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¶
4.1.1.1. Required 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
4.1.1.2. Other inputs¶
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align_and_count_report.align_and_count.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
align_and_count_report.align_and_count.machine_mem_gb
Int? — Default: None
???
align_and_count_report.align_and_count.topNHits
Int — Default: 3
???
4.1.2. Outputs¶
align_and_count_report.report
File
???
align_and_count_report.report_top_hits
File
???
align_and_count_report.viral_core_version
String
???
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