Merge pull request #43 from pdimens/docs_dev

update verbiage
pdimens · Feb 19, 2024 · 776d3a4 · 776d3a4
2 parents fbe9bb5 + 90c4e71
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diff --git a/Modules/Align/bwa.md b/Modules/Align/bwa.md
@@ -81,11 +81,10 @@ if the primary alignment was marked as a duplicate. Duplicates get marked but **
 - ignores (but retains) barcode information
 - fast
 
-The [BWA MEM](https://github.com/lh3/bwa) workflow is substantially simpler and faster than the EMA workflow
- and maps all reads against the reference genome, no muss no fuss. Duplicates are marked using 
- [sambamba](https://lomereiter.github.io/sambamba/). The `BX:Z` tags in the read headers are still added 
- to the alignment headers, even though barcodes are not used to inform mapping. The `-m` threshold is used
- for alignment molecule assignment.
+The [BWA MEM](https://github.com/lh3/bwa) workflow is much simpler and faster than the EMA workflow
+and maps all reads against the reference genome. Duplicates are marked using `samtools markdup`.
+The `BX:Z` tags in the read headers are still added to the alignment headers, even though barcodes
+are not used to inform mapping. The `-m` threshold is used for alignment molecule assignment.
 
 ```mermaid
 graph LR
@@ -106,6 +105,7 @@ graph LR
 ```
 +++ :icon-file-directory: BWA output
 The `harpy align` module creates an `Align/bwa` directory with the folder structure below. `Sample1` is a generic sample name for demonstration purposes.
+The resulting folder also includes a `workflow` directory (not shown) with workflow-relevant runtime files and information.
 ```
 Align/bwa
 ├── Sample1.bam

diff --git a/Modules/Align/ema.md b/Modules/Align/ema.md
@@ -97,8 +97,7 @@ information, the EMA workflow is a bit more complicated under the hood. Reads wi
 barcodes are aligned using EMA and reads without valid barcodes are separately mapped
 using BWA before merging all the alignments together again. EMA will mark duplicates
 within alignments, but the BWA alignments need duplicates marked manually using 
-[sambamba](https://lomereiter.github.io/sambamba/). Thankfully, you shouldn't need 
-to worry about any of these details.
+`samtools markdup`.
 
 ```mermaid
 graph LR
@@ -121,7 +120,8 @@ graph LR
 
 ```
 +++ :icon-file-directory: EMA output
-The `harpy align` module creates an `Align/ema` directory with the folder structure below. `Sample1` is a generic sample name for demonstration purposes.
+The `harpy align` module creates an `Align/ema` directory with the folder structure below. `Sample1` is a generic sample name for demonstration purposes. 
+The resulting folder also includes a `workflow` directory (not shown) with workflow-relevant runtime files and information.
 ```
 Align/ema
 ├── Sample1.bam

diff --git a/Modules/SV/leviathan.md b/Modules/SV/leviathan.md
@@ -111,6 +111,7 @@ graph LR
 ```
 +++ :icon-file-directory: leviathan output
 The `harpy variants --method leviathan` module creates a `Variants/leviathan` (or `leviathan-pop`) directory with the folder structure below. `sample1` and `sample2` are generic sample names for demonstration purposes.
+The resulting folder also includes a `workflow` directory (not shown) with workflow-relevant runtime files and information.
 
 ```
 Variants/leviathan/

diff --git a/Modules/SV/naibr.md b/Modules/SV/naibr.md
@@ -149,6 +149,7 @@ graph LR
 The `harpy sv --method naibr` module creates a `Variants/naibr` (or `naibr-pop`) 
 directory with the folder structure below. `sample1` and `sample2` are generic sample 
 names for demonstration purposes.
+The resulting folder also includes a `workflow` directory (not shown) with workflow-relevant runtime files and information.
 
 ```
 Variants/naibr/

diff --git a/Modules/demultiplex.md b/Modules/demultiplex.md
@@ -80,6 +80,7 @@ graph LR
 +++ :icon-file-directory: demultiplexing output
 The `harpy demultiplex` module creates an `Demultiplex/PREFIX` directory with the folder structure below, where `PREFIX` is the prefix of your input file that Harpy
 infers by removing the file extension and forward/reverse distinction. `Sample1` and `Sample2` are generic sample names for demonstration purposes.
+The resulting folder also includes a `workflow` directory (not shown) with workflow-relevant runtime files and information.
 ```
 Demultiplex/PREFIX
 ├── Sample1.F.fq.gz

