4.2. align_and_count_multiple_report¶
Count the number of times reads map to provided reference sequences. Useful for counting spike-ins, etc.
4.2.1. Inputs¶
4.2.1.1. Required inputs¶
align_and_count_multiple_report.reads_unmapped_bams
Array[File]+ — Default: None
Unaligned reads in BAM format
align_and_count_multiple_report.ref_db
File — Default: None
File containing sequences against which reads should me aligned and counted
4.2.1.2. Other inputs¶
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align_and_count_multiple_report.align_and_count.docker
String — Default: "quay.io/broadinstitute/viral-core"
???
align_and_count_multiple_report.align_and_count.machine_mem_gb
Int? — Default: None
???
align_and_count_multiple_report.align_and_count.minScoreToFilter
Int? — Default: None
???
align_and_count_multiple_report.align_and_count.topNHits
Int? — Default: 3
???
align_and_count_multiple_report.align_and_count_summary.docker
String — Default: "quay.io/broadinstitute/viral-core"
???
align_and_count_multiple_report.align_and_count_summary.output_prefix
String? — Default: "count_summary"
???
align_and_count_multiple_report.align_and_count_summary_top_hits.docker
String — Default: "quay.io/broadinstitute/viral-core"
???
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