Merge pull request #165 from drpatelh/master

Bump versions to 1.2.0

Author: drpatelh

.github/workflows/ci.yml

@@ -35,13 +35,13 @@ jobs:
 
       - name: Build new docker image
         if: env.GIT_DIFF
-        run: docker build --no-cache . -t nfcore/chipseq:dev
+        run: docker build --no-cache . -t nfcore/chipseq:1.2.0
 
       - name: Pull docker image
         if: ${{ !env.GIT_DIFF }}
         run: |
           docker pull nfcore/chipseq:dev
-          docker tag nfcore/chipseq:dev nfcore/chipseq:dev
+          docker tag nfcore/chipseq:dev nfcore/chipseq:1.2.0
 
       - name: Install Nextflow
         run: |
@@ -75,13 +75,13 @@ jobs:
 
       - name: Build new docker image
         if: env.GIT_DIFF
-        run: docker build --no-cache . -t nfcore/chipseq:dev
+        run: docker build --no-cache . -t nfcore/chipseq:1.2.0
 
       - name: Pull docker image
         if: ${{ !env.GIT_DIFF }}
         run: |
           docker pull nfcore/chipseq:dev
-          docker tag nfcore/chipseq:dev nfcore/chipseq:dev
+          docker tag nfcore/chipseq:dev nfcore/chipseq:1.2.0
 
       - name: Install Nextflow
         run: |

CHANGELOG.md

@@ -3,21 +3,19 @@
 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).
 
-## [1.2.0] - 2020-06-04
+## [1.2.0] - 2020-07-02
 
 ### `Added`
 
 * [#138](https://github.com/nf-core/chipseq/issues/138) - Add social preview image
 * [#153](https://github.com/nf-core/chipseq/issues/153) - Add plotHeatmap
 * [#159](https://github.com/nf-core/chipseq/issues/159) - expose bwa mem -T parameter
 * [nf-core/atacseq#63](https://github.com/nf-core/atacseq/issues/63) - Added multicore support for Trim Galore!
-* [nf-core/atacseq#71](https://github.com/nf-core/atacseq/issues/71) - consensus_peaks.mLb.clN.boolean.intersect.plot.pdf not generated
 * [nf-core/atacseq#75](https://github.com/nf-core/atacseq/issues/75) - Include gene annotation versions in multiqc report
 * [nf-core/atacseq#76](https://github.com/nf-core/atacseq/issues/76) - featureCounts coupled to DESeq2
 * [nf-core/atacseq#79](https://github.com/nf-core/atacseq/issues/79) - Parallelize DESeq2
 * [nf-core/atacseq#97](https://github.com/nf-core/atacseq/issues/97) - PBC1, PBC2 from pipeline?
 * [nf-core/atacseq#107](https://github.com/nf-core/atacseq/issues/107) - Add options to change MACS2 parameters
-* [nf-core/atacseq#109](https://github.com/nf-core/atacseq/issues/109) - Specify custom gtf but gene bed is not generated from that gtf?
 * Regenerated screenshots and added collapsible sections for output files in `docs/output.md`
 * Update template to tools `1.9`
 * Replace `set` with `tuple` and `file()` with `path()` in all processes
@@ -34,53 +32,54 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### `Removed`
 
-* `--tss_bed`
+* `--tss_bed` parameter
 
 ### `Fixed`
 
 * [#118](https://github.com/nf-core/chipseq/issues/118) - Running on with SGE
 * [#132](https://github.com/nf-core/chipseq/issues/132) - BigWig Error: sort: cannot create temporary file in '': Read-only file system
 * [#154](https://github.com/nf-core/chipseq/issues/154) - computeMatrix.val.mat.gz files not zipped
+* [nf-core/atacseq#71](https://github.com/nf-core/atacseq/issues/71) - consensus_peaks.mLb.clN.boolean.intersect.plot.pdf not generated
 * [nf-core/atacseq#73](https://github.com/nf-core/atacseq/issues/73) - macs_annotatePeaks.mLb.clN.summary.txt file is not created
 * [nf-core/atacseq#86](https://github.com/nf-core/atacseq/issues/86) - bug in the plot_homer_annotatepeaks.r script
 * [nf-core/atacseq#102](https://github.com/nf-core/atacseq/issues/102) - Incorrect Group ID assigned by featurecounts_deseq2.r
+* [nf-core/atacseq#109](https://github.com/nf-core/atacseq/issues/109) - Specify custom gtf but gene bed is not generated from that gtf?
 * Make executables in `bin/` compatible with Python 3
 
