2.1.3: fixes

config/config.yaml

@@ -1,5 +1,5 @@
 version: 2.1.3
-ashleys_pipeline_version: 2.1.2
+ashleys_pipeline_version: 2.1.3
 #######################################
 #   MOSAICATCHER CONFIGURATION FILE   #
 #######################################

github-actions-runner/Dockerfile-2.1.3.dockerfile

@@ -0,0 +1,235 @@
+Config file config/config.yaml is extended by additional config specified via the command line.
+localrules directive specifies rules that are not present in the Snakefile:
+symlink_bam_ashleys
+ashleys_genecore_symlink
+
+Building DAG of jobs...
+Hashing conda environment https://github.com/friendsofstrandseq/ashleys-qc-pipeline/raw/2.1.3/workflow/envs/ashleys_base.yaml.
+Hashing conda environment https://github.com/friendsofstrandseq/ashleys-qc-pipeline/raw/2.1.3/workflow/envs/ashleys_rtools.yaml.
+Hashing conda environment https://github.com/snakemake/snakemake-wrappers/raw/v1.7.0/bio/bwa/index/environment.yaml.
+Hashing conda environment https://github.com/snakemake/snakemake-wrappers/raw/v1.7.0/bio/fastqc/environment.yaml.
+Hashing conda environment workflow/envs/mc_base.yaml.
+Hashing conda environment workflow/envs/mc_bioinfo_tools.yaml.
+Hashing conda environment workflow/envs/rtools.yaml.
+FROM condaforge/mambaforge:latest
+LABEL io.github.snakemake.containerized="true"
+LABEL io.github.snakemake.conda_env_hash="94a1aeb6a853dc669a56425707c8ab0bed50fc300640ba9254ff0e9927af2159"
+
+# Step 1: Retrieve conda environments
+
+# Conda environment:
+#   source: https://github.com/friendsofstrandseq/ashleys-qc-pipeline/raw/2.1.3/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://github.com/friendsofstrandseq/ashleys-qc-pipeline/raw/2.1.3/workflow/envs/ashleys_base.yaml /conda-envs/87c04f5d115eff742eca84455513deba/environment.yaml
+
+# Conda environment:
+#   source: https://github.com/friendsofstrandseq/ashleys-qc-pipeline/raw/2.1.3/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://github.com/friendsofstrandseq/ashleys-qc-pipeline/raw/2.1.3/workflow/envs/ashleys_rtools.yaml /conda-envs/9b847fc31baae8e01dfb7ce438a56b71/environment.yaml
+
+# 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/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/261d620cc100b901beec2634c6032c4f
+#   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
+RUN mkdir -p /conda-envs/261d620cc100b901beec2634c6032c4f
+COPY workflow/envs/rtools.yaml /conda-envs/261d620cc100b901beec2634c6032c4f/environment.yaml
+
+# Step 2: Generate conda environments
+
+RUN 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/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/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/261d620cc100b901beec2634c6032c4f --file /conda-envs/261d620cc100b901beec2634c6032c4f/environment.yaml && \
+    mamba clean --all -y

workflow/rules/scNOVA.smk

@@ -85,7 +85,7 @@ rule remove_low_quality_reads:
         None
     input:
         bam="{folder}/{sample}/selected/{cell}.sort.mdup.bam",
-        check="workflow/data/scNOVA/log/dl.ok",
+        # check="workflow/data/scNOVA/log/dl.ok",
     output:
         bam_pre="{folder}/{sample}/scNOVA_bam_modified/{cell}.sc_pre_mono.bam",
         bam_header="{folder}/{sample}/scNOVA_bam_modified/{cell}.header_test.sam",