From ad83b64bc1a0cef8617a12f69b3f9294d5d07578 Mon Sep 17 00:00:00 2001 From: "Jalees A. Nasir" <60946013+jaleezyy@users.noreply.github.com> Date: Thu, 16 Feb 2023 15:47:35 -0500 Subject: [PATCH] Update README --- README.md | 40 ++++++++++++++++++++++++++++------------ 1 file changed, 28 insertions(+), 12 deletions(-) diff --git a/README.md b/README.md index 9f93e28..f9cbea7 100644 --- a/README.md +++ b/README.md @@ -87,17 +87,22 @@ To display the help screen: python signal.py -h Output: -usage: signal.py [-h] [-c CONFIGFILE] [-d DIRECTORY] [--cores CORES] [--config-only] [--remove-freebayes] [--add-breseq] [-neg NEG_PREFIX] [--dependencies] +usage: signal.py [-h] [-c CONFIGFILE] [-d DIRECTORY] [--cores CORES] [--config-only] [--remove-freebayes] [--add-breseq] + [-neg NEG_PREFIX] [--dependencies] [-ri] [--unlock] [-F] [-n] [--verbose] [-v] [all ...] [postprocess ...] [ncov_tools ...] -SARS-CoV-2 Illumina GeNome Assembly Line (SIGNAL) aims to take Illumina short-read sequences and perform consensus assembly + variant calling for ongoing surveillance and research efforts towards -the emergent coronavirus: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). +SARS-CoV-2 Illumina GeNome Assembly Line (SIGNAL) aims to take Illumina short-read sequences and perform consensus assembly + +variant calling for ongoing surveillance and research efforts towards the emergent coronavirus: Severe Acute Respiratory Syndrome +Coronavirus 2 (SARS-CoV-2). positional arguments: - all Run SIGNAL with all associated assembly rules. Does not include postprocessing '--configfile' or '--directory' required. The latter will automatically generate a - configuration file and sample table. If both provided, then '--configfile' will take priority - postprocess Run SIGNAL postprocessing on completed SIGNAL run. '--configfile' is required but will be generated if '--directory' is provided - ncov_tools Generate configuration file and filesystem setup required and then execute ncov-tools quality control assessment. '--configfile' is required but will be generated if '-- + all Run SIGNAL with all associated assembly rules. Does not include postprocessing '--configfile' or '-- + directory' required. The latter will automatically generate a configuration file and sample table. If + both provided, then '--configfile' will take priority + postprocess Run SIGNAL postprocessing on completed SIGNAL run. '--configfile' is required but will be generated if ' + --directory' is provided + ncov_tools Generate configuration file and filesystem setup required and then execute ncov-tools quality control + assessment. Requires 'ncov-tools' submodule! '--configfile' is required but will be generated if '-- directory' is provided optional arguments: @@ -108,12 +113,23 @@ optional arguments: Path to directory containing reads. Will be used to generate sample table and configuration file --cores CORES Number of cores. Default = 1 --config-only Generate sample table and configuration file (i.e., config.yaml) and exit. '--directory' required - --remove-freebayes Configuration file generator parameter. Set flag to DISABLE freebayes variant calling (improves overall speed) - --add-breseq Configuration file generator parameter. Set flag to ENABLE optional breseq step (will take more time for analysis to complete) + --remove-freebayes Configuration file generator parameter. Set flag to DISABLE freebayes variant calling (improves overall + speed) + --add-breseq Configuration file generator parameter. Set flag to ENABLE optional breseq step (will take more time for + analysis to complete) -neg NEG_PREFIX, --neg-prefix NEG_PREFIX - Configuration file generator parameter. Comma-separated list of negative sontrol sample name(s) or prefix(es). For example, 'Blank' will cover Blank1, Blank2, etc. Recommend - if running ncov-tools. Will be left empty, if not provided - --dependencies Download data dependencies (under a created 'data' directory) required for SIGNAL analysis and exit. Note: Will override other flags! (~10 GB storage required) + Configuration file generator parameter. Comma-separated list of negative sontrol sample name(s) or + prefix(es). For example, 'Blank' will cover Blank1, Blank2, etc. Recommended if running ncov-tools. Will + be left empty, if not provided + --dependencies Download data dependencies (under a created 'data' directory) required for SIGNAL analysis and exit. + Note: Will override other flags! (~10 GB storage required) + -ri, --rerun-incomplete + Snakemake parameter. Re-run any incomplete samples from a previously failed run + --unlock Snakemake parameter. Remove a lock on the working directory after a failed run + -F, --forceall Snakemake parameter. Force the re-run of all rules regardless of prior output + -n, --dry-run Snakemake parameter. Do not execute anything and only display what would be done + --verbose Snakemake parameter. Display snakemake debugging output + -v, --version Display version number ``` ## Summary: