Reverting last two commits.

As I was trying to add mafs as a targetable output, the way I handled polarization of major/minor seemed needlessy complicated. Instead, maf can just be done separately in a single rule or two and it cuts down on complexity a lot.
zjnolen · Sep 30, 2024 · 00ba4a3 · 00ba4a3
1 parent a6fdf70
commit 00ba4a3
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Showing 13 changed files with 124 additions and 236 deletions.
diff --git a/.test/config/config.yaml b/.test/config/config.yaml
@@ -149,14 +149,12 @@ params:
     extra_saf: "" # goes to all -doSaf runs
     extra_beagle: "" # goes to all -doGlf 2 runs
     domajorminor: 1 # Currently only compatible with values 1, 2, 4, 5
-    domaf: 1 # Currently only compatible with values 1, 2, 3
-    popmafmaj: "population" # "all" or "population"
+    domaf: 1
     snp_pval: "1e-6"
     min_maf: -1 # Set -1 to disable
     mindepthind_heterozygosity: 1
   ngsrelate:
-    ibsrelate-only-extra: ""
-    freqbased-extra: ""
+    prune: true
   ngsld:
     max_kb_dist_est-ld: 200
     rnd_sample_est-ld: 0.001

diff --git a/config/config.yaml b/config/config.yaml
@@ -148,14 +148,12 @@ params:
     extra_saf: "" # goes to all -doSaf runs
     extra_beagle: "" # goes to all -doGlf 2 runs
     domajorminor: 1 # Currently only compatible with values 1, 2, 4, 5
-    domaf: 1 # Currently only compatible with values 1, 2, 3
-    popmafmaj: "population" # "all" or "population"
+    domaf: 1
     snp_pval: "1e-6"
     min_maf: -1 # Set -1 to disable
     mindepthind_heterozygosity: 1
   ngsrelate:
-    ibsrelate-only-extra: ""
-    freqbased-extra: ""
+    prune: false
   ngsld:
     max_kb_dist_est-ld: 4000
     rnd_sample_est-ld: 0.001

diff --git a/workflow/Snakefile b/workflow/Snakefile
@@ -59,7 +59,6 @@ wildcard_constraints:
     dp=".{0}|.dp[1-9][0-9]*",
     chunk="[0-9]+",
     sites="|".join(filters),
-    maj="all|pop|anc|ref",
 
 
 # Accumulate desired output files from config file

diff --git a/workflow/rules/3.2_beagles.smk b/workflow/rules/3.2_beagles.smk
@@ -9,7 +9,7 @@ rule angsd_doGlf2:
     population beagle files, even if a population is fixed for a certain allele.
     """
     input:
-        unpack(get_sitesfile),
+        unpack(filt_depth),
         unpack(get_anc_ref),
         bam="results/datasets/{dataset}/bamlists/{dataset}.{ref}_{population}{dp}.bamlist",
         bams=get_bamlist_bams,
@@ -18,13 +18,13 @@ rule angsd_doGlf2:
         reffai="results/ref/{ref}/{ref}.fa.fai",
         regions="results/datasets/{dataset}/filters/chunks/{ref}_chunk{chunk}.rf",
     output:
-        beagle="results/datasets/{dataset}/beagles/chunks/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj.beagle.gz",
-        maf="results/datasets/{dataset}/beagles/chunks/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj.mafs.gz",
-        arg="results/datasets/{dataset}/beagles/chunks/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj.arg",
+        beagle="results/datasets/{dataset}/beagles/chunks/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.beagle.gz",
+        maf="results/datasets/{dataset}/beagles/chunks/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.mafs.gz",
+        arg="results/datasets/{dataset}/beagles/chunks/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.arg",
     log:
-        "logs/{dataset}/angsd/doGlf2/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj.log",
+        "logs/{dataset}/angsd/doGlf2/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.log",
     benchmark:
-        "benchmarks/{dataset}/angsd/doGlf2/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj.log"
+        "benchmarks/{dataset}/angsd/doGlf2/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.log"
     container:
         angsd_container
     params:
@@ -33,9 +33,10 @@ rule angsd_doGlf2:
         extra_beagle=config["params"]["angsd"]["extra_beagle"],
         mapQ=config["mapQ"],
         baseQ=config["baseQ"],
+        snp_pval=config["params"]["angsd"]["snp_pval"],
         maf=config["params"]["angsd"]["domaf"],
-        snp_pval_maf=get_snppval_maf,
-        majmin=get_majmin,
+        minmaf=config["params"]["angsd"]["min_maf"],
+        majmin=config["params"]["angsd"]["domajorminor"],
         counts=get_docounts,
         trans=get_trans,
         nind=get_nind,
@@ -48,12 +49,12 @@ rule angsd_doGlf2:
     shell:
         """
         angsd -doGlf 2 -bam {input.bam} -GL {params.gl_model} -ref {input.ref} \
-            {params.majmin} -doMaf {params.maf} {params.snp_pval_maf} \
-            -nThreads {threads} {params.extra} -minMapQ {params.mapQ} \
-            -minQ {params.baseQ} -sites {input.sites} -anc {input.anc} \
-            {params.extra_beagle} -rf {input.regions} {params.minind} \
-            -setMinDepthInd {params.mininddp} {params.counts} \
-            -rmTrans {params.trans} -out {params.out} &> {log}
+            -doMajorMinor {params.majmin} -doMaf {params.maf} -minMaf {params.minmaf} \
+            -SNP_pval {params.snp_pval} -nThreads {threads} {params.extra} \
+            -minMapQ {params.mapQ} -minQ {params.baseQ} -sites {input.sites} \
+            -anc {input.anc} {params.extra_beagle} -rf {input.regions} {params.minind} \
+            -setMinDepthInd {params.mininddp} {params.counts} -rmTrans {params.trans} \
+            -out {params.out} &> {log}
         """
 
