2.2.1: fixes

.tests/config/simple_config.yaml

@@ -3,10 +3,10 @@
 # --------------------------------------------------------
 
 # MosaiCatcher version
-version: 2.2.0
+version: 2.2.1
 
 # Ashleys-QC pipeline version
-ashleys_pipeline_version: 2.2.0
+ashleys_pipeline_version: 2.2.1
 
 # Email for notifications about the pipeline's status
 email: ""

config/config.yaml

@@ -3,10 +3,10 @@
 # --------------------------------------------------------
 
 # MosaiCatcher version
-version: 2.2.0
+version: 2.2.1
 
 # Ashleys-QC pipeline version
-ashleys_pipeline_version: 2.2.0
+ashleys_pipeline_version: 2.2.1
 
 # Email for notifications about the pipeline's status
 email: ""

github-actions-runner/Dockerfile-2.2.1.dockerfile

@@ -0,0 +1,227 @@
+FROM condaforge/mambaforge:latest
+LABEL io.github.snakemake.containerized="true"
+LABEL io.github.snakemake.conda_env_hash="77eaa388d65d5205b87324fb0adb89561bc0e532a328995990a1d580aeb894ae"
+
+# 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: https://raw.githubusercontent.com/friendsofstrandseq/ashleys-qc-pipeline/dev/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
+ADD https://raw.githubusercontent.com/friendsofstrandseq/ashleys-qc-pipeline/dev/workflow/envs/ashleys_base.yaml /conda-envs/87c04f5d115eff742eca84455513deba/environment.yaml
+
+# Conda environment:
+#   source: https://raw.githubusercontent.com/friendsofstrandseq/ashleys-qc-pipeline/dev/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
+ADD https://raw.githubusercontent.com/friendsofstrandseq/ashleys-qc-pipeline/dev/workflow/envs/ashleys_rtools.yaml /conda-envs/9b847fc31baae8e01dfb7ce438a56b71/environment.yaml
+
+# Conda environment:
+#   source: workflow/envs/mc_base.yaml
+#   prefix: /conda-envs/c80307395eddf442c2fb6870f40d822b
+#   name: mc-base
+#   channels:
+#     - conda-forge
+#     - bioconda
+#   dependencies:
+#     - pandas
+#     - intervaltree
+#     - scipy
+#     - pysam
+#     - tqdm
+#     - perl
+#     - pypdf2
+#     - parmap
+#     # NEW
+#     - pyyaml
+#     - seaborn
+#     - matplotlib
+#     # SOLVE se-pe detection
+#     - samtools
+#     # ArbiGent Hufsah deps
+#     - pytables
+#     - xopen
+RUN mkdir -p /conda-envs/c80307395eddf442c2fb6870f40d822b
+COPY workflow/envs/mc_base.yaml /conda-envs/c80307395eddf442c2fb6870f40d822b/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/598c87b6c764d05e0c66953cc67f2931
+#   name: rtools
+#   channels:
+#     - bioconda
+#     - conda-forge
+#     - r
+#     - anaconda
+#   dependencies:
+#     # # NEW
+#     - strandphaser
+#     # ###############
+#     - bioconductor-biocparallel
+#     - bioconductor-bsgenome
+#     - bioconductor-bsgenome.hsapiens.ucsc.hg38
+#     - bioconductor-complexheatmap
+#     # - bioconductor-fastseg
+#     - bioconductor-genomicalignments
+#     - bioconductor-genomicranges
+#     - bioconductor-rsamtools
+#     # - bioconductor-s4vectors
+#     - fonts-anaconda
+#     - r-assertthat
+#     - r-base
+#     - r-biocmanager
+#     - r-cairo
+#     - r-cowplot
+#     - r-data.table
+#     - r-devtools
+#     - r-doparallel
+#     - r-dplyr
+#     - r-foreach
+#     - r-ggplot2
+#     - r-gplots
+#     - r-gtools
+#     - r-mc2d
+#     - r-rcolorbrewer
+#     - r-reshape2
+#     - r-scales
+#     - r-stringr
+#     # SV_CALLS_DEV
+#     # - r-zoo
+#     - r-r.utils
+#     - r-ggnewscale
+#     # HEATMAP
+#     - r-tidyr
+#     # ARBIGENT
+#     - r-reshape
+#     - r-optparse
+#     - r-tidyr
+#     - r-ggbeeswarm
+#     - r-pheatmap
+#     # GC_correction
+#     - r-ggpubr
+#     - bioconductor-edger
+#     # SOLVE R lib issue
+#     - r-stringi=1.7.12
+RUN mkdir -p /conda-envs/598c87b6c764d05e0c66953cc67f2931
+COPY workflow/envs/rtools.yaml /conda-envs/598c87b6c764d05e0c66953cc67f2931/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 env create --prefix /conda-envs/c80307395eddf442c2fb6870f40d822b --file /conda-envs/c80307395eddf442c2fb6870f40d822b/environment.yaml && \
+    mamba env create --prefix /conda-envs/f251d84cdc9f25d0e14b48e780261d66 --file /conda-envs/f251d84cdc9f25d0e14b48e780261d66/environment.yaml && \
+    mamba env create --prefix /conda-envs/598c87b6c764d05e0c66953cc67f2931 --file /conda-envs/598c87b6c764d05e0c66953cc67f2931/environment.yaml && \
+    mamba clean --all -y

github-actions-runner/docker_procedure.md

@@ -34,7 +34,16 @@ conda activate snakemake
 snakemake --configfile .tests/config/simple_config.yaml --config ashleys_pipeline=True MultiQC=True --profile workflow/snakemake_profiles/local/conda/ -c 8 --forceall -n
 snakemake --configfile .tests/config/simple_config.yaml --config ashleys_pipeline=True MultiQC=True --profile workflow/snakemake_profiles/local/conda_singularity/ -c 8 --forceall
 
+# Solved in
 
-# Solved in 
+https://github.com/weber8thomas/workspace-images/tree/docker-apptainer-mamba
 
-https://github.com/weber8thomas/workspace-images/tree/docker-apptainer-mamba
+# Dockerfile creation
+
+snakemake --configfile .tests/config/simple_config.yaml --config ashleys_pipeline=True MultiQC=True --profile workflow/snakemake_profiles/local/conda/ -c 8 --containerize > Dockerfile
+
+# Docker commands
+
+docker login -u weber8thomas
+docker build --platform=linux/amd64 -t weber8thomas/mosaicatcher-pipeline:VERSION .
+docker push -t weber8thomas/mosaicatcher-pipeline:VERSION

workflow/Snakefile

@@ -25,9 +25,9 @@ if config["ashleys_pipeline"] is True:
             github(
                 "friendsofstrandseq/ashleys-qc-pipeline",
                 path="workflow/Snakefile",
-                # tag=str(config["ashleys_pipeline_version"])
+                tag=str(config["ashleys_pipeline_version"])
                 # branch="main",
-                branch="dev",
+                # branch="dev",
             )
         config:
             config

workflow/rules/common.smk

@@ -285,7 +285,7 @@ class HandleInput:
         # List of folders/files to not consider (restrict to samples only)
 
         l_to_process = [e for e in os.listdir(thisdir) if e not in exclude and e.endswith(".zip") is False]
-        print(l_to_process)
+        # print(l_to_process)
         if config["samples_to_process"]:
             l_to_process = [e for e in l_to_process if e in config["samples_to_process"]]
 
@@ -327,7 +327,7 @@ class HandleInput:
         complete_df = complete_df.sort_values(by=["Cell", "File"]).reset_index(
             drop=True
         )
-        print(complete_df)
+        # print(complete_df)
         return complete_df