Merge pull request #48 from friendsofstrandseq/dev

Fix import from MC

config/config.yaml

@@ -1,7 +1,7 @@
 # --------------------------------------------------------
 # Ashleys-QC pipeline Configuration
 # --------------------------------------------------------
-version: 2.3.0
+version: 2.3.1
 
 # Email for notifications about the pipeline's status
 email: ""

github-actions-runner/Dockerfile-2.3.1.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

workflow/Snakefile

@@ -31,10 +31,10 @@ if config["list_commands"] is False:
         input:
             get_final_result(),
 
-    if config["email"]:
 
-        onsuccess:
-            onsuccess_fct(log)
+# if config["email"]:
 
-        onerror:
-            onerror_fct(log)
+# onsuccess:
+#     onsuccess_fct(log)
+# onerror:
+#     onerror_fct(log)

workflow/rules/common.smk

@@ -40,7 +40,7 @@ if config["mosaicatcher_pipeline"] == False:
             "chr" + str(e) for e in list(range(1, 20)) + ["X", "Y"]
         ]
 
-    from scripts.utils import make_log_useful_ashleys, pipeline_aesthetic_start_ashleys
+    from scripts.utils import pipeline_aesthetic_start_ashleys
 
     if config["list_commands"] is True:
         pipeline_aesthetic_start_ashleys.argparse_help(config)
@@ -63,32 +63,32 @@ if config["mosaicatcher_pipeline"] == False:
         )
 
 
-def onsuccess_fct(log):
-    config_metadata = config_definitions = yaml.safe_load(
-        open(configfile_location.replace("config.yaml", "config_metadata.yaml"), "r")
-    )
-    log_path_new = make_log_useful_ashleys.make_log_useful(
-        log, "SUCCESS", config, config_metadata
-    )
-    shell(
-        'mail -s "[Snakemake] smk-wf-catalog/ashleys-qc-pipeline v{} - Run on {} - SUCCESS" {} < {}'.format(
-            config["version"], config["data_location"], config["email"], log_path_new
-        )
-    )
-
-
-def onerror_fct(log):
-    config_metadata = config_definitions = yaml.safe_load(
-        open(configfile_location.replace("config.yaml", "config_metadata.yaml"), "r")
-    )
-    log_path_new = make_log_useful_ashleys.make_log_useful(
-        log, "ERROR", config, config_metadata
-    )
-    shell(
-        'mail -s "[Snakemake] smk-wf-catalog/ashleys-qc-pipeline v{} - Run on {} - ERRROR" {} < {}'.format(
-            config["version"], config["data_location"], config["email"], log_path_new
-        )
-    )
+# def onsuccess_fct(log):
+#     config_metadata = config_definitions = yaml.safe_load(
+#         open(configfile_location.replace("config.yaml", "config_metadata.yaml"), "r")
+#     )
+#     log_path_new = make_log_useful_ashleys.make_log_useful(
+#         log, "SUCCESS", config, config_metadata
+#     )
+#     shell(
+#         'mail -s "[Snakemake] smk-wf-catalog/ashleys-qc-pipeline v{} - Run on {} - SUCCESS" {} < {}'.format(
+#             config["version"], config["data_location"], config["email"], log_path_new
+#         )
+#     )
+
+
+# def onerror_fct(log):
+#     config_metadata = config_definitions = yaml.safe_load(
+#         open(configfile_location.replace("config.yaml", "config_metadata.yaml"), "r")
+#     )
+#     log_path_new = make_log_useful_ashleys.make_log_useful(
+#         log, "ERROR", config, config_metadata
+#     )
+#     shell(
+#         'mail -s "[Snakemake] smk-wf-catalog/ashleys-qc-pipeline v{} - Run on {} - ERRROR" {} < {}'.format(
+#             config["version"], config["data_location"], config["email"], log_path_new
+#         )
+#     )
 
 
 # Simple class to retrieve automatically files in the fastq/bam folder and create a config dataframe