 
@@ -63,15 +64,15 @@ rule merge_beagle:
     """
     input:
         lambda w: expand(
-            "results/datasets/{{dataset}}/beagles/chunks/{{dataset}}.{{ref}}_{{population}}{{dp}}_chunk{chunk}_{{sites}}-filts.{{maj}}maj.beagle.gz",
+            "results/datasets/{{dataset}}/beagles/chunks/{{dataset}}.{{ref}}_{{population}}{{dp}}_chunk{chunk}_{{sites}}-filts.beagle.gz",
             chunk=chunklist,
         ),
     output:
-        beagle="results/datasets/{dataset}/beagles/{dataset}.{ref}_{population}{dp}_{sites}-filts.{maj}maj.beagle.gz",
+        beagle="results/datasets/{dataset}/beagles/{dataset}.{ref}_{population}{dp}_{sites}-filts.beagle.gz",
     log:
-        "logs/{dataset}/angsd/doGlf2/{dataset}.{ref}_{population}{dp}_{sites}-filts.{maj}maj_merge-beagle.log",
+        "logs/{dataset}/angsd/doGlf2/{dataset}.{ref}_{population}{dp}_{sites}-filts_merge-beagle.log",
     benchmark:
-        "benchmarks/{dataset}/angsd/doGlf2/{dataset}.{ref}_{population}{dp}_{sites}-filts.{maj}maj_merge-beagle.log"
+        "benchmarks/{dataset}/angsd/doGlf2/{dataset}.{ref}_{population}{dp}_{sites}-filts_merge-beagle.log"
     container:
         shell_container
     resources:
@@ -93,15 +94,15 @@ rule merge_maf:
     """
     input:
         lambda w: expand(
-            "results/datasets/{{dataset}}/beagles/chunks/{{dataset}}.{{ref}}_{{population}}{{dp}}_chunk{chunk}_{{sites}}-filts.{{maj}}maj.mafs.gz",
+            "results/datasets/{{dataset}}/beagles/chunks/{{dataset}}.{{ref}}_{{population}}{{dp}}_chunk{chunk}_{{sites}}-filts.mafs.gz",
             chunk=chunklist,
         ),
     output:
-        maf="results/datasets/{dataset}/beagles/{dataset}.{ref}_{population}{dp}_{sites}-filts.{maj}maj.mafs.gz",
+        maf="results/datasets/{dataset}/mafs/{dataset}.{ref}_{population}{dp}_{sites}-filts.mafs.gz",
     log:
-        "logs/{dataset}/angsd/doGlf2/{dataset}.{ref}_{population}{dp}_{sites}-filts.{maj}maj_merge-mafs.log",
+        "logs/{dataset}/angsd/doGlf2/{dataset}.{ref}_{population}{dp}_{sites}-filts_merge-mafs.log",
     benchmark:
-        "benchmarks/{dataset}/angsd/doGlf2/{dataset}.{ref}_{population}{dp}_{sites}-filts.{maj}maj_merge-mafs.log"
+        "benchmarks/{dataset}/angsd/doGlf2/{dataset}.{ref}_{population}{dp}_{sites}-filts_merge-mafs.log"
     container:
         shell_container
     resources:
@@ -123,13 +124,13 @@ rule snpset:
     dataset.
     """
     input:
-        "results/datasets/{dataset}/beagles/{dataset}.{ref}_{population}{dp}_{sites}-filts.{maj}maj.mafs.gz",
+        "results/datasets/{dataset}/mafs/{dataset}.{ref}_{population}{dp}_{sites}-filts.mafs.gz",
     output:
-        "results/datasets/{dataset}/filters/snps/{dataset}.{ref}_{population}{dp}_{sites}-filts.{maj}maj_snps.sites",
+        "results/datasets/{dataset}/filters/snps/{dataset}.{ref}_{population}{dp}_{sites}-filts_snps.sites",
     log:
-        "logs/{dataset}/filters/snps/{dataset}.{ref}_{population}{dp}_{sites}-filts.{maj}maj_snps.log",
+        "logs/{dataset}/filters/snps/{dataset}.{ref}_{population}{dp}_{sites}-filts_snps.log",
     benchmark:
-        "benchmarks/{dataset}/filters/snps/{dataset}.{ref}_{population}{dp}_{sites}-filts.{maj}maj_snps.log"
+        "benchmarks/{dataset}/filters/snps/{dataset}.{ref}_{population}{dp}_{sites}-filts_snps.log"
     container:
         shell_container
     shell:

