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Implement samplesheet support for mapping constrains #49

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Joon-Klaps opened this issue Dec 15, 2023 · 1 comment · Fixed by #60
Closed
13 tasks done

Implement samplesheet support for mapping constrains #49

Joon-Klaps opened this issue Dec 15, 2023 · 1 comment · Fixed by #60
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enhancement New feature or request priority An issue with priority
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Release 0.1.1

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@Joon-Klaps
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Joon-Klaps commented Dec 15, 2023 •
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Description of feature

Constrained mapping sequence should support metadata. This metadata needs to have:

  • ncbi ID
  • NCBI definition (optional)
  • Sequence file location
  • Samples that need to map towards the sequence (optional)
  • Species name (optional)
  • Segment (optional)

This metadata needs to be implemented in the in sample table overview & should create an additional table mapping_constrains.{tsv/excel} with more in depth information (standard information that is already given).

Additional columns to include in the sample table for each unique combination of species and segment (if given):

  • # reads mapped
  • Variants called (total SNPs)
  • Consensus length
  • Coverage 10X
  • median coverage depth for 100% of genome
  • min coverage depth
  • max coverage depth
@Joon-Klaps Joon-Klaps added the enhancement New feature or request label Dec 15, 2023
@Joon-Klaps Joon-Klaps added this to the Release 0.1.1 milestone Dec 15, 2023
@Joon-Klaps Joon-Klaps linked a pull request Jan 1, 2024 that will close this issue
49 samplesheet mapping constrains #60
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@Joon-Klaps Joon-Klaps added the priority An issue with priority label Jan 3, 2024
@Joon-Klaps
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Waiting for approval of MultiQC/MultiQC#2257 to have min & max coverage included.

@Joon-Klaps Joon-Klaps mentioned this issue Jan 19, 2024
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49 samplesheet mapping constrains Joon-Klaps/viralgenie
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