Merge pull request #97 from hydra-genetics/develop

chore: dev to master

.github/workflows/compatibility.yaml

@@ -36,8 +36,4 @@ jobs:
       - name: snakemake dry run
         working-directory: .tests/compatibility
         run: |
-          snakemake -n -s Snakefile -c
-      - name: snakemake dry run fastp_pe config
-        working-directory: .tests/compatibility
-        run: |
-          snakemake -n -s Snakefile
+          snakemake -n -s Snakefile --configfile config.yaml

.github/workflows/integration.yaml

@@ -22,6 +22,7 @@ jobs:
           echo $CONDA/bin >> $GITHUB_PATH
       - name: Install dependencies
         run: |
+          conda config --set channel_priority strict
           conda install -c conda-forge mamba=0.15.3
       - name: Install requirements.txt
         run: |
@@ -32,7 +33,7 @@ jobs:
       - name: Integration test - small dataset
         working-directory: .tests/integration
         run: |
-          snakemake -s ../../workflow/Snakefile -j 1 --use-conda
+          snakemake -s ../../workflow/Snakefile -j 1 --configfile config.yaml --use-conda
   integration-small-singularity:
     name: integration small data set singularity
     runs-on: ubuntu-latest
@@ -47,6 +48,7 @@ jobs:
           echo $CONDA/bin >> $GITHUB_PATH
       - name: Install dependencies
         run: |
+          conda config --set channel_priority strict
           conda install -c conda-forge mamba=0.15.3
       - name: Install requirements.txt
         run: |
@@ -58,4 +60,4 @@ jobs:
         working-directory: .tests/integration
         run: |
           mamba install -c conda-forge -c bioconda singularity=3.8.6
-          snakemake -s ../../workflow/Snakefile -j 1 --show-failed-logs --use-singularity --singularity-args  " --cleanenv --bind /home/runner "
+          snakemake -s ../../workflow/Snakefile -j 1 --show-failed-logs  --configfile config.yaml --use-singularity --singularity-args  " --cleanenv --bind /home/runner "

.github/workflows/lint.yaml

@@ -23,5 +23,5 @@ jobs:
         with:
           directory: ".tests/integration"
           snakefile: "workflow/Snakefile"
-          args: "--lint"
+          args: "--lint --configfile .tests/integration/config.yaml"
           stagein: "pip install -r requirements.txt"

.github/workflows/snakemake-dry-run.yaml

@@ -33,4 +33,4 @@ jobs:
       - name: snakemake dry run
         working-directory: .tests/integration
         run: |
-          snakemake -n -s ../../workflow/Snakefile
+          snakemake -n -s ../../workflow/Snakefile --configfile config.yaml

COMPATIBLITY.md

@@ -3,6 +3,7 @@
 
 | alignment version | snv_indels version |
 | --- | --- |
+| v0.3.0 | v0.3.0 |
 | v0.2.0 | v0.2.0 |
 | v0.2.0 | v0.1.1 |
 | v0.1.0 | v0.1.1 |

README.md

@@ -30,6 +30,8 @@ In order to use this module, the following dependencies are required:
 [![snakemake](https://img.shields.io/badge/snakemake-6.10.0-blue)](https://snakemake.readthedocs.io/en/stable/)
 [![singularity](https://img.shields.io/badge/singularity-3.0.0-blue)](https://sylabs.io/docs/)
 
+*Note! Releases of snv_indels <= v0.2.0 needs tabulate<0.9.0 added in requirements.txt**
+
 ## :school_satchel: Preparations
 
 ### Sample and unit data
@@ -94,7 +96,7 @@ use rule * from snv_indels as snv_indels_*
 ### Compatibility
 
 Latest:
- - alignment:v0.2.0
+ - alignment:v0.3.0
 
  See [COMPATIBLITY.md](../master/COMPATIBLITY.md) file for a complete list of module compatibility.
 

requirements.txt

@@ -3,4 +3,5 @@ jinja2==3.0.1
 networkx==2.5
 pandas>=1.3.1
 singularity==3.0.0
-snakemake==6.10.0
+snakemake==7.8.0
+tabulate<0.9.0

workflow/rules/common.smk

@@ -13,12 +13,12 @@ from snakemake.exceptions import WorkflowError
 from snakemake.utils import min_version
 from snakemake.utils import validate
 
-min_version("6.10.0")
+min_version("7.8.0")
 
 ### Set and validate config file
 
-
-configfile: "config.yaml"
+if not workflow.overwrite_configfiles:
+    sys.exit("At least one config file must be passed using --configfile/--configfiles, by command line or a profile!")
 
 
 validate(config, schema="../schemas/config.schema.yaml")

workflow/scripts/mutect2_pass_filter.py

@@ -5,5 +5,5 @@
 vcf_out = VariantFile(snakemake.output.vcf, 'w', header=vcf_in.header)
 
 for record in vcf_in.fetch():
-    if record.filter.keys() == ["PASS"]:
+    if record.filter.keys() == ["PASS"] or record.filter.keys() == ["multiallelic"]:
         vcf_out.write(record)