taxfilt"),".clean")
???

assemble_refbased.align_to_self.aligner
String? — Default: "novoalign"
Short read aligner to use: novoalign or bwa. (Default: novoalign)

assemble_refbased.align_to_self.docker
String — Default: "quay.io/broadinstitute/viral-core"
???

assemble_refbased.align_to_self.sample_name
String — Default: basename(basename(basename(reads_unmapped_bam,".bam"),".taxfilt"),".clean")
???

assemble_refbased.call_consensus.docker
String — Default: "quay.io/broadinstitute/viral-assemble"
???

assemble_refbased.call_consensus.machine_mem_gb
Int? — Default: None
???

assemble_refbased.call_consensus.major_cutoff
Float? — Default: 0.5
???

assemble_refbased.call_consensus.mark_duplicates
Boolean? — Default: false
???

assemble_refbased.call_consensus.min_coverage
Int? — Default: 2
???

assemble_refbased.ivar_trim.docker
String — Default: "andersenlabapps/ivar"
???

assemble_refbased.ivar_trim.machine_mem_gb
Int? — Default: None
???

assemble_refbased.ivar_trim.min_keep_length
Int? — Default: None
Minimum length of read to retain after trimming (Default: 30)

assemble_refbased.ivar_trim.min_quality
Int? — Default: None
Minimum quality threshold for sliding window to pass (Default: 20)

assemble_refbased.ivar_trim.sliding_window
Int? — Default: None
Width of sliding window for quality trimming (Default: 4)

assemble_refbased.merge_align_to_ref.docker
String — Default: "quay.io/broadinstitute/viral-core"
???

assemble_refbased.merge_align_to_ref.reheader_table
File? — Default: None
???

assemble_refbased.merge_align_to_self.docker
String — Default: "quay.io/broadinstitute/viral-core"
???

assemble_refbased.merge_align_to_self.reheader_table
File? — Default: None
???

assemble_refbased.multiqc_align_to_ref.comment
String? — Default: None
???

assemble_refbased.multiqc_align_to_ref.config
File? — Default: None
???

assemble_refbased.multiqc_align_to_ref.config_yaml
String? — Default: None
???

assemble_refbased.multiqc_align_to_ref.data_dir
Boolean — Default: false
???

assemble_refbased.multiqc_align_to_ref.docker
String — Default: "quay.io/biocontainers/multiqc:1.8--py_2"
???

assemble_refbased.multiqc_align_to_ref.exclude_modules
Array[String]+? — Default: None
???

assemble_refbased.multiqc_align_to_ref.export
Boolean — Default: false
???

assemble_refbased.multiqc_align_to_ref.file_name
String? — Default: None
???

assemble_refbased.multiqc_align_to_ref.flat
Boolean — Default: false
???

assemble_refbased.multiqc_align_to_ref.force
Boolean — Default: false
???

assemble_refbased.multiqc_align_to_ref.full_names
Boolean — Default: false
???

assemble_refbased.multiqc_align_to_ref.ignore_analysis_files
String? — Default: None
???

assemble_refbased.multiqc_align_to_ref.ignore_sample_names
String? — Default: None
???

assemble_refbased.multiqc_align_to_ref.interactive
Boolean — Default: true
???

assemble_refbased.multiqc_align_to_ref.lint
Boolean — Default: false
???

assemble_refbased.multiqc_align_to_ref.megaQC_upload
Boolean — Default: false
???

assemble_refbased.multiqc_align_to_ref.module_to_use
Array[String]+? — Default: None
???

assemble_refbased.multiqc_align_to_ref.no_data_dir
Boolean — Default: false
???

assemble_refbased.multiqc_align_to_ref.out_dir
String — Default: "./multiqc-output"
???

assemble_refbased.multiqc_align_to_ref.output_data_format
String? — Default: None
[tsv|yaml|json] default:tsv

assemble_refbased.multiqc_align_to_ref.pdf
Boolean — Default: false
???

assemble_refbased.multiqc_align_to_ref.sample_names
File? — Default: None
???

assemble_refbased.multiqc_align_to_ref.tag
String? — Default: None
???

assemble_refbased.multiqc_align_to_ref.template
String? — Default: None
???

assemble_refbased.multiqc_align_to_ref.title
String? — Default: None
???

assemble_refbased.multiqc_align_to_ref.zip_data_dir
Boolean — Default: false
???

assemble_refbased.novocraft_license
File? — Default: None
The default Novoalign short read aligner is a commercially licensed software that is available in a much slower, single-threaded version for free. If you have a paid license file, provide it here to run in multi-threaded mode. If this is omitted, it will run in single-threaded mode.

assemble_refbased.plot_ref_coverage.bin_large_plots
Boolean? — Default: false
???

assemble_refbased.plot_ref_coverage.binning_summary_statistic
String? — Default: "max"
???

assemble_refbased.plot_ref_coverage.docker
String — Default: "quay.io/broadinstitute/viral-core"
???

assemble_refbased.plot_ref_coverage.plot_only_non_duplicates
Boolean? — Default: false
???

assemble_refbased.plot_ref_coverage.skip_mark_dupes
Boolean? — Default: false
???

assemble_refbased.plot_self_coverage.bin_large_plots
Boolean? — Default: false
???

assemble_refbased.plot_self_coverage.binning_summary_statistic
String? — Default: "max"
???

assemble_refbased.plot_self_coverage.docker
String — Default: "quay.io/broadinstitute/viral-core"
???

assemble_refbased.plot_self_coverage.plot_only_non_duplicates
Boolean? — Default: false
???

assemble_refbased.plot_self_coverage.skip_mark_dupes
Boolean? — Default: false
???

assemble_refbased.skip_mark_dupes
Boolean? — Default: false
skip Picard MarkDuplicates step after alignment. This is recommended to be set to true for PCR amplicon based data. (Default: false)

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