Fix naming mistakes in output docs (#546)

* Fix naming mistakes in output docs * Changelog and prettier * Update docs/output.md Co-authored-by: Anders Jemt <[email protected]> * prettier --------- Co-authored-by: Anders Jemt <[email protected]>
genomic-medicine-sweden · Jan 24, 2025 · db09834 · db09834
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -24,7 +24,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
-- [#546](https://github.com/genomic-medicine-sweden/nallo/pull/546) - Fixed output filename descriptions in documentation not matching actual output
+- [#546](https://github.com/genomic-medicine-sweden/nallo/pull/546) - Fixed output filenames missmatches in documentation compared to pipeline
 
 ### Parameters
 

diff --git a/docs/output.md b/docs/output.md
@@ -36,12 +36,13 @@ This document describes the pipeline output files and the tools used to generate
 
 [Modkit](https://github.com/nanoporetech/modkit) is used to create methylation pileups, producing bedMethyl files for both haplotagged and ungrouped reads. Additionally, methylation information can be viewed in the BAM files, for example in IGV. When phasing is on, modkit outputs pileups per haplotype.
 
-| Path                                                                         | Description                                               | Alignment          | Alignment & phasing |
-| ---------------------------------------------------------------------------- | --------------------------------------------------------- | ------------------ | ------------------- |
-| `methylation/modkit/pileup/{sample}/*.modkit_pileup_phased_*.bed.gz`         | bedMethyl file with summary counts from haplotagged reads |                    | :white_check_mark:  |
-| `methylation/modkit/pileup/{sample}/*.modkit_pileup_phased_ungrouped.bed.gz` | bedMethyl file for ungrouped reads                        |                    | :white_check_mark:  |
-| `methylation/modkit/pileup/{sample}/*.modkit_pileup.bed.gz`                  | bedMethyl file with summary counts from all reads         | :white_check_mark: |                     |
-| `methylation/modkit/pileup/{sample}/*.bed.gz.tbi`                            | Index of the corresponding bedMethyl file                 | :white_check_mark: |                     |
+| Path                                                                  | Description                                                             | Alignment          | Alignment & phasing |
+| --------------------------------------------------------------------- | ----------------------------------------------------------------------- | ------------------ | ------------------- |
+| `methylation/modkit/pileup/{sample}/*.modkit_pileup_1.bed.gz`         | bedMethyl file with summary counts from haplotagged reads (haplotype 1) |                    | :white_check_mark:  |
+| `methylation/modkit/pileup/{sample}/*.modkit_pileup_2.bed.gz`         | bedMethyl file with summary counts from haplotagged reads (haplotype 2) |                    | :white_check_mark:  |
+| `methylation/modkit/pileup/{sample}/*.modkit_pileup_ungrouped.bed.gz` | bedMethyl file for ungrouped reads                                      |                    | :white_check_mark:  |
+| `methylation/modkit/pileup/{sample}/*.modkit_pileup.bed.gz`           | bedMethyl file with summary counts from all reads                       | :white_check_mark: |                     |
+| `methylation/modkit/pileup/{sample}/*.bed.gz.tbi`                     | Index of the corresponding bedMethyl files                              | :white_check_mark: |                     |
 
 ## MultiQC
 
@@ -166,10 +167,10 @@ In general, annotated variant calls are output per family while unannotated call
 
 [Stranger](https://github.com/Clinical-Genomics/stranger) is used to annotate repeats.
 
-| Path                                                                                | Description                           | Call repeats | Call & annotate repeats |
-| ----------------------------------------------------------------------------------- | ------------------------------------- | ------------ | ----------------------- |
-| `repeat_expansions/family/{family}/{family}_repeat_expansions_annotated.vcf.gz`     | Merged, annotated VCF file per family |              | :white_check_mark:      |
-| `repeat_expansions/family/{family}/{family}_repeat_expansions_annotated.vcf.gz.tbi` | Index of the VCF file                 |              | :white_check_mark:      |
+| Path                                                                      | Description                           | Call repeats | Call & annotate repeats |
+| ------------------------------------------------------------------------- | ------------------------------------- | ------------ | ----------------------- |
+| `repeats/family/{family}/{family}_repeat_expansions_annotated.vcf.gz`     | Merged, annotated VCF file per family |              | :white_check_mark:      |
+| `repeats/family/{family}/{family}_repeat_expansions_annotated.vcf.gz.tbi` | Index of the VCF file                 |              | :white_check_mark:      |
 
 ### SNVs