Changed executable name to fix errors, still need to update README

README.md

@@ -1,22 +1,105 @@
-# SeqQC
+# BioExcel_SeqQC
 
-TO BE UPDATED SOON.
-
-Python scripts for a Sequence Quality Control pipeline, based on workflows
+Python package to run a Sequence Quality Control pipeline, based on workflows
 defined by IGMM.
 
-Each tool can be run standalone, or as a whole workflow.
-
-Requirements:
+## Requirements:
 
 - FastQC
 - Cutadapt
-- Python (only tested with 2.7.10/13)
+- Python 3.x
+- Pyyaml
+
+We recommend using the conda package manager, and making use of virtual 
+environments. This tool also exists in the bioconda channel. This has the 
+benefit of automatically installing all pre-requisites when installing this 
+tool.
+
+## Installation
+
+There are two main ways to install the package.
+
+### Conda package installation
+
+#### Set up a new conda environment (optional):
+
+```bash
+$ conda create -n my_env -c bioconda python=3 
+```
+
+This creates a clean Python3 environment in which to install and run the tool. 
+If you have a conda environment you already wish to use, make sure you add the 
+bioconda channel to the environment, or your conda package as a whole.
+
+#### Install BioExcel_SeqQC
+```bash
+$ conda install bioexcel_seqqc
+```
+
+This one line will install BioExcel_SeqQC and all of it's dependencies.
+
+### Manual installation
+
+If you wish to install manually, follow the steps below. We still recommend 
+using some kind of virtual environment. Before running the workflow, install
+the pre-requisite tools and ensure they are contained in your $PATH
+
+```bash
+$ git clone https://github.com/bioexcel/BioExcel_SeqQC.git
+$ cd BioExcel_SeqQC
+$ python setup.py install
+```
+
+## Usage
+
+Once installed, there are several ways to use the tool. The easiest is to call
+the executable script, which runs the whole workflow based on several options 
+and arguments the user can modify. Find these using
+
+```bash
+$ bioexcel_seqqc -h
+```
+
+An example of basic usage of the pipeline is:
+
+```bash
+$ bioexcel_seqqc --files in1.fa in2.fa --threads 4 --outdir ./output
+```
+
+### Editing configuration for checkFastQC stage
+
+The tool runs an automated set of checks based on output from FastQC. The 
+default decision making is based on our partner preference, but these can be
+changed. First, output an example configuration file (which contains the
+default values):
+
+```bash
+$ bioexcel_seqqc --printconfig
+```
+
+The file lists the summary outputs from FastQC, and what decisions to make 
+depending on whether the files should be trimmed, rechecked, and take into
+account whether they have been trimmed automatically.
+
+### Python Module
+
+In addition to the executable version, the tool is installed as a Python 
+package, so each stage can be imported as a module into other scripts, if the 
+user wishes to perform more unique/complicated/expanded workflows. Each function
+creates and returns a python subprocess.
+
+```python
+import bioexcel_seqqc
+import bioexcel_seqqc.runfastqc as rfq
+import bioexcel_seqqc.runtrim as rt
+
+# Do things before running FastQC
 
-Above packages can be easily obtained via installing BCBio, which also includes packages used in further downstream analysis. - Make sure paths are correctly set up if done so.
+fqc_process = rfq.run_fqc(infiles, fqcdir, tmpdir, threads)
+fqc.wait()
 
-## Future plans
+# Do things after FastQC, and before trimming low quality reads
 
-- Provide CWL-compliant examples and tool-descriptors for basic usage (cannot do loops within CWL so must still use Python as workflow management, but CWL runners could run whole scripts/workflow with correct tool descriptions)
-- Create Singularity container of workflow
-- Make it easier for user to configure logic behind PASS/WARN/FAIL flags from FastQC
+trim_process = rt.trimQC(infiles, trimdir, threads):
+trim_process.wait()
+```

setup.py

@@ -16,7 +16,7 @@
     description=('Sequence Quality Control workflow python package'),
     author='Darren White',
     author_email='[email protected]',
-    scripts=['bin/bioexcel_seqqc'],
+    scripts=['bin/bxcl_seqqc'],
     packages=['bioexcel_seqqc'],
     package_dir={'bioexcel_seqqc': 'bioexcel_seqqc'},
     install_requires=['pyyaml'],