diff --git a/workflow/rules/4.0_estimate_LD.smk b/workflow/rules/4.0_estimate_LD.smk
@@ -8,19 +8,19 @@ rule ngsLD_estLD:
     Estimates pairwise linkage disequilibrium between SNPs.
     """
     input:
-        beagle="results/datasets/{dataset}/beagles/chunks/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj.beagle.gz",
+        beagle="results/datasets/{dataset}/beagles/chunks/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.beagle.gz",
         bamlist="results/datasets/{dataset}/bamlists/{dataset}.{ref}_{population}{dp}.bamlist",
     output:
         ld=temp(
-            "results/datasets/{dataset}/{path}/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj.ld_maxkbdist-{maxkb}_rndsample-{rndsmp}.gz"
+            "results/datasets/{dataset}/{path}/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.ld_maxkbdist-{maxkb}_rndsample-{rndsmp}.gz"
         ),
         pos=temp(
-            "results/datasets/{dataset}/{path}/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj.ld_maxkbdist-{maxkb}_rndsample-{rndsmp}.pos",
+            "results/datasets/{dataset}/{path}/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.ld_maxkbdist-{maxkb}_rndsample-{rndsmp}.pos",
         ),
     log:
-        "logs/{dataset}/ngsLD/estLD/{path}/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj.ld_maxkbdist-{maxkb}_rndsample-{rndsmp}.log",
+        "logs/{dataset}/ngsLD/estLD/{path}/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.ld_maxkbdist-{maxkb}_rndsample-{rndsmp}.log",
     benchmark:
-        "benchmarks/{dataset}/ngsLD/estLD/{path}/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj.ld_maxkbdist-{maxkb}_rndsample-{rndsmp}.log"
+        "benchmarks/{dataset}/ngsLD/estLD/{path}/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.ld_maxkbdist-{maxkb}_rndsample-{rndsmp}.log"
     container:
         ngsld_container
     threads: lambda wildcards, attempt: attempt
@@ -50,9 +50,8 @@ rule ngsLD_estLD:
 rule combine_LD_files:
     input:
         ldgz=expand(
-            "results/datasets/{{dataset}}/analyses/ngsLD/chunks/{{dataset}}.{{ref}}_{{population}}{{dp}}_chunk{chunk}_{{sites}}-filts.{maj}maj.ld_maxkbdist-{{maxkb}}_rndsample-{{rndsmp}}.gz",
+            "results/datasets/{{dataset}}/analyses/ngsLD/chunks/{{dataset}}.{{ref}}_{{population}}{{dp}}_chunk{chunk}_{{sites}}-filts.ld_maxkbdist-{{maxkb}}_rndsample-{{rndsmp}}.gz",
             chunk=chunklist,
-            maj=get_maj,
         ),
     output:
         ldgz="results/datasets/{dataset}/analyses/ngsLD/{dataset}.{ref}_{population}{dp}_{sites}-filts.ld_maxkbdist-{maxkb}_rndsample-{rndsmp}.gz",

