Merge pull request #65 from nservant/dev

Dev

.github/workflows/ci.yml

@@ -22,7 +22,7 @@ jobs:
       - name: Pull docker image
         run: |
           docker pull nfcore/hic:dev
-          docker tag nfcore/hic:dev nfcore/hic:dev
+          docker tag nfcore/hic:dev nfcore/hic:1.2.0
       - name: Run pipeline with test data
         run: |
           # nf-core: You can customise CI pipeline run tests as required

CHANGELOG.md

@@ -3,11 +3,11 @@
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
-## v1.2.0dev - 2020-05-12
+## v1.2.0 - 2020-06-18
 
 ### `Added`
 
-* Bump v1.2.0dev
+* Bump v1.2.0
 * Merge template nf-core 1.9
 * Move some options to camel_case
 * Update python scripts for python3
@@ -33,6 +33,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### `Fixed`
 
+* Fix error in doc for Arima kit usage
 * Sort output of `get_valid_interaction` process as the input files of `remove_duplicates`
 are expected to be sorted (sort -m)
 

Dockerfile

@@ -7,8 +7,8 @@ RUN apt-get update && apt-get install -y gcc g++ && apt-get clean -y
 
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/nf-core-hic-1.2.0dev/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-hic-1.2.0/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-hic-1.2.0dev > nf-core-hic-1.2.0dev.yml
+RUN conda env export --name nf-core-hic-1.2.0 > nf-core-hic-1.2.0.yml
 

docs/usage.md

@@ -398,7 +398,7 @@ Here are a few examples:
 * DpnII: ^GATC
 * BglII: A^GATCT
 * HindIII: A^AGCTT
-* ARIMA kit: ^GATC,^GANT
+* ARIMA kit: ^GATC,G^ANTC
 
 Note that multiples restriction motifs can be provided (comma-separated) and
 that 'N' base are supported.
@@ -419,7 +419,7 @@ Default: 'AAGCTAGCTT'
 --ligation_site '[Ligation motif]'
 ```
 
-Exemple of the ARIMA kit: GATCGATC,GATCGANT,GANTGATC,GANTGANT
+Exemple of the ARIMA kit: GATCGATC,GANTGATC,GANTANTC,GATCANTC
 
 #### `--min_restriction_fragment_size`
 

environment.yml

 # You can use this file to create a conda environment for this pipeline:
 #   conda env create -f environment.yml
-name: nf-core-hic-1.2.0dev
+name: nf-core-hic-1.2.0
 channels:
   - conda-forge
   - bioconda

nextflow.config

@@ -64,7 +64,7 @@ params {
 
 // Container slug. Stable releases should specify release tag!
 // Developmental code should specify :dev
-process.container = 'nfcore/hic:dev'
+process.container = 'nfcore/hic:1.2.0'
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
@@ -135,7 +135,7 @@ manifest {
   description = 'Analysis of Chromosome Conformation Capture data (Hi-C)'
   mainScript = 'main.nf'
   nextflowVersion = '>=19.10.0'
-  version = '1.2.0dev'
+  version = '1.2.0'
 }
 
 // Function to ensure that resource requirements don't go beyond