Merge pull request #34 from 3d-omics/ci

fix: rename and replace rules

profile/default/config.yaml

@@ -32,40 +32,37 @@ set-resources:
         mem_mb: 4G
     # align
     align__index__:
-        mem_mb: 64 * 1024
-        runtime: 24 * 60
+        mem_mb: 64G
+        runtime: 1d
     align__map__:
-        mem_mb: 64 * 1024
-        runtime: 24 * 60
+        mem_mb: 64G
+        runtime: 1d
     align__mark_duplicates__:
-        mem_mb: 8 * 1024
-        runtime: 6 * 60
+        mem_mb: 8G
+        runtime: 6h
     align__mark_duplicates__bam_to_cram__:
-        mem_mb: 8 * 1024
-        runtime: 12 * 60
+        mem_mb: 8G
+        runtime: 12h
+    align__bcftools__call__:
+        mem_mb: 8G
+        runtime: 1d
     align__recalibrate__baserecalibrator__:
-        mem_mb: 8 * 1024
-        runtime: 24 * 60
-    align__recalibrate__applybqsr__:
-        mem_mb: 8 * 1024
-        runtime: 24 * 60
-    align__recalibrate__bam_to_cram__:
-        mem_mb: 4 * 1024
-        runtime: 24 * 60
-    # variants
-    variants__call__haplotype_caller__:
         mem_mb: 8G
         runtime: 1d
-    variants__combine_gvcfs__:
+    align__recalibrate__applybqsr__:
         mem_mb: 8G
         runtime: 1d
-    variants__genotype_gvcfs__:
+    align__recalibrate__bam_to_cram__:
+        mem_mb: 4G
+        runtime: 6h
+    # variants
+    variants__call__haplotype_caller__:
         mem_mb: 8G
         runtime: 1d
-    variants__calculate_genotype_posteriors__:
+    variants__call__combine_gvcfs__:
         mem_mb: 8G
         runtime: 1d
-    variants__variant_filtration__:
+    variants__genotype__genotype_gvcfs__:
         mem_mb: 8G
         runtime: 1d
     # annotate

workflow/Snakefile

@@ -47,14 +47,14 @@ include: "rules/swaps/__main__.smk"
 include: "rules/report/__main__.smk"
 
 
-rule cache:
-    input:
-        rules.reference.input,
-        rules.align__index.input,
-
-
 rule all:
     """Run the entire pipeline"""
     input:
         rules.report__step.input,
         rules.report__sample.input,
+
+
+rule cache:
+    input:
+        rules.reference.input,
+        rules.align__index.input,

workflow/rules/variants/__functions__.smk

@@ -43,18 +43,23 @@ def get_ploidy_of_sample_and_chromosome(wildcards):
         return 1
     if chromosome in autosomes:
         return 2
-    if sex == "male" and chromosome not in male_chromosomes:
-        return 0
-    if sex == "female" and chromosome not in female_chromosomes:
-        return 0
-    if chromosome in male_chromosomes and len(male_chromosomes) == 1:
-        return 2
-    if chromosome in female_chromosomes and len(female_chromosomes) == 1:
-        return 2
-    if chromosome in male_chromosomes and len(male_chromosomes) == 2:
+    if sex == "male" and len(male_chromosomes) == 2 and chromosome in male_chromosomes:
         return 1
-    if chromosome in female_chromosomes and len(female_chromosomes) == 2:
+    if sex == "male" and len(male_chromosomes) == 1 and chromosome in male_chromosomes:
+        return 2
+    if (
+        sex == "female"
+        and len(female_chromosomes) == 2
+        and chromosome in female_chromosomes
+    ):
         return 1
+    if (
+        sex == "female"
+        and len(female_chromosomes) == 1
+        and chromosome in female_chromosomes
+    ):
+        return 2
+    return 0
 
 
 def generate_mock_interval(wildcards):

workflow/rules/variants/genotype.smk

@@ -1,4 +1,4 @@
-rule variants__genotype_gvcfs__:
+rule variants__genotype__genotype_gvcfs__:
     """Genotype a single region"""
     input:
         vcf_gz=CALL / "{region}.vcf.gz",
@@ -22,7 +22,7 @@ rule variants__genotype_gvcfs__:
         """
 
 
-rule variants__genotype_gvcfs__merge_vcfs__:
+rule variants__genotype__merge_vcfs__:
     """Join all the GVCFs into a single one
 
     Mysterioustly MergeVcfs fucks up the file