feat: annotate access patterns

Author: johanneskoester

workflow/Snakefile

@@ -13,6 +13,10 @@ scattergather:
     calling=16,
 
 
+input_default:
+    access.seq,
+
+
 # Allow users to fix the underlying OS via singularity.
 container: "docker://continuumio/miniconda3"
 

workflow/rules/annotation.smk

@@ -1,9 +1,9 @@
 rule annotate_candidate_variants:
     input:
         calls="results/candidate-calls/{group}.{caller}.{scatteritem}.bcf",
-        cache="resources/vep/cache",
-        plugins="resources/vep/plugins",
-        fasta=genome,
+        cache=access.random("resources/vep/cache"),
+        plugins=access.random("resources/vep/plugins"),
+        fasta=access.random(genome),
         fai=genome_fai,
     output:
         calls="results/candidate-calls/{group}.{caller}.{scatteritem}.annotated.bcf",
@@ -25,11 +25,11 @@ rule annotate_candidate_variants:
 rule annotate_variants:
     input:
         calls="results/calls/{group}.{calling_type}.{scatteritem}.bcf",
-        cache="resources/vep/cache",
-        plugins="resources/vep/plugins",
+        cache=access.random("resources/vep/cache"),
+        plugins=access.random("resources/vep/plugins"),
         revel=lambda wc: get_plugin_aux("REVEL"),
         revel_tbi=lambda wc: get_plugin_aux("REVEL", True),
-        fasta=genome,
+        fasta=access.random(genome),
         fai=genome_fai,
     output:
         calls="results/calls/{group}.{calling_type}.{scatteritem}.annotated.bcf",

workflow/rules/calling.smk

@@ -44,7 +44,7 @@ rule varlociraptor_preprocess:
     input:
         ref=genome,
         ref_idx=genome_fai,
-        candidates=get_candidate_calls,
+        candidates=access.multi(get_candidate_calls),
         bam="results/recal/{sample}.bam",
         bai="results/recal/{sample}.bai",
         alignment_props=get_alignment_props,

workflow/rules/candidate_calling.smk

@@ -1,10 +1,10 @@
 rule freebayes:
     input:
-        ref=genome,
+        ref=access.random(genome),
         ref_idx=genome_fai,
         regions="results/regions/{group}.expanded_regions.filtered.bed",
         # you can have a list of samples here
-        alns=lambda w: get_group_bams(w),
+        alns=access.random(lambda w: get_group_bams(w)),
         idxs=lambda w: get_group_bams(w, bai=True),
     output:
         "results/candidate-calls/{group}.freebayes.bcf",
@@ -25,9 +25,9 @@ rule freebayes:
 
 rule delly:
     input:
-        ref=genome,
+        ref=access.random(genome),
         ref_idx=genome_fai,
-        alns=lambda w: get_group_bams(w),
+        alns=access.random(lambda w: get_group_bams(w)),
         index=lambda w: get_group_bams(w, bai=True),
         exclude=get_delly_excluded_regions(),
     output:

workflow/rules/fusion_calling.smk

@@ -62,7 +62,7 @@ rule annotate_exons:
         """
 
 
-# Use script provide by arriba once new version is released
+# Use script provided by arriba once new version is released
 rule convert_fusions:
     input:
         fasta=rules.get_genome.output,

workflow/rules/mapping.smk

@@ -1,7 +1,7 @@
 rule map_reads_bwa:
     input:
         reads=get_map_reads_input,
-        idx=rules.bwa_index.output,
+        idx=access.random(rules.bwa_index.output),
     output:
         temp("results/mapped/bwa/{sample}.bam"),
     log:
@@ -50,10 +50,10 @@ rule create_reference_paths:
 rule map_reads_vg:
     input:
         reads=get_map_reads_input,
-        graph=f"{pangenome_prefix}.gbz",
-        kmers="results/kmers/{sample}.kff",
-        hapl=f"{pangenome_prefix}.hapl",
-        paths="resources/reference_paths.txt",
+        graph=access.random(f"{pangenome_prefix}.gbz"),
+        kmers=access.random("results/kmers/{sample}.kff"),
+        hapl=access.random(f"{pangenome_prefix}.hapl"),
+        paths=access.random("resources/reference_paths.txt"),
     output:
         bam=temp("results/mapped/vg/{sample}.preprocessed.bam"),
         indexes=temp(
@@ -226,7 +226,7 @@ rule calc_consensus_reads:
 rule map_consensus_reads:
     input:
         reads=get_processed_consensus_input,
-        idx=rules.bwa_index.output,
+        idx=access.random(rules.bwa_index.output),
     output:
         temp("results/consensus/{sample}.consensus.{read_type}.mapped.bam"),
     params:

workflow/rules/primers.smk

@@ -47,7 +47,7 @@ rule trim_primers:
 rule map_primers:
     input:
         reads=lambda wc: get_panel_primer_input(wc.panel),
-        idx=rules.bwa_index.output,
+        idx=access.random(rules.bwa_index.output),
     output:
         "results/primers/{panel}_primers.bam",
     log: