Merge pull request friendsofstrandseq#51 from friendsofstrandseq/dev

2.2.4: minor fixes for scNOVA new container mode

.gitignore

@@ -218,4 +218,8 @@ LOGS_DEV/
 
 # scTRIP multiplot
 workflow/scripts/plotting/scTRIP_multiplot/scTRIPmultiplot
-workflow/config/scTRIP_multiplot.ok
+workflow/config/scTRIP_multiplot.ok
+args.output
+scNOVA_env_costea.yaml
+.keras/keras.json
+hs_err_pid2227945.log

afac/update_timestamps.py

@@ -0,0 +1,25 @@
+import os, sys
+import time
+from pathlib import Path
+
+
+def update_timestamps(directory):
+    """
+    Update the access and modification times of all files in the given directory and its subdirectories.
+
+    :param directory: Path to the directory
+    """
+    for root, dirs, files in os.walk(directory):
+        for file in files:
+            if file.endswith(".fastq.gz"):
+                continue
+            file_path = Path(root) / file
+            current_time = time.time()
+            print(file_path)
+            os.utime(file_path, (current_time, current_time))
+            print(f"Updated timestamp for: {file_path}")
+
+
+# Example usage
+directory_path = sys.argv[1]
+update_timestamps(directory_path)

config/config.yaml

@@ -3,17 +3,20 @@
 # --------------------------------------------------------
 
 # MosaiCatcher version
-version: 2.2.2
+version: 2.2.4
 
 # Ashleys-QC pipeline version
-ashleys_pipeline_version: 2.2.2
+ashleys_pipeline_version: 2.2.3
 
 # Email for notifications about the pipeline's status
 email: ""
 
 # List of samples to process if multiple are specified
 samples_to_process: []
 
+# Plate size
+plate_size: 96
+
 # --------------------------------------------------------
 # Data location & I/O
 # --------------------------------------------------------

config/config_metadata.yaml

@@ -135,3 +135,9 @@ use_strandscape_labels::
   required: False
   default: False
   lint_check: False
+plate_size::
+  desc: "Plate size used for the sequencing (96/384)"
+  type: int
+  required: True
+  default: 96
+  lint_check: False

github-actions-runner/Dockerfile-2.2.2.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/2.2.2/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/2.2.2/workflow/envs/ashleys_base.yaml /conda-envs/87c04f5d115eff742eca84455513deba/environment.yaml
+
+# Conda environment:
+#   source: https://raw.githubusercontent.com/friendsofstrandseq/ashleys-qc-pipeline/2.2.2/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/2.2.2/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