diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 34410af1c7acb71904ab68cd8cd99e2475776381..a7f734daefe5cd9b35292fd669e0ce404ecf397e 100644 --- a/.github/workflows/ci.yml +++ b/.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 diff --git a/CHANGELOG.md b/CHANGELOG.md index 5543ec9a1028cd8a5f9acfdc72a93c24d3d05fca..685212830b29d24e0c02269c104f83284d4994c1 100644 --- a/CHANGELOG.md +++ b/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) diff --git a/Dockerfile b/Dockerfile index cbb686fa3407b15196c7673932d1b8e9db6f721a..5aecaa6236984f7b4a2aa7b79422b454b6e74f9b 100644 --- a/Dockerfile +++ b/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 diff --git a/docs/usage.md b/docs/usage.md index 66d19457950bbd8a5038bad785862b5f558cb640..cef7bf3b60752e918d11dbfb9023aed8ca2d9242 100644 --- a/docs/usage.md +++ b/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` diff --git a/environment.yml b/environment.yml index fd6119ad8dc77461ad220cadf76747a518b47294..b9e6c0218828ade3813a07574bec46380ac7d3f9 100644 --- a/environment.yml +++ b/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-hic-1.2.0dev +name: nf-core-hic-1.2.0 channels: - conda-forge - bioconda diff --git a/nextflow.config b/nextflow.config index 7ad9a223c8d0a40e16fdc7727f78c217fac76364..f7a5af77d3153338ba5b149f37262cac2439cd9c 100644 --- a/nextflow.config +++ b/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