Initial commit

.editorconfig

+# EditorConfig is awesome: http://EditorConfig.org
+
+# top-most EditorConfig file
+root = true
+
+[*]
+end_of_line = lf
+insert_final_newline = true
+charset = utf-8
+indent_style = space
+indent_size = 4
+
+[*.{yml,yaml}]
+indent_style = space
+indent_size = 2

.gitattributes

+*.smk linguist-language=Python
+Snakefile linguist-language=Python

.gitignore

+*
+!scripts
+!scripts/*
+!scripts/common
+!scripts/common/*
+scripts/.snakemake*
+!Snakefile
+!config.yaml
+!samples.tsv
+!resources
+!resources/*
+!envs
+!envs/*
+!environment.yaml
+!LICENSE
+!README.md
+!rules
+!rules/*
+!.gitignore
+!.gitattributes
+!.editorconfig
+!.travis.yml
+!.test

.travis.yml

+language: python
+python:
+  # We don't actually use the Travis Python, but this keeps it organized.
+  - "3.6"
+
+install:
+  - sudo apt-get update
+  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+  - bash miniconda.sh -b -p $HOME/miniconda
+  - export PATH="$HOME/miniconda/bin:$PATH"
+  - hash -r
+  - conda config --set always_yes yes --set changeps1 no
+  - conda update -q conda
+  # Useful for debugging any issues with conda
+  - conda info -a
+  - conda config --add channels defaults
+  - conda config --add channels conda-forge
+  - conda config --add channels bioconda
+  # create snakemake env
+  - conda create -q -n snakemake snakemake python=$TRAVIS_PYTHON_VERSION
+  # add additional stuff to setup below
+
+script:
+  - source activate snakemake
+  # run the workflow
+  # put a test case into the subfolder .test (e.g., use https://github.com/snakemake-workflows/ngs-test-data as a submodule)
+  - snakemake --use-conda --directory .test

LICENSE

+MIT License
+
+Copyright (c) 2019, Monica R. Ticlla
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

+# MetagenomicSnake
+
+[![Snakemake](https://img.shields.io/badge/snakemake-≥5.4.4-brightgreen.svg)](https://snakemake.bitbucket.io)
+[![Build Status](https://travis-ci.org/snakemake-workflows/metagenomicsnake.svg?branch=master)](https://travis-ci.org/snakemake-workflows/metagenomicsnake)
+
+## Description
+
+MetagenomicSnake is a new Snakemake workflow for analysis of metagenomic datasets from human microbiomes.
+
+## Authors
+
+* Monica R. Ticlla (@mticllacc)
+
+## Requirements
+
+### Datasets
+- Paired-end Illumina sequences
+
+### Dependencies
+- Snakemake >= 5.4.4
+- Singularity >= 2.6
+
+## Usage
+
+### Simple
+
+#### Step 1: Install workflow
+
+If you simply want to use this workflow, download and extract the [latest release](https://github.com/snakemake-workflows/metagenomicsnake/releases).
+If you intend to modify and further extend this workflow or want to work under version control, fork this repository as outlined in [Advanced](#advanced). The latter way is recommended.
+
+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).
+
+#### Step 2: Configure workflow
+
+Configure the workflow according to your needs via editing the file `config.yaml`.
+
+#### Step 3: Execute workflow
+
+Test your configuration by performing a dry-run via
+
+    snakemake --use-conda -n
+
+Execute the workflow locally via
+
+    snakemake --use-conda --cores $N
+
+using `$N` cores or run it in a cluster environment via
+
+    snakemake --use-conda --cluster qsub --jobs 100
+
+or
+
+    snakemake --use-conda --drmaa --jobs 100
+
+If you not only want to fix the software stack but also the underlying OS, use
+
+    snakemake --use-conda --use-singularity
+
+in combination with any of the modes above.
+See the [Snakemake documentation](https://snakemake.readthedocs.io/en/stable/executable.html) for further details.
+
+# Step 4: Investigate results
+
+After successful execution, you can create a self-contained interactive HTML report with all results via:
+
+    snakemake --report report.html
+
+This report can, e.g., be forwarded to your collaborators.
+
+### Advanced
+
+The following recipe provides established best practices for running and extending this workflow in a reproducible way.
+
+1. [Fork](https://help.github.com/en/articles/fork-a-repo) the repo to a personal or lab account.
+2. [Clone](https://help.github.com/en/articles/cloning-a-repository) the fork to the desired working directory for the concrete project/run on your machine.
+3. [Create a new branch](https://git-scm.com/docs/gittutorial#_managing_branches) (the project-branch) within the clone and switch to it. The branch will contain any project-specific modifications (e.g. to configuration, but also to code).
+4. Modify the config, and any necessary sheets (and probably the workflow) as needed.
+5. Commit any changes and push the project-branch to your fork on github.
+6. Run the analysis.
+7. Optional: Merge back any valuable and generalizable changes to the [upstream repo](https://github.com/snakemake-workflows/metagenomicsnake) via a [**pull request**](https://help.github.com/en/articles/creating-a-pull-request). This would be **greatly appreciated**.
+8. Optional: Push results (plots/tables) to the remote branch on your fork.
+9. Optional: Create a self-contained workflow archive for publication along with the paper (snakemake --archive).
+10. Optional: Delete the local clone/workdir to free space.
+
+
+## Testing
+
+Tests cases are in the subfolder `.test`. They are automtically executed via continuous integration with Travis CI.

Snakefile

+# The main entry point of your workflow.
+# After configuring, running snakemake -n in a clone of this repository should successfully execute a dry-run of the workflow.
+
+
+configfile: "config.yaml"
+report: "report/workflow.rst"
+
+# Allow users to fix the underlying OS via singularity.
+singularity: "docker://continuumio/miniconda3"
+
+
+rule all:
+    input:
+        # The first rule should define the default target files
+        # Subsequent target rules can be specified below. They should start with all_*.
+
+
+include: "rules/other.smk"

config.yaml

+# This file should contain everything to configure the workflow on a global scale.
+# In case of sample based data, it should be complemented by a samples.tsv file that contains
+# one row per sample. It can be parsed easily via pandas.

envs/myenv.yaml

+# conda environments needed for the workflow should be stored here.

rules/other.smk

+# An example collection of Snakemake rules imported in the main Snakefile.

scripts/common.py

+# Any Python script in the scripts folder will be able to import from this module.