diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 734d985bda7b57a590be1f60487f2220a45f8c71..0f0db1a211d8626b14bb0d38fa65e12c819d5030 100644 --- a/.github/workflows/ci.yml +++ b/.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 ${GITHUB_WORKSPACE} -profile test,docker \ No newline at end of file diff --git a/CHANGELOG.md b/CHANGELOG.md index cbc5699280ee52cb6fdaba41e6587b219f840a62..5f781faafaab20204a3f66205e3366456e916514 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,11 +3,12 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v1.3.0dev +## v1.3.0 - 2021-13-05 * Fix bug in stats export * Change the /tmp/ folder by ./tmp/ folder so that all tmp files are now in the work (#24) * Add `--hicpro_maps` options to generate the raw and normalized HiC-Pro maps. The default is now to use cooler +* Add chromosome compartments calling with cooltools (#53) * Add HiCExplorer distance decay quality control (#54) * Add HiCExplorer TADs calling (#55) * Add insulation score TADs calling (#55) diff --git a/Dockerfile b/Dockerfile index 18af828827fec11b7c15b7278c9b4591b8bc00dc..8490e29545a1aa84b13fecc14bdf5c18d1e2d5d8 100644 --- a/Dockerfile +++ b/Dockerfile @@ -10,11 +10,11 @@ COPY environment.yml / RUN conda env create --quiet -f /environment.yml && conda clean -a # Add conda installation dir to PATH (instead of doing 'conda activate') -ENV PATH /opt/conda/envs/nf-core-hic-1.3.0dev/bin:$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 diff --git a/docs/output.md b/docs/output.md index d73bce332fae54e6248816828b963d38b24f5eac..8b3fd0a40579b5ee19f107acdf6f531a8d98702f 100644 --- a/docs/output.md +++ b/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 diff --git a/environment.yml b/environment.yml index 85def0f721d3b200671fe2cc00c383dc5b226b54..9d357598b764a0dbf9adbeccd3fe6767828fa844 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-1.3.0dev +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 diff --git a/nextflow.config b/nextflow.config index c9fbf5424ba1b4f0ca5d00d54e388d134e390d9e..7296cc2af450343641614486f3cc232b25c71243 100644 --- a/nextflow.config +++ b/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