From 55e7eaaff5dc2438739ee073e3d5ab03c751c619 Mon Sep 17 00:00:00 2001
From: ticlla <monicaroxana.ticllaccenhua@unibas.ch>
Date: Tue, 19 Nov 2019 15:08:47 -0500
Subject: [PATCH] update README with information about metadata file for
samples
---
README.md | 24 +++++++++++++++++-------
1 file changed, 17 insertions(+), 7 deletions(-)
diff --git a/README.md b/README.md
index a2b3255..b4535b5 100644
--- a/README.md
+++ b/README.md
@@ -6,7 +6,9 @@
## Description
-MetaSnk is a modularized Snakemake workflow for the analysis of metagenomic datasets from human microbiomes.
+MetaSnk is a reproducible and scalable modularized Snakemake workflow for the analysis of metagenomic datasets from human microbiomes.
+
+MetaSnk wraps system and software dependencies within Singularity containers.
### Modules:
- [rawQC](README_rawQC.md)
@@ -59,6 +61,13 @@ MetaSnk is a modularized Snakemake workflow for the analysis of metagenomic data
Notice that you can have multiple paired fastq files per sample, but each SampleID-RUN_LANE combination must be unique.
+- sample_metadata.tsv: a tab-delimited table with at least two column fields
+
+ ```
+ sampleID SubjectID
+
+ ```
+
## Usage
### Simple
@@ -79,6 +88,13 @@ If you intend to modify and further extend this workflow or want to work under v
In any case, if you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this repository and, if available, its DOI (see above).
+##### Create minimal environment
+
+Some rules will use this environment.
+
+ conda env create -f ./envs/MetaSnk.yaml
+ conda activate MetaSnk
+
##### Download singularity containers and reference databases
MetaSnk wraps system requirements and software dependencies within singularity containers.
Download these containers by running rule 'pullSIFS' :
@@ -99,12 +115,6 @@ MetaSnK uses reference databases that need to be downloaded to the $METASNK_DBS
snakemake --profile ./profiles/local buildDBS
-##### Create minimal environment
-
-Some rules will use this environment.
-
- conda env create -f ./envs/MetaSnk.yaml
-
#### Step 2: Configure workflow
Configure the workflow according to your needs via editing the file `config.yaml`.
--
GitLab