diff --git a/.tests/config/simple_config.yaml b/.tests/config/simple_config.yaml index 869dd5c..4e30c84 100644 --- a/.tests/config/simple_config.yaml +++ b/.tests/config/simple_config.yaml @@ -1,7 +1,7 @@ # -------------------------------------------------------- # Ashleys-QC pipeline Configuration # -------------------------------------------------------- -version: 2.2.3 +version: 2.2.5 # Email for notifications about the pipeline's status email: "" diff --git a/README.md b/README.md index 286421a..765c093 100644 --- a/README.md +++ b/README.md @@ -469,4 +469,6 @@ snakemake --cores 12 --use-conda --config hand_selection=True data_location= MosaiCatcher v2 publication: Weber Thomas, Marco Raffaele Cosenza, and Jan Korbel. 2023. ‘MosaiCatcher v2: A Single-Cell Structural Variations Detection and Analysis Reference Framework Based on Strand-Seq’. Bioinformatics 39 (11): btad633. https://doi.org/10.1093/bioinformatics/btad633. + > Gros, Christina, Ashley D Sanders, Jan O Korbel, Tobias Marschall, and Peter Ebert. “ASHLEYS: Automated Quality Control for Single-Cell Strand-Seq Data.” Bioinformatics 37, no. 19 (October 1, 2021): 3356–57. https://doi.org/10.1093/bioinformatics/btab221. diff --git a/config/config.yaml b/config/config.yaml index 1d435f5..beb16fa 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -1,7 +1,7 @@ # -------------------------------------------------------- # Ashleys-QC pipeline Configuration # -------------------------------------------------------- -version: 2.2.3 +version: 2.2.5 # Email for notifications about the pipeline's status email: "" @@ -9,9 +9,6 @@ email: "" # List of samples to process if multiple are specified samples_to_process: [] -# Plate size -plate_size: 96 - # -------------------------------------------------------- # Data location & I/O # -------------------------------------------------------- diff --git a/github-actions-runner/Dockerfile-2.2.5.dockerfile b/github-actions-runner/Dockerfile-2.2.5.dockerfile new file mode 100644 index 0000000..eba6242 --- /dev/null +++ b/github-actions-runner/Dockerfile-2.2.5.dockerfile @@ -0,0 +1,118 @@ +FROM condaforge/mambaforge:latest +LABEL io.github.snakemake.containerized="true" +LABEL io.github.snakemake.conda_env_hash="e9bc3082704cbf20eaa004e1360fb45da1359e3288296fb66dfad7e245e22563" + +# Step 1: Retrieve conda environments + +# Conda environment: +# source: https://github.com/snakemake/snakemake-wrappers/raw/v1.7.0/bio/bwa/index/environment.yaml +# prefix: /conda-envs/5681728a49bd83ceed09ba194330c858 +# channels: +# - bioconda +# - conda-forge +# - defaults +# dependencies: +# - bwa ==0.7.17 +RUN mkdir -p /conda-envs/5681728a49bd83ceed09ba194330c858 +ADD https://github.com/snakemake/snakemake-wrappers/raw/v1.7.0/bio/bwa/index/environment.yaml /conda-envs/5681728a49bd83ceed09ba194330c858/environment.yaml + +# Conda environment: +# source: https://github.com/snakemake/snakemake-wrappers/raw/v1.7.0/bio/fastqc/environment.yaml +# prefix: /conda-envs/08d4368302a4bdf7eda6b536495efe7d +# channels: +# - bioconda +# - conda-forge +# - defaults +# dependencies: +# - fastqc ==0.11.9 +RUN mkdir -p /conda-envs/08d4368302a4bdf7eda6b536495efe7d +ADD https://github.com/snakemake/snakemake-wrappers/raw/v1.7.0/bio/fastqc/environment.yaml /conda-envs/08d4368302a4bdf7eda6b536495efe7d/environment.yaml + +# Conda environment: +# source: workflow/envs/ashleys_base.yaml +# prefix: /conda-envs/87c04f5d115eff742eca84455513deba +# name: ashleys_base +# channels: +# - conda-forge +# - bioconda +# dependencies: +# - samtools +# - tabix +# - bwa +# - sambamba +# - mosaicatcher +# # - alfred +# - ashleys-qc +# - pandas +# # PUBLISHDIR +# - rsync +# # MULTIQC +# - multiqc +# # Fix sklearn update +# - scikit-learn=1.2.2 +RUN mkdir -p /conda-envs/87c04f5d115eff742eca84455513deba +COPY workflow/envs/ashleys_base.yaml /conda-envs/87c04f5d115eff742eca84455513deba/environment.yaml + +# Conda environment: +# source: workflow/envs/ashleys_rtools.yaml +# prefix: /conda-envs/9b847fc31baae8e01dfb7ce438a56b71 +# name: rtools +# channels: +# - conda-forge +# - bioconda +# - r +# - anaconda +# dependencies: +# # - bioconductor-biocparallel +# # - bioconductor-bsgenome +# # - bioconductor-bsgenome.hsapiens.ucsc.hg19 +# # - bioconductor-bsgenome.hsapiens.ucsc.hg38 +# # - bioconductor-fastseg +# # - bioconductor-genomicalignments +# - bioconductor-genomicranges +# # - bioconductor-rsamtools +# # - bioconductor-s4vectors +# - r-assertthat +# - r-base +# # - r-biocmanager +# - r-cowplot +# - r-data.table +# # - r-devtools +# # - r-doparallel +# # - r-foreach +# - r-ggplot2 +# # - r-gtools +# - r-reshape2 +# # - r-zoo +# # - r-dplyr +# # - r-mc2d +# # - r-pheatmap +# # - bioconductor-complexheatmap +# # - r-gplots +# - r-scales +# - r-rcolorbrewer +# # - r-stringr +# - r-cairo +# - fonts-anaconda +# # NEW +# - bioconductor-edger +# - r-r.utils +# # PLATE PLOT +# - r-dplyr +# - r-platetools +# - r-viridis +# # GC_correction +# - r-tidyr +# - r-ggpubr +# # SOLVE R lib issue +# - r-stringi=1.7.12 +RUN mkdir -p /conda-envs/9b847fc31baae8e01dfb7ce438a56b71 +COPY workflow/envs/ashleys_rtools.yaml /conda-envs/9b847fc31baae8e01dfb7ce438a56b71/environment.yaml + +# Step 2: Generate conda environments + +RUN mamba env create --prefix /conda-envs/5681728a49bd83ceed09ba194330c858 --file /conda-envs/5681728a49bd83ceed09ba194330c858/environment.yaml && \ + mamba env create --prefix /conda-envs/08d4368302a4bdf7eda6b536495efe7d --file /conda-envs/08d4368302a4bdf7eda6b536495efe7d/environment.yaml && \ + mamba env create --prefix /conda-envs/87c04f5d115eff742eca84455513deba --file /conda-envs/87c04f5d115eff742eca84455513deba/environment.yaml && \ + mamba env create --prefix /conda-envs/9b847fc31baae8e01dfb7ce438a56b71 --file /conda-envs/9b847fc31baae8e01dfb7ce438a56b71/environment.yaml && \ + mamba clean --all -y