[BUMP] version 1.3.0

.github/workflows/ci.yml

@@ -37,13 +37,13 @@ jobs:
 
       - name: Build new docker image
         if: env.MATCHED_FILES
-        run: docker build --no-cache . -t nfcore/hic:dev
+        run: docker build --no-cache . -t nfcore/hic:1.3.0
 
       - name: Pull docker image
         if: ${{ !env.MATCHED_FILES }}
         run: |
           docker pull nfcore/hic:dev
-          docker tag nfcore/hic:dev nfcore/hic:dev
+          docker tag nfcore/hic:dev nfcore/hic:1.3.0
 
       - name: Install Nextflow
         env:
@@ -54,4 +54,4 @@ jobs:
 
       - name: Run pipeline with test data
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker
\ No newline at end of file

CHANGELOG.md

@@ -3,11 +3,12 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v1.3.0dev
+## v1.3.0 - 2021-13-05
 
 * Fix bug in stats export
 * Change the /tmp/ folder by ./tmp/ folder so that all tmp files are now in the work (#24)
 * Add `--hicpro_maps` options to generate the raw and normalized HiC-Pro maps. The default is now to use cooler
+* Add chromosome compartments calling with cooltools (#53)
 * Add HiCExplorer distance decay quality control (#54)
 * Add HiCExplorer TADs calling (#55)
 * Add insulation score TADs calling (#55)

Dockerfile

@@ -10,11 +10,11 @@ COPY environment.yml /
 RUN conda env create --quiet -f /environment.yml && conda clean -a
 
 # Add conda installation dir to PATH (instead of doing 'conda activate')
-ENV PATH /opt/conda/envs/nf-core-hic-1.3.0dev/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-hic-1.3.0/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-hic-1.3.0dev > nf-core-hic-1.3.0dev.yml
+RUN conda env export --name nf-core-hic-1.3.0 > nf-core-hic-1.3.0.yml
 
 # Instruct R processes to use these empty files instead of clashing with a local version
 RUN touch .Rprofile
-RUN touch .Renviron
+RUN touch .Renviron
\ No newline at end of file

docs/output.md

@@ -18,7 +18,7 @@ and processes data using the following steps:
 * [Hi-C contact maps](#hic-contact-maps)
 * [Downstream analysis](#downstream-analysis)
   * [Distance decay](#distance-decay)
-  * [Compartments calling](#compartments calling)
+  * [Compartments calling](#compartments-calling)
   * [TADs calling](#tads-calling)
 * [MultiQC](#multiqc) - aggregate report and quality controls, describing
 results of the whole pipeline

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-1.3.0dev
+name: nf-core-hic-1.3.0
 channels:
   - conda-forge
   - bioconda
@@ -28,4 +28,4 @@ dependencies:
   - conda-forge::cython=0.29.19
   - pip:
     - cooltools==0.4.0
-    - fanc==0.8.30
+    - fanc==0.8.30
\ No newline at end of file

nextflow.config

@@ -117,7 +117,7 @@ params {
 
 // Container slug. Stable releases should specify release tag!
 // Developmental code should specify :dev
-process.container = 'nfcore/hic:dev'
+process.container = 'nfcore/hic:1.3.0'
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
@@ -225,7 +225,7 @@ manifest {
   description = 'Analysis of Chromosome Conformation Capture data (Hi-C)'
   mainScript = 'main.nf'
   nextflowVersion = '>=20.04.0'
-  version = '1.3.0dev'
+  version = '1.3.0'
 }
 
 // Function to ensure that resource requirements don't go beyond
@@ -259,4 +259,4 @@ def check_max(obj, type) {
       return obj
     }
   }
-}
+}
\ No newline at end of file