diff --git a/Modules/impute.md b/Modules/impute.md
@@ -190,6 +190,7 @@ The `harpy impute` module creates an `Imputation` directory with the folder stru
 are generic contig names from an imaginary `genome.fasta` for demonstration purposes. The directory `model1/`
 is a generic name to reflect the corresponding parameter row in the stitch parameter
 file, which would have explicit names in real use (e.g. `modelpseudoHaploid_useBXTrue_k10_s1_nGen50/`).
+The resulting folder also includes a `workflow` directory (not shown) with workflow-relevant runtime files and information.
 
 ```
 Impute/

diff --git a/Modules/phase.md b/Modules/phase.md
@@ -99,6 +99,7 @@ graph LR
 +++ :icon-file-directory: phasing output
 The `harpy phase` module creates an `Phase` directory with the folder structure below. `Sample1` is a generic sample name for demonstration purposes.
 If using the `--ignore-bx` option, the output directory will be named `Phase.noBX` instead.
+The resulting folder also includes a `workflow` directory (not shown) with workflow-relevant runtime files and information.
 
 ```
 Phase/

diff --git a/Modules/qc.md b/Modules/qc.md
@@ -50,6 +50,7 @@ graph LR
 
 +++ :icon-file-directory: qc output
 The `harpy qc` module creates a `QC` directory with the folder structure below. `Sample1` and `Sample2` are generic sample names for demonstration purposes. 
+The resulting folder also includes a `workflow` directory (not shown) with workflow-relevant runtime files and information.
 ```
 QC/
 ├── Sample1.R1.fq.gz

diff --git a/Modules/snp.md b/Modules/snp.md
@@ -117,6 +117,7 @@ graph LR
 The `harpy snp` module creates a `Variants/METHOD` directory with the folder structure below where `METHOD` is what
 you specify as the `--method` (mpileup or freebayes). `contig1` and `contig2` are generic contig names from an imaginary
 `genome.fasta` for demonstration purposes.
+The resulting folder also includes a `workflow` directory (not shown) with workflow-relevant runtime files and information.
 ```
 Variants/METHOD
 ├── variants.normalized.bcf

diff --git a/software.md b/software.md
@@ -9,27 +9,31 @@ HARPY is the sum of its parts, and out of tremendous respect for the developers
 
 Issues with specific tools might warrant a discussion with the authors/developers on the repositories of these projects.
 
