Merge pull request #59 from pdimens/docs_dev

0.8.x changes
pdimens · Mar 22, 2024 · 43f435f · 43f435f
2 parents 50efb18 + e157f38
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diff --git a/Modules/Align/bwa.md b/Modules/Align/bwa.md
@@ -105,7 +105,7 @@ graph LR
     end
 ```
 +++ :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 default output directory is `Align/bwa` 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

diff --git a/Modules/Align/ema.md b/Modules/Align/ema.md
@@ -121,7 +121,7 @@ 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 default output directory is `Align/ema` 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

diff --git a/Modules/SV/leviathan.md b/Modules/SV/leviathan.md
@@ -110,11 +110,11 @@ graph LR
     C-->E([generate reports])
 ```
 +++ :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 default output directory is `SV/leviathan` 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/
+SV/leviathan
 ├── sample1.bcf
 ├── sample2.bcf
 ├── logs

diff --git a/Modules/SV/naibr.md b/Modules/SV/naibr.md
@@ -146,13 +146,12 @@ graph LR
     B-->C([generate reports])
 ```
 +++ :icon-file-directory: naibr output
-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 
+The default output directory is `SV/naibr` 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/
+SV/naibr
 ├── sample1.bedpe
 ├── sample2.bedpe
 ├── configs

diff --git a/Modules/demultiplex.md b/Modules/demultiplex.md
@@ -78,7 +78,7 @@ 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
+The default output directory is `Demultiplex/PREFIX` 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.
 ```

diff --git a/Modules/impute.md b/Modules/impute.md
@@ -186,7 +186,7 @@ graph LR
     G([create file list])-->E
 ```
 +++ :icon-file-directory: impute output
-The `harpy impute` module creates an `Imputation` directory with the folder structure below. `contig1` and `contig2` 
+The default output directory is `Impute` with the folder structure below. `contig1` and `contig2` 
 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/`).

diff --git a/Modules/phase.md b/Modules/phase.md
@@ -97,8 +97,7 @@ 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 default output directory is `Phase` 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.
 
 ```

diff --git a/Modules/preflight.md b/Modules/preflight.md
@@ -74,9 +74,7 @@ of the language such as when "any" and "all" are written.
 |BX:Z: last tag| **all** reads have `BX:Z`: as final tag in alignment records | **at least 1 read** doesn't have `BX:Z:` tag as final tag|
 
 +++ output
-Unlike the other modules. `preflight` will not create a new folder in your working directory. Instead, it will create 
-a `Preflight` folder in the same directory that was provided for `-d` (`--directory`). This design is intended to keep
-the reports near the source data.
+The default output directory is `Preflight/fastq` or `Preflight/bam` depending on which mode you are using.
 
 +++ Reports
 The result of `preflight` is a single HTML report in `inputdir/Preflight/filecheck.xxx.html` where `xxx` is either `fastq` or `bam`

diff --git a/Modules/qc.md b/Modules/qc.md
@@ -49,7 +49,7 @@ 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 default output directory is `QC` 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/

diff --git a/Modules/snp.md b/Modules/snp.md
@@ -114,12 +114,11 @@ graph LR
 ```
 
 +++ :icon-file-directory: snp output
-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 default output directory is `SNP/mpileup` or `SNP/freebayes`(depending on workflow) with the folder structure below.
+Below, `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
+SNP/method
 ├── variants.normalized.bcf
 ├── variants.normalized.bcf.csi
 ├── variants.raw.bcf

diff --git a/commonoptions.md b/commonoptions.md
@@ -42,14 +42,14 @@ parameters that don't impact the results of the module, but instead control the
 of calling the module. These runtime parameters are listed in the modules' help strings and can be 
 configured using these arguments:
 
-| argument      | short name | type    | default | required | description                                                                       |
-|:------------- |:----------:|:------- |:-------:|:--------:|:--------------------------------------------------------------------------------- |
-| `--threads`   | `-t`       | integer | 4       | no       | Number of threads to use                                                          |
-| `--print-only` |           | toggle  |         | no       | Perform internal validations, build the workflow environment, and print the resulting Snakemake command, but don't run anything |
-| `--skipreports` | `-r`     | toggle  |         | no       | Skip the processing and generation of HTML reports in a workflow                  |
-| `--snakemake` | `-s`       | string  |         | no       | Additional [Snakemake](snakemake/#adding-snakamake-parameters) options, in quotes |
-| `--quiet`     | `-q`       | toggle  |         | no       | Supressing Snakemake printing to console                                          |
-| `--help`      |            |         |         |          | Show the module docstring                                                         |
+| argument        | short name | type    | default | required | description                                                                       |
+|:--------------- |:----------:|:------- |:-------:|:--------:|:--------------------------------------------------------------------------------- |
+| `--output-dir`  | `-o`       | string  | varies  | no       | Name of output directory                                                          |
+| `--threads`     | `-t`       | integer | 4       | no       | Number of threads to use                                                          |
+| `--skipreports` | `-r`       | toggle  |         | no       | Skip the processing and generation of HTML reports in a workflow                  |
+| `--snakemake`   | `-s`       | string  |         | no       | Additional [Snakemake](snakemake/#adding-snakamake-parameters) options, in quotes |
+| `--quiet`       | `-q`       | toggle  |         | no       | Supressing Snakemake printing to console                                          |
+| `--help`        |            |         |         |          | Show the module docstring                                                         |
 
 As as example, you could call the `harpy align` module and specify 20 threads with no output to console:
 

diff --git a/retype.yml b/retype.yml
@@ -17,7 +17,7 @@ footer:
   copyright: "&copy; Copyright {{ year }}. All rights reserved."
 branding:
   title: Harpy
-  label: v0.7.x
+  label: v0.8.x
   logo: static/favicon.png
   logoDark: static/favicon.png
   logoAlign: left