Refactor assay-specific Snakefiles to include SCALE_RESOURCES variable

alsmith151 · Jul 23, 2024 · 6ff4793 · 6ff4793
1 parent 7c54954
commit 6ff4793
Show file tree

Hide file tree

Showing 4 changed files with 4 additions and 4 deletions.
diff --git a/seqnado/workflow/snakefile_atac b/seqnado/workflow/snakefile_atac
@@ -17,7 +17,7 @@ from seqnado.helpers import format_config_dict, symlink_fastq_files, remove_unwa
 ####################
 
 ASSAY = "ATAC"
-SCALE_RESOURCES = os.environ.get("SCALE_RESOURCES", "1")
+SCALE_RESOURCES = float(os.environ.get("SCALE_RESOURCES", "1"))
 
 configfile: "config_atac.yml"
 container: "library://asmith151/seqnado/seqnado_pipeline:latest"

diff --git a/seqnado/workflow/snakefile_chip b/seqnado/workflow/snakefile_chip
@@ -16,7 +16,7 @@ from seqnado.helpers import format_config_dict, symlink_fastq_files, get_scale_m
 ####################
 
 ASSAY = "ChIP"
-SCALE_RESOURCES = os.environ.get("SCALE_RESOURCES", "1")
+SCALE_RESOURCES = float(os.environ.get("SCALE_RESOURCES", "1"))
 configfile: "config_chip.yml"
 container: "library://asmith151/seqnado/seqnado_pipeline:latest"
 

diff --git a/seqnado/workflow/snakefile_rna b/seqnado/workflow/snakefile_rna
@@ -14,7 +14,7 @@ from seqnado.helpers import format_config_dict, symlink_fastq_files, remove_unwa
 # Hardcoded config #
 ####################
 ASSAY = "RNA"
-SCALE_RESOURCES = os.environ.get("SCALE_RESOURCES", "1")
+SCALE_RESOURCES = float(os.environ.get("SCALE_RESOURCES", "1"))
 
 
 configfile: "config_rna.yml"

diff --git a/seqnado/workflow/snakefile_snp b/seqnado/workflow/snakefile_snp
@@ -17,7 +17,7 @@ from seqnado.helpers import format_config_dict, symlink_fastq_files, remove_unwa
 ####################
 
 ASSAY = "SNP"
-SCALE_RESOURCES = os.environ.get("SCALE_RESOURCES", "1")
+SCALE_RESOURCES = float(os.environ.get("SCALE_RESOURCES", "1"))
 configfile: "config_snp.yml"
 container: "library://asmith151/seqnado/seqnado_pipeline:latest"