Merge pull request #82 from NBISweden/dev

Updates for GenErode version 0.6.1

.github/workflows/gerp.yaml

@@ -67,9 +67,9 @@ jobs:
       - name: gerp_dry
         shell: bash -l {0}
         run: |
-          snakemake -npr --configfile .test/config/config_gerp.yaml -j 4 --cores 1 --use-singularity
+          snakemake -np -k --configfile .test/config/config_gerp.yaml -j 4 --cores 1 --use-singularity
 
       - name: gerp
         shell: bash -l {0}
         run: |
-          snakemake --configfile .test/config/config_gerp.yaml -j 4 --cores 1 --use-singularity
+          snakemake -k --configfile .test/config/config_gerp.yaml -j 4 --cores 1 --use-singularity

.github/workflows/mitogenome_mapping.yaml

@@ -91,10 +91,10 @@ jobs:
       - name: mitogenome_mapping_dry
         shell: bash -l {0}
         run: |
-          snakemake -npr --configfile .test/config/config_mitogenomes.yaml -j 4 --cores 1 --use-singularity
+          snakemake -np -k --configfile .test/config/config_mitogenomes.yaml -j 4 --cores 1 --use-singularity
 
       - name: mitogenome_mapping
         shell: bash -l {0}
         run: |
-          snakemake --configfile .test/config/config_mitogenomes.yaml -j 4 --cores 1 --use-singularity
+          snakemake -k --configfile .test/config/config_mitogenomes.yaml -j 4 --cores 1 --use-singularity
 

.github/workflows/mlRho_options.yaml

@@ -73,9 +73,9 @@ jobs:
       - name: mlRho_options_dry
         shell: bash -l {0}
         run: |
-          snakemake -npr --configfile .test/config/config_mlRho_options.yaml -j 4 --cores 1 --use-singularity
+          snakemake -np -k --configfile .test/config/config_mlRho_options.yaml -j 4 --cores 1 --use-singularity
 
       - name: mlRho_options
         shell: bash -l {0}
         run: |
-          snakemake --configfile .test/config/config_mlRho_options.yaml -j 4 --cores 1 --use-singularity
+          snakemake -k --configfile .test/config/config_mlRho_options.yaml -j 4 --cores 1 --use-singularity

.github/workflows/pca_roh.yaml

@@ -65,9 +65,9 @@ jobs:
       - name: pca_roh_dry
         shell: bash -l {0}
         run: |
-          snakemake -npr --configfile .test/config/config_pca_roh.yaml -j 4 --cores 1 --use-singularity
+          snakemake -np -k --configfile .test/config/config_pca_roh.yaml -j 4 --cores 1 --use-singularity
 
       - name: pca_roh
         shell: bash -l {0}
         run: |
-          snakemake --configfile .test/config/config_pca_roh.yaml -j 4 --cores 1 --use-singularity
+          snakemake -k --configfile .test/config/config_pca_roh.yaml -j 4 --cores 1 --use-singularity

.github/workflows/snpeff.yaml

@@ -67,9 +67,9 @@ jobs:
       - name: snpeff_dry
         shell: bash -l {0}
         run: |
-          snakemake -npr --configfile .test/config/config_snpeff.yaml -j 4 --cores 1 --use-singularity
+          snakemake -np -k --configfile .test/config/config_snpeff.yaml -j 4 --cores 1 --use-singularity
 
       - name: snpeff
         shell: bash -l {0}
         run: |
-          snakemake --configfile .test/config/config_snpeff.yaml -j 4 --cores 1 --use-singularity
+          snakemake -k --configfile .test/config/config_snpeff.yaml -j 4 --cores 1 --use-singularity

.test/config/config_pca_roh.yaml

@@ -153,13 +153,13 @@ zerocoverage: False
 # to set a minimum depth threshold. For ultra low coverage samples, a 
 # minimum hard threshold of 3X is applied that overrides this parameter.
 # A minimum depth of 6X should be aimed for.
-minDP: 0.33
+minDP: 0.1
 
 # Maximum depth threshold calculation per sample.
 # Will be applied to mlRho analysis and in VCF file filtering.
 # Factor by which the average genome-wide depth should be multiplied 
 # to set a maximum depth threshold.
-maxDP: 10
+maxDP: 100
 #####
 
 

config/slurm/README.md

@@ -0,0 +1,71 @@
+# GenErode execution on Dardel (PDC/KTH)
+
+1) Load the following modules:
+
+```
+module load PDC UPPMAX bioinfo-tools conda singularity tmux
+```
+
+> Note that tmux is only available as a module on Dardel 
+but the equivalent tool screen is pre-installed and does 
+not need to be loaded. 
+
+2) After cloning the repository, change permissions for the 
+Snakefile:
+
+```
+chmod 755 Snakefile
+```
+
+3) Create the GenErode conda environment or update an earlier 
+version. The latest conda environment contains the Snakemake 
+executor plugin for slurm:
+
+```
+conda create -f environment.yaml -n generode
+```
+
+4) Copy the configuration file `config/slurm/profile/config_plugin_dardel.yaml` 
+to `slurm/config.yaml`. This file specifies compute resources 
+for each rule or group jobs to be run on Dardel. Any rule or 
+group job that is not listed under `set-threads` or `set-resources` 
+uses default resources specified under `default-resources`. If 
+any rule or group job fails due to too little memory or run 
+time, their compute resources can be updated in this file. 
+
+> Note that memory requirements are specified three times in 
+the configuration file: 1) under `set-threads` (used by Snakemake 
+to specify threads in rules), 2) under `set-resources` and therein 
+under `mem_mb`, specifying the memory in Megabytes (multiplying 
+the number of threads with the available memory per thread), 
+and 3) under `set-resources` and therein under `cpus-per-task` 
+(the same number as specified under `set-threads`, required for 
+correct memory assignment on Dardel). 
+
+5) Start GenErode the following:
+
+- Open a tmux session (alternatively, you can use screen)
+
+- Activate the GenErode conda environment (create or update 
+from `environment.yaml`), replacing the path to the location 
+of the conda environment:
+
+```
+export CONDA_ENVS_PATH=/cfs/klemming/home/.../
+conda activate generode
+```
+
+- Start the dry run:
+
+```
+snakemake --profile slurm -n &> YYMMDD_dry.out
+```
+
+- Start the main run:
+
+```
+snakemake --profile slurm &> YYMMDD_main.out
+```
+
+> Useful flags for running the pipeline: `--ri` to re-run 
+incomplete jobs and `-k` to keep going in case a job fails.