-| Software   | Website                                                      | Publication                                                                                            |
-|:-----------|:-------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------|
-| bash       | [website](https://www.gnu.org/software/bash/)                |                                                                                                        |
-| bcftools   | [website](https://samtools.github.io/bcftools/bcftools.html) |                                                                                                        |
-| bgzip      | [website](http://www.htslib.org/doc/bgzip.html)              |                                                                                                        |
-| bwa        | [website](https://github.com/lh3/bwa)                        | [pubication](http://arxiv.org/abs/1303.3997)                                                           |
-| click      | [website](https://github.com/pallets/click)                  |                                                                                                        |
-| conda      | [website](https://github.com/conda)                          |                                                                                                        |
-| EMA        | [website](https://github.com/arshajii/ema)                   | [publication](https://www.biorxiv.org/content/early/2017/11/16/220236)                                 |
-| fastp      | [website](https://github.com/OpenGene/fastp)                 | [publication](https://doi.org/10.1093/bioinformatics/bty560)                                           |
-| HapCUT2    | [website](https://github.com/vibansal/HapCUT2)               | [publication](https://doi.org/10.1101/gr.213462.116)                                                   |
-| LEVIATHAN  | [website](https://github.com/morispi/LEVIATHAN)              | [publication](https://doi.org/10.1101/2021.03.25.437002)                                               |
-| LRez       | [website](https://github.com/morispi/LRez)                   | [publication](https://academic.oup.com/bioinformaticsadvances/article/1/1/vbab022/6375438?login=false) |
-| mamba      | [website](https://github.com/mamba-org/mamba)                |                                                                                                        |
-| NAIBR      | [website](https://github.com/raphael-group/NAIBR) + [fork](https://github.com/pontushojer/NAIBR) | [publication](https://doi.org/10.1093/bioinformatics/btx712)       |
-| python     | [website](https://www.python.org/)                           |                                                                                                        |
-| rich       | [webiste](https://github.com/Textualize/rich)                |                                                                                                        |
-| rich-click | [website](https://github.com/ewels/rich-click)               |                                                                                                        |
-| sambamba   | [website](https://github.com/biod/sambamba)                  | [publication](https://doi.org/10.1093/bioinformatics/btv098)                                           |
-| samtools   | [website](http://www.htslib.org/)                            |                                                                                                        |
-| seqtk      | [website](https://github.com/lh3/seqtk)                      |                                                                                                        |
-| Snakemake  | [website](https://github.com/snakemake/snakemake)            | [publication](https://f1000research.com/articles/10-33/v1)                                             |
-| STITCH     | [website](https://github.com/rwdavies/STITCH)                | [publication](https://doi.org/10.1038%2Fng.3594)                                                       |
-| whatshap   | [website](https://github.com/whatshap/whatshap)              | [publication](https://doi.org/10.1101/085050)                                                          |
+| Software    | Links                                                                                                               |
+|:------------|:--------------------------------------------------------------------------------------------------------------------|
+| bash        | [website](https://www.gnu.org/software/bash/)                                                                       |
+| bcftools    | [website](https://samtools.github.io/bcftools/bcftools.html)                                                        |
+| bgzip       | [website](http://www.htslib.org/doc/bgzip.html)                                                                     |
+| bwa         | [website](https://github.com/lh3/bwa), [publication](http://arxiv.org/abs/1303.3997)                                 |
+| click       | [website](https://github.com/pallets/click)                                                                         |
+| conda       | [website](https://github.com/conda)                                                                                 |
+| EMA         | [website](https://github.com/arshajii/ema), [publication](https://www.biorxiv.org/content/early/2017/11/16/220236)  |
+| fastp       | [website](https://github.com/OpenGene/fastp), [publication](https://doi.org/10.1093/bioinformatics/bty560)          |
+| HapCUT2     | [website](https://github.com/vibansal/HapCUT2), [publication](https://doi.org/10.1101/gr.213462.116)                |
+| LEVIATHAN   | [website](https://github.com/morispi/LEVIATHAN), [publication](https://doi.org/10.1101/2021.03.25.437002)           |
+| LRez        | [website](https://github.com/morispi/LRez), [publication](https://academic.oup.com/bioinformaticsadvances/article/1/1/vbab022/6375438?login=false) |
+| mamba       | [website](https://github.com/mamba-org/mamba)                                                                       |
+| NAIBR       | [website](https://github.com/raphael-group/NAIBR), [fork](https://github.com/pontushojer/NAIBR), [publication](https://doi.org/10.1093/bioinformatics/btx712) |
+| plotly      | [website](https://plotly.com/)                                                                                      |
+| python      | [website](https://www.python.org/)                                                                                  |
+| R           | [website](https://www.r-project.org/)                                                                               |
+| r-circlize  | [website](https://github.com/jokergoo/circlize), [publication](https://doi.org/10.1093/bioinformatics/btu393)       |
+| r-tidyverse | [website](https://www.tidyverse.org/), [publication](https://doi.org/10.21105/joss.01686)                           |
+| r-DT        | [website](https://rstudio.github.io/DT/), [js-website](http://datatables.net)                                             |
+| rich        | [website](https://github.com/Textualize/rich)                                                                       |
+| rich-click  | [website](https://github.com/ewels/rich-click)                                                                      |
+| samtools    | [website](http://www.htslib.org/)                                                                                   |
+| seqtk       | [website](https://github.com/lh3/seqtk)                                                                             |
+| Snakemake   | [website](https://github.com/snakemake/snakemake), [publication](https://f1000research.com/articles/10-33/v1)       |
+| STITCH      | [website](https://github.com/rwdavies/STITCH), [publication](https://doi.org/10.1038%2Fng.3594)                 |
+| whatshap    | [website](https://github.com/whatshap/whatshap), [publication](https://doi.org/10.1101/085050)                    |