4.1. align_and_count_report¶

Align reads to reference with minimap2 and count the number of hits. Results are returned in the format of ‘samtools idxstats’.

4.1.1. Inputs¶

align_and_count_report.align_and_count.reads_bam
File — Default: None
Unaligned reads in BAM format

align_and_count_report.align_and_count.ref_db
File — Default: None
Reference genome in FASTA format

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align_and_count_report.align_and_count.cpu
Int? — Default: None
???

align_and_count_report.align_and_count.docker
String — Default: "ghcr.io/broadinstitute/viral-ngs:3.0.4-core"
???

align_and_count_report.align_and_count.machine_mem_gb
Int? — Default: None
???

align_and_count_report.align_and_count.topNHits
Int — Default: 3
???

align_and_count_report.pct_mapped_of_total_reads
String
???

align_and_count_report.pct_mapped_to_lesser_hits
String
???

align_and_count_report.pct_top_hit_of_total_reads
String
???

align_and_count_report.report
File
???

align_and_count_report.report_top_hits
File
???

align_and_count_report.tophit
String
???

align_and_count_report.viral_core_version
String
???

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