Merge pull request #50 from maxibor/dev

Update environment to fix broken dependancies

.github/workflows/ci.yml

@@ -22,7 +22,7 @@ jobs:
       - name: Pull docker image
         run: |
           docker pull nfcore/coproid:dev
-          docker tag nfcore/coproid:dev nfcore/coproid:1.1
+          docker tag nfcore/coproid:dev nfcore/coproid:1.1.1
       - name: Run pipeline with test data
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker

.github/workflows/linting.yml

@@ -45,6 +45,6 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install nf-core
+          pip install nf-core==1.9
       - name: Run nf-core lint
         run: nf-core lint ${GITHUB_WORKSPACE}

CHANGELOG.md

@@ -1,5 +1,11 @@
 # nf-core/coproid: Changelog
 
+## v.1.1.1
+
+### Fixed
+
+- Fix [#37](https://github.com/nf-core/coproid/issues/37) with conda environment and docker container update
+
 ## v1.1
 
 - Update mapped basepair count to be quicker and include it in report [#14](https://github.com/nf-core/coproid/pull/14)

Dockerfile

@@ -1,15 +1,12 @@
-FROM nfcore/base:1.9
+FROM condaforge/mambaforge
 LABEL authors="Maxime Borry" \
     description="Docker image containing all software requirements for the nf-core/coproid pipeline"
 
 # Install the conda environment
 COPY environment.yml /
-RUN conda env create -f /environment.yml && conda clean -a
-RUN conda env export --name nf-core-coproid-1.1 > nf-core-coproid-1.1.yml
-ENV PATH /opt/conda/envs/nf-core-coproid-1.1/bin:$PATH
-
-# Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-coproid-1.1 > nf-core-coproid-1.1.yml
+RUN mamba env create -f /environment.yml && mamba clean -a
+RUN mamba env export --name nf-core-coproid-1.1.1 > nf-core-coproid-1.1.1.yml
+ENV PATH /opt/conda/envs/nf-core-coproid-1.1.1/bin:$PATH
 
 # Numba cache dir patch
 ENV NUMBA_CACHE_DIR /tmp

environment.yml

@@ -1,32 +1,70 @@
-# You can use this file to create a conda environment for this pipeline:
-#   conda env create -f environment.yml
-name: nf-core-coproid-1.1
+name: nf-core-coproid-1.1.1
 channels:
   - conda-forge
-  - maxibor
   - bioconda
   - defaults
 dependencies:
-  - conda-forge::openblas=0.3.7
-  - bioconda::adapterremoval=2.3.1
-  - conda-forge::bokeh=2.0.1
-  - bioconda::bowtie2=2.3.5.1
-  - bioconda::damageprofiler=0.4.9
-  - bioconda::fastqc=0.11.9
-  - conda-forge::jupyter=1.0.0
-  - bioconda::kraken2=2.0.8_beta
-  - conda-forge::notebook=6.0.3
-  - conda-forge::nbconvert=5.6.1
-  - bioconda::pmdtools=0.60
-  - bioconda::pysam=0.15.3
-  - bioconda::samtools=1.10
-  - maxibor::sourcepredict=0.5
-  - conda-forge::scipy=1.4.1
-  - conda-forge::matplotlib=3.2.1
-  - bioconda::multiqc=1.7
-  - conda-forge::jupyter_contrib_nbextensions=0.5.1
-  - conda-forge::plotnine=0.6.0
-  - conda-forge::markdown=3.2.1
-  - conda-forge::pymdown-extensions=7.0
-  - conda-forge::pygments=2.6.1
-  - conda-forge::tbb=2020.1
+  - adapterremoval=2.3.1
+  - blast=2.11.0
+  - bokeh=2.4.3
+  - bottleneck=1.3.5
+  - bowtie2=2.5.0
+  - damageprofiler=0.4.9
+  - fastqc=0.11.9
+  - htslib=1.12
+  - ipykernel=6.16.2
+  - ipython=8.6.0
+  - ipython_genutils=0.2.0
+  - ipywidgets=8.0.2
+  - jupyter=1.0.0
+  - jupyter_contrib_core=0.4.0
+  - jupyter_contrib_nbextensions=0.5.1
+  - jupyter_core=4.11.2
+  - jupyter_highlight_selected_word=0.2.0
+  - jupyter_latex_envs=1.4.6
+  - jupyter_nbextensions_configurator=0.4.1
+  - jupyterlab_widgets=3.0.3
+  - kraken2=2.1.2
+  - make=4.3
+  - markdown=3.2.1
+  - multiqc=1.7
+  - nbconvert=5.6.1
+  - networkx=2.5.1
+  - numpy=1.22.4
+  - openjdk=11.0.8
+  - pandas=1.5.1
+  - pandocfilters=1.5.0
+  - pip=22.3
+  - plotnine=0.6.0
+  - pmdtools=0.60
+  - pysam=0.16.0.1
+  - python=3.9.9
+  - samtools=1.12
+  - sed=4.8
+  - sqlite=3.37.0
+  - yaml=0.2.5
+  - pip:
+    - cachecontrol==0.12.11
+    - cython==0.29.32
+    - ete3==3.1.2
+    - h5py==3.7.0
+    - hdmedians==0.14.2
+    - joblib==1.2.0
+    - jupyter-client==6.1.12
+    - jupyter-console==6.4.0
+    - llvmlite==0.39.1
+    - lockfile==0.12.2
+    - matplotlib==3.5.3
+    - msgpack==1.0.4
+    - natsort==8.2.0
+    - numba==0.56.3
+    - pynndescent==0.5.8
+    - pyyaml==5.4.1
+    - scikit-bio==0.5.7
+    - scikit-learn==1.1.3
+    - scipy==1.8.1
+    - sourcepredict==0.5
+    - threadpoolctl==3.1.0
+    - tqdm==4.64.1
+    - umap-learn==0.5.3
+    - pymdown-extensions

nextflow.config

@@ -133,7 +133,7 @@ manifest {
   description = 'Coprolite Identification'
   mainScript = 'main.nf'
   nextflowVersion = '>=19.10.0'
-  version = '1.1'
+  version = '1.1.1'
 }
 
 // Function to ensure that resource requirements don't go beyond