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¶

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

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align_and_count_multiple_report.align_and_count.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???

align_and_count_multiple_report.align_and_count.machine_mem_gb
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:2.1.33"
???

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:2.1.33"
???

align_and_count_multiple_report.report
File
???

align_and_count_multiple_report.report_top_hits
File
???

align_and_count_multiple_report.viral_core_version
String
???

Generated using WDL AID (1.0.0)