 ### `Dependencies`
 
-* Add python `3.7.6`
+* Add bioconductor-biocparallel `1.20.0`
 * Add markdown `3.2.2`
-* Add pymdown-extensions `7.1`
-* Add pygments `2.6.1`
 * Add pigz `2.3.4`
-* Add r-tidyr `1.1.0`
+* Add pygments `2.6.1`
+* Add pymdown-extensions `7.1`
+* Add python `3.7.6`
 * Add r-reshape2 `1.4.4`
-* Add bioconductor-biocparallel `1.20.0`
+* Add r-tidyr `1.1.0`
+* Update bedtools `2.27.1` -> `2.29.2`
+* Update bioconductor-deseq2 `1.20.0` -> `1.26.0`
+* Update bioconductor-vsn `3.46.0` -> `3.54.0`
+* Update deeptools `3.2.1` -> `3.4.3`
+* Update fastqc `0.11.8` -> `0.11.9`
 * Update gawk `4.2.1` -> `5.1.0`
+* Update homer `4.9.1` -> `4.11`
+* Update macs2 `2.1.2` -> `2.2.7.1`
+* Update multiqc `1.7` -> `1.8`
+* Update phantompeakqualtools `1.2` -> `1.2.2`
+* Update picard `2.19.0` -> `2.23.1`
+* Update pysam `0.15.2` -> `0.15.3`
 * Update r-base `3.4.1` -> `3.6.2`
-* Update r-optparse `1.6.0` -> `1.6.6`
 * Update r-ggplot2 `3.1.0` -> `3.3.2`
-* Update r-pheatmap `1.0.10` -> `1.0.12`
 * Update r-lattice `0.20_35` -> `0.20_41`
-* Update r-upsetr `1.3.3` -> `1.4.0`
+* Update r-optparse `1.6.0` -> `1.6.6`
+* Update r-pheatmap `1.0.10` -> `1.0.12`
 * Update r-scales `1.0.0` -> `1.1.1`
+* Update r-upsetr `1.3.3` -> `1.4.0`
 * Update r-xfun `0.3` -> `0.15`
-* Update fastqc `0.11.8` -> `0.11.9`
-* Update trim-galore `0.5.0` -> `0.6.5`
 * Update samtools `1.9` -> `1.10`
-* Update picard `2.19.0` -> `2.23.1`
-* Update pysam `0.15.2` -> `0.15.3`
-* Update bedtools `2.27.1` -> `2.29.2`
-* Update ucsc-bedgraphtobigwig `377` -> `357`
-* Update deeptools `3.2.1` -> `3.4.3`
-* Update macs2 `2.1.2` -> `2.2.7.1`
-* Update homer `4.9.1` -> `4.11`
 * Update subread `1.6.4` -> `2.0.1`
-* Update multiqc `1.7` -> `1.8`  
-* Update phantompeakqualtools `1.2` -> `1.2.2`
-* Update bioconductor-deseq2 `1.20.0` -> `1.26.0`
-* Update bioconductor-vsn `3.46.0` -> `3.54.0`
-* Remove r-reshape2 `1.4.3`
+* Update trim-galore `0.5.0` -> `0.6.5`
+* Update ucsc-bedgraphtobigwig `377` -> `357`
 
 ## [1.1.0] - 2019-11-05
 

Dockerfile

@@ -7,10 +7,10 @@ COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
 
 # Add conda installation dir to PATH (instead of doing 'conda activate')
-ENV PATH /opt/conda/envs/nf-core-chipseq-1.1.1dev/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-chipseq-1.2.0/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-chipseq-1.1.1dev > nf-core-chipseq-1.1.1dev.yml
+RUN conda env export --name nf-core-chipseq-1.2.0 > nf-core-chipseq-1.2.0.yml
 
 # Instruct R processes to use these empty files instead of clashing with a local version
 RUN touch .Rprofile

environment.yml

@@ -1,6 +1,6 @@
 # You can use this file to create a conda environment for this pipeline:
 #   conda env create -f environment.yml
-name: nf-core-chipseq-1.1.1dev
+name: nf-core-chipseq-1.2.0
 channels:
   - conda-forge
   - bioconda

nextflow.config

@@ -96,7 +96,7 @@ params {
 
 // Container slug. Stable releases should specify release tag!
 // Developmental code should specify :dev
-process.container = 'nfcore/chipseq:dev'
+process.container = 'nfcore/chipseq:1.2.0'
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
@@ -169,7 +169,7 @@ manifest {
   description = 'ChIP-seq peak-calling and differential analysis pipeline.'
   mainScript = 'main.nf'
   nextflowVersion = '>=19.10.0'
-  version = '1.1.1dev'
+  version = '1.2.0'
 }
 
 // Function to ensure that resource requirements don't go beyond