ROI files for coverage analysis

[ToonRosseel]

Description of feature

• make the use of 1 seperated BED file per sample possible for coverage analysis (posssible that this is already working with the "roi" samplesheet field)
• WES profile: generation of *mosdepth.region.dist.txt only for genelists with "Exoom + publieke website" tag in CMGG Bio module
• new SeqCap profile:

params {
aligner =   "snap"
markdup  =   "samtools"
umi_aware  = true
run_coverage = true
disable_picard_metrics  = false
genelists  =   "/kyukon/data/gent/shared/000/gvo00082/genomes/Hsapiens/GRCh38/regions/SeqCap-panels/designs"
}

[matthdsm]

make the use of 1 seperated BED file per sample possible for coverage analysis (posssible that this is already working with the "roi" samplesheet field)

Possible with ROI samplesheet field

[matthdsm]

WES profile: generation of *mosdepth.region.dist.txt only for genelists with "Exoom + publieke website" tag in CMGG Bio module

Impossible to infer bed filename from "Gene Panels" field in Smaple. Too many non overlapping names, which would result in missing information.

[ToonRosseel]

make the use of 1 seperated BED file per sample possible for coverage analysis (posssible that this is already working with the "roi" samplesheet field)

Possible with ROI samplesheet field

I tested this on the HPC in /kyukon/data/gent/vo/000/gvo00082/projects/NF_validations/HyperCap_giab_samples/NVQ_944_Connective_tissue_v6/preprocessing/. Remaining problem:

• When using full path's of BED files, I get error below. Solution: loosing regex of

  preprocessing/assets/schema_input.json

  Line 72 in e3021ca

  "pattern": "^[a-zA-Z0-9_]+.bed$",

* --input   (/kyukon/data/gent/vo/000/gvo00082/projects/NF_validations/HyperCap_giab_samples/NVQ_944_Connective_tissue_v6/preprocessing/NVQ_944.csv):   Validation of file failed:
--
  | -> Entry 1: Error for field 'roi'   (/kyukon/data/gent/shared/000/gvo00082/genomes/Hsapiens/GRCh38/regions/SeqCap-panels/designs/Connective_tissue_v6_cds15_e105_sorted.bed):   "/kyukon/data/gent/shared/000/gvo00082/genomes/Hsapiens/GRCh38/regions/SeqCap-panels/designs/Connective_tissue_v6_cds15_e105_sorted.bed"   does not match regular expression [^[a-zA-Z0-9_]+.bed$]
  | -> Entry 2: Error for field 'roi'   (/kyukon/data/gent/shared/000/gvo00082/genomes/Hsapiens/GRCh38/regions/SeqCap-panels/designs/FamCanc_v3_cds15_e105_sorted.bed):   "/kyukon/data/gent/shared/000/gvo00082/genomes/Hsapiens/GRCh38/regions/SeqCap-panels/designs/FamCanc_v3_cds15_e105_sorted.bed"   does not match regular expression [^[a-zA-Z0-9_]+.bed$]