Merge pull request #462 from ewels/conda-py3

Conda - use Python 3
nf-core · Dec 10, 2019 · c8d3c57 · c8d3c57
2 parents bddec20 + 6a971d5
commit c8d3c57
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -38,9 +38,16 @@
 * Added support for nf-tower in the travis tests, using public mailbox [email protected]
 * Add link to [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) and [Semantic Versioning](http://semver.org/spec/v2.0.0.html) to CHANGELOG
 * Adjusted `.travis.yml` checks to allow for `patch` branches to be tested
+* Add Python 3.7 dependency to the `environment.yml` file
 * Remove awsbatch profile cf [nf-core/configs#71](https://github.com/nf-core/configs/pull/71)
 * Make `scrape_software_versions.py` compatible with Python3 to enable miniconda3 in    [base image PR](https://github.com/nf-core/tools/pull/462)
 
+### Base Docker image
+
+* Use miniconda3 instead of miniconda for a Python 3k base environment
+  * If you still need Python 2 for your pipeline, add `conda-forge::python=2.7.4` to the dependencies in your `environment.yml`
+* Update conda version to 4.7.12
+
 ### Other
 
 * Updated Base Dockerfile to Conda 4.7.10

diff --git a/Dockerfile b/Dockerfile
@@ -1,6 +1,6 @@
-FROM continuumio/miniconda:4.7.10
+FROM continuumio/miniconda3:4.7.12
 LABEL authors="[email protected],[email protected]" \
       description="Docker image containing base requirements for the nfcore pipelines"
 
 # Install procps so that Nextflow can poll CPU usage
-RUN apt-get update && apt-get install -y procps && apt-get clean -y
+RUN apt-get update && apt-get install -y procps && apt-get clean -y
diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/README.md b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/README.md
@@ -31,6 +31,7 @@ nextflow run {{ cookiecutter.name }} -profile test,<docker/singularity/conda/ins
 iv. Start running your own analysis!
 
 <!-- TODO nf-core: Update the default command above used to run the pipeline -->
+
 ```bash
 nextflow run {{ cookiecutter.name }} -profile <docker/singularity/conda/institute> --reads '*_R{1,2}.fastq.gz' --genome GRCh37
 ```

diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/docs/usage.md b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/docs/usage.md
@@ -2,8 +2,6 @@
 
 ## Table of contents
 
-<!-- Install Atom plugin markdown-toc-auto for this ToC to auto-update on save -->
-<!-- TOC START min:2 max:3 link:true asterisk:true update:true -->
 * [Table of contents](#table-of-contents)
 * [Introduction](#introduction)
 * [Running the pipeline](#running-the-pipeline)
@@ -39,7 +37,6 @@
   * [`--plaintext_email`](#--plaintext_email)
   * [`--monochrome_logs`](#--monochrome_logs)
   * [`--multiqc_config`](#--multiqc_config)
-<!-- TOC END -->
 
 ## Introduction
 
@@ -185,6 +182,7 @@ params {
 ```
 
 <!-- TODO nf-core: Describe reference path flags -->
+
 ### `--fasta`
 
 If you prefer, you can specify the full path to your reference genome when you run the pipeline:

diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/environment.yml b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/environment.yml
@@ -6,6 +6,7 @@ channels:
   - bioconda
   - defaults
 dependencies:
+  - conda-forge::python=3.7.3
   # TODO nf-core: Add required software dependencies here
   - bioconda::fastqc=0.11.8
   - bioconda::multiqc=1.7
-Original file line number
+Diff line change
@@ Expand Up @@
     iv. Start running your own analysis!
     <!-- TODO nf-core: Update the default command above used to run the pipeline -->
     ```bash
     nextflow run {{ cookiecutter.name }} -profile <docker/singularity/conda/institute> --reads '*_R{1,2}.fastq.gz' --genome GRCh37
     ```
@@ Expand Down @@