Merge pull request #5 from nf-core/dev

Assembly/Binning

.gitignore

@@ -3,3 +3,5 @@ work/
 results/
 .DS_Store
 tests/test_data
+.vscode
+db/

.travis.yml

@@ -11,9 +11,9 @@ before_install:
   # PRs made to 'master' branch should always orginate from another repo or the 'dev' branch
   - '[ $TRAVIS_PULL_REQUEST = "false" ] || [ $TRAVIS_BRANCH != "master" ] || ([ $TRAVIS_PULL_REQUEST_SLUG = $TRAVIS_REPO_SLUG ] && [ $TRAVIS_PULL_REQUEST_BRANCH = "dev" ])'
   # Pull the docker image first so the test doesn't wait for this
-  - docker pull hadrieng/mag
+  - docker pull nfcore/mag:dev
   # Fake the tag locally so that the pipeline runs properly
-  - docker tag hadrieng/mag hadrieng/mag:0.1.0
+  - docker tag nfcore/mag:dev nfcore/mag:1.0.0
 
 install:
   # Install Nextflow
@@ -27,11 +27,11 @@ install:
   - cd ${TRAVIS_BUILD_DIR}
 
 env:
-  - NXF_VER=0.30.0 # Specify a minimum NF version that should be tested and work
+  - NXF_VER='0.32.0' # Specify a minimum NF version that should be tested and work
   - NXF_VER='' # Plus: get the latest NF version and check, that it works
 
 script:
   # Lint the pipeline code
   - nf-core lint ${TRAVIS_BUILD_DIR}
   # Run the pipeline with the test profile
-  - make test
+  - nextflow run main.nf -profile test,docker

CHANGELOG.md

@@ -1,3 +1,3 @@
+## nf-core/mag version 1.0.0 -
 
-## nf-core/mag version 0.1.0dev -
 Initial release of nf-core/mag, created with the [nf-core](http://nf-co.re/) template.

Dockerfile

@@ -1,8 +1,9 @@
 FROM nfcore/base
-=======
-MAINTAINER Hadrien Gourlé <[email protected]>
+
+LABEL maintainer="Hadrien Gourlé <[email protected]>"
 LABEL description="Docker image containing all requirements for nf-core/mag pipeline"
 
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/nf-core-mag-1.0dev/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-mag-1.0.0/bin:$PATH
+

README.md

@@ -1,28 +1,32 @@
-# [UNDER CONSTRUCTION] nf-core/mag
+# ![mag](https://raw.githubusercontent.com/nf-core/mag/master/docs/images/mag_logo.png)
+
+# nf-core/mag
+
 **Assembly, binning and annotation of metagenomes**
 
 [![Build Status](https://travis-ci.org/nf-core/mag.svg?branch=master)](https://travis-ci.org/nf-core/mag)
-[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.30.0-brightgreen.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.32.0-brightgreen.svg)](https://www.nextflow.io/)
 
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](http://bioconda.github.io/)
 [![Docker](https://img.shields.io/docker/automated/hadrieng/mag.svg)](https://hub.docker.com/r/hadrieng/mag)
-![Singularity Container available](
-https://img.shields.io/badge/singularity-available-7E4C74.svg)
+![Singularity Container available](https://img.shields.io/badge/singularity-available-7E4C74.svg)
 
 ### Introduction
-The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.
 
+The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.
 
 ### Documentation
+
 The nf-core/mag pipeline comes with documentation about the pipeline, found in the `docs/` directory:
 
 1. [Installation](docs/installation.md)
 2. Pipeline configuration
-    * [Local installation](docs/configuration/local.md)
-    * [Adding your own system](docs/configuration/adding_your_own.md)
+   - [Local installation](docs/configuration/local.md)
+   - [Adding your own system](docs/configuration/adding_your_own.md)
 3. [Running the pipeline](docs/usage.md)
 4. [Output and how to interpret the results](docs/output.md)
 5. [Troubleshooting](docs/troubleshooting.md)
 
 ### Credits
+
 This pipeline was written by [Hadrien Gourlé](https://hadriengourle.com) at [SLU](https://slu.se).

Singularity

@@ -5,10 +5,10 @@ Bootstrap:docker
 =======
     MAINTAINER Hadrien Gourlé <[email protected]>
     DESCRIPTION Singularity image containing all requirements for nf-core/mag pipeline
-    VERSION 0.1.0
+    VERSION 1.0.0
 
 %environment
-    PATH=/opt/conda/envs/nf-core-mag-1.0dev/bin:$PATH
+    PATH=/opt/conda/envs/nf-core-mag-1.0.0/bin:$PATH
     export PATH
 
 %files

bin/filter_ssu.py

@@ -0,0 +1,61 @@
+#!/usr/bin/env python
+
+from __future__ import print_function
+
+import os
+import sys
+import argparse
+
+
+def filter(args):
+    """filter blast hits from refinem
+
+    Args:
+        args (obj): arguments from argparse
+    """
+    with open(args.ssu, "r") as i, open(args.output, "w") as o:
+        header = i.readline()
+        for line in i:
+            splitted_line = line.split()
+            evalue = splitted_line[7]
+            align_length = splitted_line[8]
+            percent_ident = splitted_line[9]
+
+            if int(evalue) <= args.evalue:
+                o.write(line)
+            else:
+                continue
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        prog="filter_ssu.py",
+        usage="filter ssu hits from refinem"
+    )
+    parser.add_argument(
+        "--evalue",
+        help="evalue threshold"
+    )
+    parser.add_argument(
+        "ssu",
+        metavar="ssu.tsv",
+        help="ssu tsv file generated by refinem"
+    )
+    parser.add_argument(
+        "output",
+        metavar="output.tsv",
+        default="output.tsv",
+        help="output file name"
+    )
+    parser.set_defaults(func=filter)
+    args = parser.parse_args()
+
+    try:
+        args.func(args)
+    except AttributeError as e:
+        parser.print_help()
+        raise
+
+
+if __name__ == "__main__":
+    main()