update

Modules/SV/leviathan.md

@@ -25,8 +25,8 @@ This file is optional and only useful if you want variant calling to happen on a
     - spaces can be used as delimeters too
 - the groups can be numbers or text (_i.e._ meaningful population names)
 - you can comment out lines with `#` for Harpy to ignore them
-- create with `harpy extra -p <samplefolder>` or manually
-- if created with `harpy extra -p`, all the samples will be assigned to group `pop1`
+- create with `harpy extra popgroup -d <samplefolder>` or manually
+- if created with `harpy extra popgroup`, all the samples will be assigned to group `pop1`
     - make sure to edit the second column to reflect your data correctly.
 
 ``` example file for --populations

Modules/SV/naibr.md

@@ -20,8 +20,8 @@ This file is optional and only useful if you want variant calling to happen on a
     - spaces can be used as delimeters too
 - the groups can be numbers or text (_i.e._ meaningful population names)
 - you can comment out lines with `#` for Harpy to ignore them
-- create with `harpy extra -p <samplefolder>` or manually
-- if created with `harpy extra -p`, all the samples will be assigned to group `pop1`
+- create with `harpy extra popgroup -d <samplefolder>` or manually
+- if created with `harpy extra popgroup`, all the samples will be assigned to group `pop1`
     - make sure to edit the second column to reflect your data correctly.
 
 ``` example file for --populations

Modules/snp.md

@@ -18,8 +18,8 @@ This file is optional and useful if you want variant calling to happen on a per-
     - spaces can be used as delimeters too
 - the groups can be numbers or text (_i.e._ meaningful population names)
 - you can comment out lines with `#` for Harpy to ignore them
-- create with `harpy extra -p <samplefolder>` or manually
-- if created with `harpy extra -p`, all the samples will be assigned to group `pop1`, so make sure to edit the second column to reflect your data correctly.
+- create with `harpy extra popgroup -d <samplefolder>` or manually
+- if created with `harpy extra popgroup`, all the samples will be assigned to group `pop1`, so make sure to edit the second column to reflect your data correctly.
 
 ``` example file for --populations
 sample1 pop1

commonoptions.md

@@ -5,7 +5,7 @@ order: 4
 ---
 
 # :icon-list-unordered: Common Harpy Options
-
+## Common command-line options
 Every Harpy module has a series of configuration parameters. These are arguments you need to input
 to configure the module to run on your data, such as the directory with the reads/alignments,
 the genome assembly, etc. All main modules (e.g. `qc`) also share a series of common runtime
@@ -37,6 +37,7 @@ When you run one of the main Harpy modules, the output directory will contain a
 both necessary for the module to run and is very useful to understand what the module did, be it for your own
 understanding or as a point of reference when writing the Methods within a manuscript. The presence of the folder
 and the contents therein also allow you to rerun the workflow manually. The `workflow` folder may contain the following:
+
 | item | contents | utility |
 |:-----|:---------|:--------|
 |`*.smk`| Snakefile with the full recipe of the workflow | useful for understanding the workflow |

retype.yml

@@ -17,7 +17,7 @@ footer:
   copyright: "© Copyright {{ year }}. All rights reserved."
 branding:
   title: Harpy           # Your custom website title; keep it short.
-  label: v0.4.0
+  label: v0.5.0
   logo: static/favicon.png          # Path to a logo file.
   logoDark: static/favicon.png # Path to a logo file to use in dark mode.
   logoAlign: left

snakemake.md

@@ -26,9 +26,11 @@ is allowed. The reserved (**forbidden**) arguments are:
 - `--directory`
 - `--cores`
 - `--snakefile`
-- `--config`
+- `--configfile`
 - `--rerun-incomplete`
 - `--nolock`
+- `--use-conda`
+- `--conda-prefix`
 !!!
 
 ### Common use cases
@@ -42,14 +44,14 @@ run the Harpy workflow. Useful for knowing what you're getting yourself into
 ahead of time. It's also useful for debugging during development. Here is an 
 example of dry-running variant calling:
 ```bash
-harpy variants snp -g genome.fasta  -d Align/ema -s "--dry-run"
+harpy snp mpileup -g genome.fasta  -d Align/ema -s "--dry-run"
 ```
 ==- Specific file target
 Sometimes you want to generate a specific intermediate file (or files) rather than running the entire module to completion. For example,
 you want the beadtag report Harpy makes from the output of `EMA count`. To do this, just list the file/files (relative
 to your working directory) without any flags. Example for the beadtag report:
 ```bash
-harpy align -g genome.fasta -d QC/ -t 4 -s "Align/ema/stats/reads.bxstats.html"
+harpy align bwa -g genome.fasta -d QC/ -t 4 -s "Align/ema/stats/reads.bxstats.html"
 ```
 This of course necessitates knowing the names of the files ahead of time. See the individual modules for a breakdown of expected outputs. 
 
@@ -62,6 +64,6 @@ your files into that workspace storage to make sure you keep the output of your
 you may use `--shadow-prefix <dirname>` where `<dirname>` is the path to the mandatory directory you need to work out of. By 
 configuring this "shadow directory" setting, Snakemake will automatically move the files in/out of that directory for you:
 ```bash
-harpy variants sv --method leviathan -g genome.fasta  -d Align/bwa --threads 8 -p samples.groups -s "--shadow-prefix /SCRATCH/username/"
+harpy sv leviathan -g genome.fasta  -d Align/bwa --threads 8 -p samples.groups -s "--shadow-prefix /SCRATCH/username/"
 ```
 ===