diff --git a/.tests b/.tests index f4d3eda3..603fade9 160000 --- a/.tests +++ b/.tests @@ -1 +1 @@ -Subproject commit f4d3eda328a2b5ff59e8c9ce1a3d6ca88808844c +Subproject commit 603fade9c5aa33f4f511af59f8ccdfa53834fa36 diff --git a/github-actions-runner/Dockerfile-2.3.5.dockerfile b/github-actions-runner/Dockerfile-2.3.5.dockerfile new file mode 100644 index 00000000..63402789 --- /dev/null +++ b/github-actions-runner/Dockerfile-2.3.5.dockerfile @@ -0,0 +1,255 @@ +FROM condaforge/mambaforge:latest +LABEL io.github.snakemake.containerized="true" +LABEL io.github.snakemake.conda_env_hash="72e8bd41499b7a00b23bf8b7611bc709b4cf39ef9dda6af310328b74cc86321b" + +# Step 1: Retrieve conda environments + +# Conda environment: +# source: https://github.com/friendsofstrandseq/ashleys-qc-pipeline/raw/2.3.5/workflow/envs/ashleys_base.yaml +# prefix: /conda-envs/32c736a65a401b33605acfa7a0241299 +# name: ashleys_base +# channels: +# - conda-forge +# - bioconda +# dependencies: +# - ashleys-qc +# - bwa +# - mosaicatcher +# - multiqc +# - pandas +# - python=3.10 +# - pysam +# - rsync +# - sambamba +# - samtools +# - scikit-learn=1.2.2 +# - tabix +RUN mkdir -p /conda-envs/32c736a65a401b33605acfa7a0241299 +ADD https://github.com/friendsofstrandseq/ashleys-qc-pipeline/raw/2.3.5/workflow/envs/ashleys_base.yaml /conda-envs/32c736a65a401b33605acfa7a0241299/environment.yaml + +# Conda environment: +# source: https://github.com/friendsofstrandseq/ashleys-qc-pipeline/raw/2.3.5/workflow/envs/ashleys_rtools.yaml +# prefix: /conda-envs/fc1f554e9ee82b99f4350430ee3ae0a0 +# name: rtools +# channels: +# - conda-forge +# - bioconda +# dependencies: +# - bioconductor-edger +# - bioconductor-genomicranges +# - fonts-conda-forge +# - r-assertthat +# - r-base +# - r-cairo +# - r-cowplot +# - r-data.table +# - r-dplyr +# - r-ggplot2 +# - r-ggpubr +# - r-platetools +# - r-r.utils +# - r-rcolorbrewer +# - r-reshape2 +# - r-scales +# - r-stringi=1.7.12 +# - r-tidyr +# - r-viridis +RUN mkdir -p /conda-envs/fc1f554e9ee82b99f4350430ee3ae0a0 +ADD https://github.com/friendsofstrandseq/ashleys-qc-pipeline/raw/2.3.5/workflow/envs/ashleys_rtools.yaml /conda-envs/fc1f554e9ee82b99f4350430ee3ae0a0/environment.yaml + +# 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/mc_base.yaml +# prefix: /conda-envs/e5cbb476a12203f97f2a0bb44963061d +# name: mc-base +# channels: +# - conda-forge +# - bioconda +# dependencies: +# - intervaltree +# - matplotlib +# - pandas +# - parmap +# - perl +# - pybigwig +# - pypdf2 +# - pysam +# - pytables +# - pyyaml +# - samtools +# - scipy +# - seaborn +# - tqdm +# - xopen +RUN mkdir -p /conda-envs/e5cbb476a12203f97f2a0bb44963061d +COPY workflow/envs/mc_base.yaml /conda-envs/e5cbb476a12203f97f2a0bb44963061d/environment.yaml + +# Conda environment: +# source: workflow/envs/mc_bioinfo_tools.yaml +# prefix: /conda-envs/f251d84cdc9f25d0e14b48e780261d66 +# name: mc-bioinfo-tools +# channels: +# - conda-forge +# - bioconda +# dependencies: +# - bcftools +# - freebayes +# - mosaicatcher +# - samtools +# - tabix +# - whatshap +RUN mkdir -p /conda-envs/f251d84cdc9f25d0e14b48e780261d66 +COPY workflow/envs/mc_bioinfo_tools.yaml /conda-envs/f251d84cdc9f25d0e14b48e780261d66/environment.yaml + +# Conda environment: +# source: workflow/envs/rtools.yaml +# prefix: /conda-envs/905757e298f80370141afb02667ced2e +# name: rtools +# channels: +# - bioconda +# - conda-forge +# dependencies: +# - bioconductor-biocparallel +# - bioconductor-breakpointr +# - bioconductor-bsgenome +# - bioconductor-bsgenome.hsapiens.ucsc.hg38 +# - bioconductor-complexheatmap +# - bioconductor-edger +# - bioconductor-genomicalignments +# - bioconductor-genomicranges +# - bioconductor-rsamtools +# - fonts-conda-forge +# - r-assertthat +# - r-base +# - r-biocmanager +# - r-cairo +# - r-cowplot +# - r-data.table +# - r-devtools +# - r-doparallel +# - r-dplyr +# - r-foreach +# - r-ggbeeswarm +# - r-ggnewscale +# - r-ggplot2 +# - r-ggpubr +# - r-gplots +# - r-gtools +# - r-mc2d +# - r-optparse +# - r-pheatmap +# - r-r.utils +# - r-rcolorbrewer +# - r-reshape +# - r-reshape2 +# - r-scales +# - r-stringi=1.7.12 +# - r-stringr +# - r-tidyr +# - r-tidyr +# - strandphaser +RUN mkdir -p /conda-envs/905757e298f80370141afb02667ced2e +COPY workflow/envs/rtools.yaml /conda-envs/905757e298f80370141afb02667ced2e/environment.yaml + +# Conda environment: +# source: workflow/envs/scNOVA/scNOVA_DL.yaml +# prefix: /conda-envs/fdeedf32561210c2a9762946a26b4cca +# name: scNOVA_DL +# channels: +# - conda-forge +# dependencies: +# - h5py=2.10.0 +# - matplotlib=3.1.1 +# - numpy +# - pandas=0.25.3 +# - python=3.7.4 +# - scikit-learn=0.21.3 +# - tensorflow=1.15.0 +# - unzip +# - pip: +# - cffi +RUN mkdir -p /conda-envs/fdeedf32561210c2a9762946a26b4cca +COPY workflow/envs/scNOVA/scNOVA_DL.yaml /conda-envs/fdeedf32561210c2a9762946a26b4cca/environment.yaml + +# Conda environment: +# source: workflow/envs/scNOVA/scNOVA_R.yaml +# prefix: /conda-envs/e4c4fbc0d8d5fdeeb1f51bb8c0e86716 +# name: scNOVA +# channels: +# - bioconda +# - conda-forge +# dependencies: +# - bioconductor-bsgenome.hsapiens.ucsc.hg38=1.4.3 +# - bioconductor-chromvar=1.12.0 +# - bioconductor-deseq2=1.30.0 +# - bioconductor-jaspar2016=1.18.0 +# - bioconductor-motifmatchr=1.12.0 +# - r-codetools=0.2_18 +# - r-doparallel +# - r-factoextra=1.0.7 +# - r-fitdistrplus +# - r-foreach +# - r-gplots=3.1.1 +# - r-matrixstats=0.58.0 +# - r-nabor=0.5.0 +# - r-pheatmap=1.0.12 +# - r-pracma=2.3.3 +# - r-rtsne=0.15 +# - r-umap=0.2.7.0 +RUN mkdir -p /conda-envs/e4c4fbc0d8d5fdeeb1f51bb8c0e86716 +COPY