bump freebayes and move regions to results

workflow/envs/variants.yaml

@@ -4,6 +4,6 @@ channels:
 dependencies:
   - hisat2
   - samtools
-  - freebayes=1.3.2
+  - freebayes=1.3.8
   - bcftools
   - samblaster

workflow/rules/common.smk

@@ -163,15 +163,6 @@ def GetDesiredOutputs(wildcards):
             )
         )
 
-        if config['QualityControl']['coverage']['activate']:
-            wanted_input.extend(
-                expand(
-                    [
-                        "results/qc/coverage/{sample}.mosdepth.summary.txt",
-                    ],
-                sample=samples,
-                )
-            )
 
         if config["VariantAnalysis"]["selection"]["activate"]:
             wanted_input.extend(
@@ -189,19 +180,53 @@ def GetDesiredOutputs(wildcards):
                 )
             )
 
-    if config["VariantAnalysis"]["ancestry"]["activate"]:
+        if config["VariantAnalysis"]["ancestry"]["activate"]:
+            wanted_input.extend(
+                expand(
+                    [
+                        "results/variantAnalysis/ancestry/AIMs_summary.tsv",
+                        "results/variantAnalysis/ancestry/AIM_fraction_whole_genome.svg",
+                        "results/variantAnalysis/ancestry/n_AIMS_per_chrom.tsv",
+                        "results/variantAnalysis/ancestry/AIM_fraction_{contig}.tsv",
+                    ],
+                    contig=config["contigs"],
+                )
+            )
+
+        if config["VariantAnalysis"]["karyotype"]["activate"]:
+            wanted_input.extend(
+                expand(
+                    [
+                        "results/karyotype/{karyo}.{dataset}.karyo.txt",
+                        "results/karyotype/karyoFreqs.svg",
+                    ],
+                    karyo=config["VariantAnalysis"]["karyotype"]["inversions"],
+                    dataset=config["dataset"],
+                )
+            )
+
+        if (
+        config["VariantAnalysis"]['selection']["activate"]
+        and config["DifferentialExpression"]["GSEA"]["activate"]
+        ):
+            wanted_input.extend(
+                expand(
+                    ["results/gsea/fst/{comp}.fst.tsv"],
+                    comp=config["contrasts"],
+                )
+            )
+
+    if config['QualityControl']['coverage']['activate']:
         wanted_input.extend(
             expand(
                 [
-                    "results/variantAnalysis/ancestry/AIMs_summary.tsv",
-                    "results/variantAnalysis/ancestry/AIM_fraction_whole_genome.svg",
-                    "results/variantAnalysis/ancestry/n_AIMS_per_chrom.tsv",
-                    "results/variantAnalysis/ancestry/AIM_fraction_{contig}.tsv",
+                    "results/qc/coverage/{sample}.mosdepth.summary.txt",
                 ],
-                contig=config["contigs"],
+            sample=samples,
             )
         )
 
+
     if config["miscellaneous"]["VariantsOfInterest"]["activate"]:
         wanted_input.extend(
             [
@@ -221,29 +246,6 @@ def GetDesiredOutputs(wildcards):
             )
         )
 
-    if (
-        config["VariantAnalysis"]['selection']["activate"]
-        and config["DifferentialExpression"]["GSEA"]["activate"]
-    ):
-        wanted_input.extend(
-            expand(
-                ["results/gsea/fst/{comp}.fst.tsv"],
-                comp=config["contrasts"],
-            )
-        )
-
-    if config["VariantAnalysis"]["karyotype"]["activate"]:
-        wanted_input.extend(
-            expand(
-                [
-                    "results/karyotype/{karyo}.{dataset}.karyo.txt",
-                    "results/karyotype/karyoFreqs.svg",
-                ],
-                karyo=config["VariantAnalysis"]["karyotype"]["inversions"],
-                dataset=config["dataset"],
-            )
-        )
-
     if config["miscellaneous"]["sweeps"]["activate"]:
         if config["DifferentialExpression"]['gene-level']["activate"]:
             wanted_input.extend(

workflow/rules/hisat2-freebayes.smk

@@ -59,7 +59,7 @@ rule GenerateFreebayesParams:
         bamlist="results/alignments/bam.list",
         pops="results/alignments/populations.tsv",
         regions=expand(
-            "resources/regions/genome.{contig}.region.{i}.bed",
+            "results/variantAnalysis/regions/genome.{contig}.region.{i}.bed",
             contig=config["contigs"],
             i=chunks,
         ),
@@ -83,9 +83,9 @@ rule VariantCallingFreebayes:
         bams=expand("results/alignments/{sample}.hisat2.bam", sample=samples),
         index=expand("results/alignments/{sample}.hisat2.bam.bai", sample=samples),
         ref=config["reference"]["genome"].rstrip(".gz"),
-        samples=ancient("results/alignments/bam.list"),
-        pops=ancient("results/alignments/populations.tsv"),
-        regions=ancient("resources/regions/genome.{contig}.region.{i}.bed"),
+        samples="results/alignments/bam.list",
+        pops="results/alignments/populations.tsv",
+        regions="results/variantAnalysis/regions/genome.{contig}.region.{i}.bed",
     output:
         temp("results/variantAnalysis/vcfs/freebayes/{contig}/variants.{i}.vcf"),
     log:

workflow/scripts/GenerateFreebayesParams.R

@@ -43,7 +43,7 @@ for (contig in contigs){
    for (i in 1:(chunks-1)){
       #write bed file, one for each chunk/interval, which will be passed as input to freebayes
       row = c(contig, bedseq[i], bedseq[i+1])
-      data.frame(row) %>% t() %>% fwrite(., glue("resources/regions/genome.{contig}.region.{i}.bed"), sep="\t", col.names = FALSE)
+      data.frame(row) %>% t() %>% fwrite(., glue("results/variantAnalysis/regions/genome.{contig}.region.{i}.bed"), sep="\t", col.names = FALSE)
    }
 }