Skip to content

Commit

Permalink
add docs
Browse files Browse the repository at this point in the history
  • Loading branch information
@rannick
rannick committed Feb 14, 2025
1 parent c22628e commit 077b53d
Showing 1 changed file with 52 additions and 0 deletions.
52 changes: 52 additions & 0 deletions docs/nallo_map.md
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,52 @@
| Nallo tags | Mandatory | HK tags | Used by |
|-----------------------------------------------------|-------------|-------------------------------------|---------------------------------------------|
| alignment_haplotags, alignment | True | bam, haplotags | scout, clinical-delivery, long-term-storage |
| alignment, alignment_haplotags_index | True | bam-index, haplotags | scout, clinical-delivery, long-term-storage |
| assembly, summary_hap1 | True | hap1, assembly, assembly-summary | clinical-delivery, long-term-storage |
| summary_hap2, assembly | True | hap2, assembly, assembly-summary | clinical-delivery, long-term-storage |
| assembly, assembly_hap1_mapped | True | bed, hap1, modkit-pileup | clinical-delivery, long-term-storage |
| assembly, assembly_hap1_mapped_index | True | bed-index, hap1, modkit-pileup | clinical-delivery, long-term-storage |
| assembly_hap2_mapped, assembly | True | bam, hap2, assembly | clinical-delivery, long-term-storage |
| assembly, assembly_hap2_mapped_index | True | bam-index, hap2, assembly | clinical-delivery, long-term-storage |
| summary_counts, hap1 | True | bed, hap1, modkit-pileup | clinical-delivery, long-term-storage |
| hap1_index, summary_counts | True | bed-index, hap1, modkit-pileup | clinical-delivery, long-term-storage |
| summary_counts, hap2 | True | bed, hap2, modkit-pileup | clinical-delivery, long-term-storage |
| summary_counts, hap2_index | True | bed-index, hap2, modkit-pileup | clinical-delivery, long-term-storage |
| summary_counts, ungrouped | True | bed, ungrouped, modkit-pileup | clinical-delivery, long-term-storage |
| ungrouped_index, summary_counts | True | bed-index, ungrouped, modkit-pileup | clinical-delivery, long-term-storage |
| mosdepth_d4, qc_bam | True | coverage, d4 | scout, clinical-delivery, long-term-storage |
| multiqc-html, multiqc | True | multiqc-html | scout, clinical-delivery, long-term-storage |
| multiqc, multiqc-json | True | multiqc-json | long-term-storage |
| pedigree_fam, pedigree | True | pedigree | clinical-delivery, scout, long-term-storage |
| relate_html, somalier | True | somalier, relate-html | clinical-delivery, scout, long-term-storage |
| somalier, relate_pairs | True | somalier, relate-pairs | scout, long-term-storage |
| somalier, relate_samples | True | somalier, relate-samples | scout, long-term-storage |
| deepvariant, report | True | deepvariant-report | clinical-delivery, long-term-storage |
| paraphase | True | bam, paraphase | clinical-delivery, long-term-storage |
| paraphase_index, paraphase | True | bam-index, paraphase | clinical-delivery, long-term-storage |
| json, paraphase | True | paraphase, json | clinical-delivery, long-term-storage |
| vcf, paraphase | False | bam-index, paraphase, vcf | clinical-delivery, long-term-storage |
| vcf_index, paraphase | False | bam-index, paraphase, vcf-index | clinical-delivery, long-term-storage |
| sorted_repeats, vcf_str | True | repeats, sorted, vcf | long-term-storage |
| sorted_repeats, vcf_str_index | True | repeats, sorted, vcf-index | long-term-storage |
| bam, spanning_repeats | True | repeats, spanning, bam | long-term-storage |
| bam_index, spanning_repeats | True | repeats, spanning, bam-index | long-term-storage |
| repeats_annotated, vcf_str | True | vcf-str | scout, clinical-delivery, long-term-storage |
| repeats_annotated, vcf_str_index | True | vcf-str-index | scout, clinical-delivery, long-term-storage |
| vcf_snv_research, snv_annotated | True | vcf-snv-research | scout, clinical-delivery, long-term-storage |
| vcf_snv_research_index, snv_annotated | True | vcf-snv-research-index | scout, clinical-delivery, long-term-storage |
| snv_annotated_filtered, vcf_snv_clinical | True | vcf-snv-clinical | scout, clinical-delivery, long-term-storage |
| snv_annotated_filtered, vcf_snv_clinical_index | True | vcf-snv-clinical-index | scout, clinical-delivery, long-term-storage |
| vcf_sv_research, sv_annotated_ranked | True | vcf-sv-research | scout, clinical-delivery, long-term-storage |
| sv_annotated_ranked, vcf_sv_research_index | True | vcf-sv-research-index | scout, clinical-delivery, long-term-storage |
| vcf_sv_clinical, sv_annotated_ranked_filtered | True | vcf-sv-clinical | scout, clinical-delivery, long-term-storage |
| vcf_sv_clinical_index, sv_annotated_ranked_filtered | True | vcf-sv-clinical-index | scout, clinical-delivery, long-term-storage |
| copy_number, bedgraph | True | cnv, bedgraph | clinical-delivery, long-term-storage |
| bigwig, depth_track | True | hificnv, bigwig | clinical-delivery, long-term-storage |
| bigwig, maf_depth_track | True | hificnv, bigwig, maf | clinical-delivery, long-term-storage |
| nextflow-params | True | nextflow-params | cg, long-term-storage |
| nextflow-config | True | nextflow-config | cg, long-term-storage |
| samplesheet | True | nextflow-samplesheet | cg, long-term-storage |
| software-versions | True | software-versions | cg, clinical-delivery, long-term-storage |
| qc-metrics | True | qc-metrics, deliverable | cg, long-term-storage |
| manifest | False | manifest | scout, long-term-storage |

0 comments on commit 077b53d

Please sign in to comment.