workflow/envs/scNOVA/scNOVA_R.yaml /conda-envs/e4c4fbc0d8d5fdeeb1f51bb8c0e86716/environment.yaml + +# Conda environment: +# source: workflow/envs/scNOVA/scNOVA_bioinfo_tools.yaml +# prefix: /conda-envs/8b150c19ea62e29d0bbc47d682a8db8e +# name: scNOVA_bioinfo_tools +# channels: +# - conda-forge +# - bioconda +# dependencies: +# - bedtools +# - biobambam +# - samtools +RUN mkdir -p /conda-envs/8b150c19ea62e29d0bbc47d682a8db8e +COPY workflow/envs/scNOVA/scNOVA_bioinfo_tools.yaml /conda-envs/8b150c19ea62e29d0bbc47d682a8db8e/environment.yaml + +# Step 2: Generate conda environments + +RUN mamba env create --prefix /conda-envs/32c736a65a401b33605acfa7a0241299 --file /conda-envs/32c736a65a401b33605acfa7a0241299/environment.yaml && \ + mamba env create --prefix /conda-envs/fc1f554e9ee82b99f4350430ee3ae0a0 --file /conda-envs/fc1f554e9ee82b99f4350430ee3ae0a0/environment.yaml && \ + 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/e5cbb476a12203f97f2a0bb44963061d --file /conda-envs/e5cbb476a12203f97f2a0bb44963061d/environment.yaml && \ + mamba env create --prefix /conda-envs/f251d84cdc9f25d0e14b48e780261d66 --file /conda-envs/f251d84cdc9f25d0e14b48e780261d66/environment.yaml && \ + mamba env create --prefix /conda-envs/905757e298f80370141afb02667ced2e --file /conda-envs/905757e298f80370141afb02667ced2e/environment.yaml && \ + mamba env create --prefix /conda-envs/fdeedf32561210c2a9762946a26b4cca --file /conda-envs/fdeedf32561210c2a9762946a26b4cca/environment.yaml && \ + mamba env create --prefix /conda-envs/e4c4fbc0d8d5fdeeb1f51bb8c0e86716 --file /conda-envs/e4c4fbc0d8d5fdeeb1f51bb8c0e86716/environment.yaml && \ + mamba env create --prefix /conda-envs/8b150c19ea62e29d0bbc47d682a8db8e --file /conda-envs/8b150c19ea62e29d0bbc47d682a8db8e/environment.yaml && \ + mamba clean --all -y +# CUSTOM PART +RUN wget https://zenodo.org/record/7697400/files/BSgenome.T2T.CHM13.V2_1.0.0.tar.gz -P /workflow/data/ref_genomes/ +COPY /workflow/scripts/utils/install_R_package.R /conda-envs/ +RUN chmod -R 0777 /conda-envs/905757e298f80370141afb02667ced2e/lib/R/library && /conda-envs/905757e298f80370141afb02667ced2e/bin/Rscript /conda-envs/install_R_package.R /workflow/data/ref_genomes/BSgenome.T2T.CHM13.V2_1.0.0.tar.gz diff --git a/workflow/data b/workflow/data index 5b5e4c3e..25c696e2 160000 --- a/workflow/data +++ b/workflow/data @@ -1 +1 @@ -Subproject commit 5b5e4c3ebc948ae16ea25012cf77e50536bf877a +Subproject commit 25c696e243578a6b3b7b0f982aefdbf2765acd47 diff --git a/workflow/snakemake_profiles b/workflow/snakemake_profiles index f666be2a..68bce283 160000 --- a/workflow/snakemake_profiles +++ b/workflow/snakemake_profiles @@ -1 +1 @@ -Subproject commit f666be2acce84c12701d6890d8fb3f5c5edccc87 +Subproject commit 68bce283f865546d0db958fbb64106d14f24d2ce