diff --git a/workflow/rules/4.1_linkage_pruning.smk b/workflow/rules/4.1_linkage_pruning.smk
@@ -7,13 +7,13 @@ rule ngsLD_prune_sites:
     Prunes SNPs to produce a list of SNPs in linkage equilibrium.
     """
     input:
-        ld="results/datasets/{dataset}/beagles/pruned/ngsLD/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj.ld_maxkbdist-{maxkb}_rndsample-1.gz",
+        ld="results/datasets/{dataset}/beagles/pruned/ngsLD/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.ld_maxkbdist-{maxkb}_rndsample-1.gz",
     output:
-        sites="results/datasets/{dataset}/beagles/pruned/ngsLD/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj.pruned_maxkbdist-{maxkb}_minr2-{r2}.sites",
+        sites="results/datasets/{dataset}/beagles/pruned/ngsLD/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.pruned_maxkbdist-{maxkb}_minr2-{r2}.sites",
     log:
-        "logs/{dataset}/ngsLD/prune_sites/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj_maxkbdist-{maxkb}_minr2-{r2}.log",
+        "logs/{dataset}/ngsLD/prune_sites/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts_maxkbdist-{maxkb}_minr2-{r2}.log",
     benchmark:
-        "benchmarks/{dataset}/ngsLD/prune_sites/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj_maxkbdist-{maxkb}_minr2-{r2}.log"
+        "benchmarks/{dataset}/ngsLD/prune_sites/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts_maxkbdist-{maxkb}_minr2-{r2}.log"
     container:
         ngsld_container
     threads: 4
@@ -36,21 +36,21 @@ rule prune_chunk_beagle:
     Subsets beagle file to pruned SNPs.
     """
     input:
-        beagle="results/datasets/{dataset}/beagles/chunks/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj.beagle.gz",
-        sites="results/datasets/{dataset}/beagles/pruned/ngsLD/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj.pruned_maxkbdist-{maxkb}_minr2-{r2}.sites",
+        beagle="results/datasets/{dataset}/beagles/chunks/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.beagle.gz",
+        sites="results/datasets/{dataset}/beagles/pruned/ngsLD/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.pruned_maxkbdist-{maxkb}_minr2-{r2}.sites",
     output:
-        prunedgz="results/datasets/{dataset}/beagles/pruned/chunks/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj.pruned_maxkbdist-{maxkb}_minr2-{r2}.beagle.gz",
+        prunedgz="results/datasets/{dataset}/beagles/pruned/chunks/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.pruned_maxkbdist-{maxkb}_minr2-{r2}.beagle.gz",
     log:
-        "logs/{dataset}/ngsLD/prune_beagle/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj.pruned_maxkbdist-{maxkb}_minr2-{r2}.log",
+        "logs/{dataset}/ngsLD/prune_beagle/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.pruned_maxkbdist-{maxkb}_minr2-{r2}.log",
     benchmark:
-        "benchmarks/{dataset}/ngsLD/prune_beagle/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj.pruned_maxkbdist-{maxkb}_minr2-{r2}.log"
+        "benchmarks/{dataset}/ngsLD/prune_beagle/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.pruned_maxkbdist-{maxkb}_minr2-{r2}.log"
     container:
         shell_container
     shadow:
         "minimal"
     threads: lambda wildcards, attempt: attempt
     params:
-        pruned="results/datasets/{dataset}/beagles/pruned/chunks/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.{maj}maj.pruned_maxkbdist-{maxkb}_minr2-{r2}.beagle",
+        pruned="results/datasets/{dataset}/beagles/pruned/chunks/{dataset}.{ref}_{population}{dp}_chunk{chunk}_{sites}-filts.pruned_maxkbdist-{maxkb}_minr2-{r2}.beagle",
     resources:
         runtime=lambda wildcards, attempt: attempt * 120,
     shell:
@@ -78,15 +78,15 @@ rule merge_pruned_beagles:
     """
     input:
         pruned=lambda w: expand(
-            "results/datasets/{{dataset}}/beagles/pruned/chunks/{{dataset}}.{{ref}}_{{population}}{{dp}}_chunk{chunk}_{{sites}}-filts.{{maj}}maj.pruned_maxkbdist-{{maxkb}}_minr2-{{r2}}.beagle.gz",
+            "results/datasets/{{dataset}}/beagles/pruned/chunks/{{dataset}}.{{ref}}_{{population}}{{dp}}_chunk{chunk}_{{sites}}-filts.pruned_maxkbdist-{{maxkb}}_minr2-{{r2}}.beagle.gz",
             chunk=chunklist,
         ),
     output:
-        beagle="results/datasets/{dataset}/beagles/pruned/{dataset}.{ref}_{population}{dp}_{sites}-filts.{maj}maj.pruned_maxkbdist-{maxkb}_minr2-{r2}.beagle.gz",
+        beagle="results/datasets/{dataset}/beagles/pruned/{dataset}.{ref}_{population}{dp}_{sites}-filts.pruned_maxkbdist-{maxkb}_minr2-{r2}.beagle.gz",
     log:
-        "logs/{dataset}/ngsLD/merge_pruned/{dataset}.{ref}_{population}{dp}_{sites}-filts.{maj}maj_merge.pruned_maxkbdist-{maxkb}_minr2-{r2}.log",
+        "logs/{dataset}/ngsLD/merge_pruned/{dataset}.{ref}_{population}{dp}_{sites}-filts_merge.pruned_maxkbdist-{maxkb}_minr2-{r2}.log",
     benchmark:
-        "benchmarks/{dataset}/ngsLD/merge_pruned/{dataset}.{ref}_{population}{dp}_{sites}-filts.{maj}maj_merge.pruned_maxkbdist-{maxkb}_minr2-{r2}.log"
+        "benchmarks/{dataset}/ngsLD/merge_pruned/{dataset}.{ref}_{population}{dp}_{sites}-filts_merge.pruned_maxkbdist-{maxkb}_minr2-{r2}.log"
     wildcard_constraints:
         population="|".join(
             ["all"]

