Merge pull request #42 from friendsofstrandseq/dev

2.2.2: fixes and small update, dockerfile

github-actions-runner/Dockerfile-2.2.2.dockerfile

@@ -0,0 +1,118 @@
+FROM condaforge/mambaforge:latest
+LABEL io.github.snakemake.containerized="true"
+LABEL io.github.snakemake.conda_env_hash="e9bc3082704cbf20eaa004e1360fb45da1359e3288296fb66dfad7e245e22563"
+
+# 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/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
+COPY workflow/envs/ashleys_base.yaml /conda-envs/87c04f5d115eff742eca84455513deba/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/87c04f5d115eff742eca84455513deba --file /conda-envs/87c04f5d115eff742eca84455513deba/environment.yaml && \
+    mamba env create --prefix /conda-envs/9b847fc31baae8e01dfb7ce438a56b71 --file /conda-envs/9b847fc31baae8e01dfb7ce438a56b71/environment.yaml && \
+    mamba clean --all -y

workflow/rules/gc.smk

@@ -77,6 +77,8 @@ if config["multistep_normalisation"] is True and config["window"] == 200000:
             "{folder}/{sample}/counts/multistep_normalisation/{sample}.txt.scaled.GC.VST.gz",
         output:
             "{folder}/{sample}/counts/multistep_normalisation/{sample}.txt.scaled.GC.VST.reformat.gz",
+        log:
+            "{folder}/{sample}/log/reformat_ms_norm/{sample}.log"
         conda:
             "../envs/ashleys_base.yaml"
         resources: