From 86e81088e453b08fdc2b56dfbcc8c264a5833bd5 Mon Sep 17 00:00:00 2001 From: Thomas Weber Date: Mon, 24 Jun 2024 12:04:37 +0000 Subject: [PATCH 1/4] No update, keeping versioning homogenous with MC --- config/config.yaml | 2 +- .../Dockerfile-2.3.2.dockerfile | 120 ++++++++++++++++++ 2 files changed, 121 insertions(+), 1 deletion(-) create mode 100644 github-actions-runner/Dockerfile-2.3.2.dockerfile diff --git a/config/config.yaml b/config/config.yaml index 88ce4cf..cb96ac0 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -1,7 +1,7 @@ # -------------------------------------------------------- # Ashleys-QC pipeline Configuration # -------------------------------------------------------- -version: 2.3.1 +version: 2.3.2 # Email for notifications about the pipeline's status email: "" diff --git a/github-actions-runner/Dockerfile-2.3.2.dockerfile b/github-actions-runner/Dockerfile-2.3.2.dockerfile new file mode 100644 index 0000000..c194dc9 --- /dev/null +++ b/github-actions-runner/Dockerfile-2.3.2.dockerfile @@ -0,0 +1,120 @@ +FROM condaforge/mambaforge:latest +LABEL io.github.snakemake.containerized="true" +LABEL io.github.snakemake.conda_env_hash="b4bf346d2b78ca78f3eab94bacc2a487b682a40690bd07db57f6c50bb52d1ce0" + +# 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/eba7cf011bffb12bcf25d066f6955913 +# 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 +# # Fix ashleys GH issue +# - python=3.10 +RUN mkdir -p /conda-envs/eba7cf011bffb12bcf25d066f6955913 +COPY workflow/envs/ashleys_base.yaml /conda-envs/eba7cf011bffb12bcf25d066f6955913/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/eba7cf011bffb12bcf25d066f6955913 --file /conda-envs/eba7cf011bffb12bcf25d066f6955913/environment.yaml && \ + mamba env create --prefix /conda-envs/9b847fc31baae8e01dfb7ce438a56b71 --file /conda-envs/9b847fc31baae8e01dfb7ce438a56b71/environment.yaml && \ + mamba clean --all -y From 7a08b210229021903b5f6a215d94b4c68f50a911 Mon Sep 17 00:00:00 2001 From: Thomas Weber Date: Mon, 24 Jun 2024 12:17:34 +0000 Subject: [PATCH 2/4] Re-enabling pre-commit hook --- .pre-commit-config.yaml | 45 ++++++++++++++++++++++------------------- 1 file changed, 24 insertions(+), 21 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 7e6b5db..26666df 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,21 +1,24 @@ -# repos: -# - hooks: -# - id: trailing-whitespace -# - id: check-added-large-files -# - id: check-yaml -# # - args: -# # - --branch -# # - master -# # id: no-commit-to-branch -# repo: https://github.com/pre-commit/pre-commit-hooks -# rev: v3.4.0 - # - hooks: - # - id: snakefmt - # repo: https://github.com/snakemake/snakefmt - # rev: 0.4.0 - # - hooks: - # - id: commitizen - # stages: - # - commit-msg - # repo: https://github.com/commitizen-tools/commitizen - # rev: v2.17.12 +repos: + - hooks: + - id: trailing-whitespace + - id: end-of-file-fixer + - id: check-added-large-files + - id: check-yaml + # - args: + # - --branch + # - master + # id: no-commit-to-branch + repo: https://github.com/pre-commit/pre-commit-hooks + rev: v3.4.0 + + - hooks: + - id: snakefmt + repo: https://github.com/snakemake/snakefmt + rev: 0.4.0 + + - hooks: + - id: commitizen + stages: + - commit-msg + repo: https://github.com/commitizen-tools/commitizen + rev: v2.17.12 From 11c17dbd805a699f76c737ae89ff3a6faf30605f Mon Sep 17 00:00:00 2001 From: Thomas Weber Date: Mon, 24 Jun 2024 12:23:04 +0000 Subject: [PATCH 3/4] No update, synchronising versions with MC --- .pre-commit-config.yaml | 52 ++++++++++++++++++++++++----------------- 1 file changed, 30 insertions(+), 22 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 26666df..02f2780 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,24 +1,32 @@ -repos: - - hooks: - - id: trailing-whitespace - - id: end-of-file-fixer - - id: check-added-large-files - - id: check-yaml - # - args: - # - --branch - # - master - # id: no-commit-to-branch - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v3.4.0 +# repos: +# - hooks: +# - id: trailing-whitespace +# args: ["--verbose"] +# - id: end-of-file-fixer +# args: ["--verbose"] +# - id: check-added-large-files +# args: ["--verbose"] +# - id: check-yaml +# args: ["--verbose"] - - hooks: - - id: snakefmt - repo: https://github.com/snakemake/snakefmt - rev: 0.4.0 +# # - args: +# # - --branch +# # - master +# # id: no-commit-to-branch +# repo: https://github.com/pre-commit/pre-commit-hooks +# rev: v3.4.0 - - hooks: - - id: commitizen - stages: - - commit-msg - repo: https://github.com/commitizen-tools/commitizen - rev: v2.17.12 +# - hooks: +# - id: snakefmt +# args: ["--verbose"] + +# repo: https://github.com/snakemake/snakefmt +# rev: 0.4.0 + +# - hooks: +# - id: commitizen +# args: ["--verbose"] +# stages: +# - commit-msg +# repo: https://github.com/commitizen-tools/commitizen +# rev: v2.17.12 From 2617f082acc1ddec60b1f055dcaf2a8ab1859044 Mon Sep 17 00:00:00 2001 From: Thomas Weber Date: Mon, 24 Jun 2024 14:24:26 +0200 Subject: [PATCH 4/4] Synchronising version --- .pre-commit-config.yaml | 31 ++++++++++--------------------- 1 file changed, 10 insertions(+), 21 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 02f2780..7e6b5db 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,32 +1,21 @@ # repos: # - hooks: # - id: trailing-whitespace -# args: ["--verbose"] -# - id: end-of-file-fixer -# args: ["--verbose"] # - id: check-added-large-files -# args: ["--verbose"] # - id: check-yaml -# args: ["--verbose"] - # # - args: # # - --branch # # - master # # id: no-commit-to-branch # repo: https://github.com/pre-commit/pre-commit-hooks # rev: v3.4.0 - -# - hooks: -# - id: snakefmt -# args: ["--verbose"] - -# repo: https://github.com/snakemake/snakefmt -# rev: 0.4.0 - -# - hooks: -# - id: commitizen -# args: ["--verbose"] -# stages: -# - commit-msg -# repo: https://github.com/commitizen-tools/commitizen -# rev: v2.17.12 + # - hooks: + # - id: snakefmt + # repo: https://github.com/snakemake/snakefmt + # rev: 0.4.0 + # - hooks: + # - id: commitizen + # stages: + # - commit-msg + # repo: https://github.com/commitizen-tools/commitizen + # rev: v2.17.12