diff --git a/workflow/rules/4.2_linkage_decay.smk b/workflow/rules/4.2_linkage_decay.smk
@@ -1,19 +1,19 @@
 rule combine_LDdecay_files:
     input:
         ldgz=expand(
-            "results/datasets/{{dataset}}/analyses/ngsLD/chunks/{{dataset}}.{{ref}}_{{population}}{{dp}}_chunk{chunk}_{{sites}}-filts.{{maj}}maj.ld_maxkbdist-{maxkb}_rndsample-{rndsmp}.gz",
+            "results/datasets/{{dataset}}/analyses/ngsLD/chunks/{{dataset}}.{{ref}}_{{population}}{{dp}}_chunk{chunk}_{{sites}}-filts.ld_maxkbdist-{maxkb}_rndsample-{rndsmp}.gz",
             chunk=chunklist,
             maxkb=config["params"]["ngsld"]["max_kb_dist_decay"],
             rndsmp=config["params"]["ngsld"]["rnd_sample_decay"],
         ),
     output:
         ldgz=temp(
-            "results/datasets/{dataset}/analyses/ngsLD/decay/{dataset}.{ref}_{population}{dp}_{sites}-filts.{maj}maj.LDdecay.gz"
+            "results/datasets/{dataset}/analyses/ngsLD/decay/{dataset}.{ref}_{population}{dp}_{sites}-filts.LDdecay.gz"
         ),
     log:
-        "logs/{dataset}/ngsLD/combine_LDdecay_files/{dataset}.{ref}_{population}{dp}_{sites}-filts.{maj}maj.ld_decay.log",
+        "logs/{dataset}/ngsLD/combine_LDdecay_files/{dataset}.{ref}_{population}{dp}_{sites}-filts.ld_decay.log",
     benchmark:
-        "benchmarks/{dataset}/ngsLD/combine_LDdecay_files/{dataset}.{ref}_{population}{dp}_{sites}-filts.{maj}maj.ld_decay.log"
+        "benchmarks/{dataset}/ngsLD/combine_LDdecay_files/{dataset}.{ref}_{population}{dp}_{sites}-filts.ld_decay.log"
     container:
         shell_container
     shell:
@@ -24,10 +24,7 @@ rule combine_LDdecay_files:
 
 rule fit_LD_decay:
     input:
-        lambda w: expand(
-            "results/datasets/{{dataset}}/analyses/ngsLD/decay/{{dataset}}.{{ref}}_{{population}}{{dp}}_{{sites}}-filts.{maj}maj.LDdecay.gz",
-            maj=get_maj,
-        ),
+        "results/datasets/{dataset}/analyses/ngsLD/decay/{dataset}.{ref}_{population}{dp}_{sites}-filts.LDdecay.gz",
     output:
         plot=report(
             "results/datasets/{dataset}/plots/LD_decay/{dataset}.{ref}_{population}{dp}_{sites}-filts.LDdecay.pdf",