diff --git a/Modules/SV/leviathan.md b/Modules/SV/leviathan.md index 929dff0f7..531d2d872 100644 --- a/Modules/SV/leviathan.md +++ b/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 ` or manually -- if created with `harpy extra -p`, all the samples will be assigned to group `pop1` +- create with `harpy extra popgroup -d ` 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 diff --git a/Modules/SV/naibr.md b/Modules/SV/naibr.md index 959e55cdd..7269dce58 100644 --- a/Modules/SV/naibr.md +++ b/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 ` or manually -- if created with `harpy extra -p`, all the samples will be assigned to group `pop1` +- create with `harpy extra popgroup -d ` 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 diff --git a/Modules/snp.md b/Modules/snp.md index 1a3029979..511a183b6 100644 --- a/Modules/snp.md +++ b/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 ` 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 ` 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 diff --git a/commonoptions.md b/commonoptions.md index d7f3931a8..8b22adef0 100644 --- a/commonoptions.md +++ b/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 | diff --git a/retype.yml b/retype.yml index 92fca628e..e7af66154 100644 --- a/retype.yml +++ b/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 diff --git a/snakemake.md b/snakemake.md index 065da352e..c69c12340 100644 --- a/snakemake.md +++ b/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 ` where `` 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/" ``` ===