Remove copying the repeatmask bed file to reduce file number and trig…

…gering reruns of downstream rules
NBISweden · Oct 25, 2023 · 8447c9b · 8447c9b
1 parent 0702bf0
commit 8447c9b
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Showing 3 changed files with 6 additions and 8 deletions.
diff --git a/workflow/rules/0.2_repeat_identification.smk b/workflow/rules/0.2_repeat_identification.smk
@@ -137,7 +137,6 @@ rule make_no_repeats_bed:
         sorted_rep_bed=rules.sort_repeats_bed.output.sorted_rep_bed,
     output:
         no_rep_bed=REF_DIR + "/" + REF_NAME + ".repma.bed",
-        no_rep_bed_dir="results/" + REF_NAME + ".repma.bed",
     group:
         "reference_group"
     log:
@@ -146,6 +145,5 @@ rule make_no_repeats_bed:
         "docker://nbisweden/generode-bedtools-2.29.2"
     shell:
         """
-        bedtools subtract -a {input.ref_bed} -b {input.sorted_rep_bed} > {output.no_rep_bed} 2> {log} &&
-        cp {output.no_rep_bed} {output.no_rep_bed_dir} 2>> {log}
+        bedtools subtract -a {input.ref_bed} -b {input.sorted_rep_bed} > {output.no_rep_bed} 2> {log}
         """
diff --git a/workflow/rules/6_autosome_sexchromosome_bed_files.smk b/workflow/rules/6_autosome_sexchromosome_bed_files.smk
@@ -51,7 +51,7 @@ rule make_autosomes_bed:
 
 rule intersect_sexchr_repma_beds:
     input:
-        no_rep_bed_dir=rules.make_no_repeats_bed.output.no_rep_bed_dir,
+        no_rep_bed=rules.make_no_repeats_bed.output.no_rep_bed,
         sexchr_bed=rules.make_sexchr_bed.output,
     output:
         repma_sex_chr="results/" + REF_NAME + ".repma.sexchr.bed",
@@ -64,13 +64,13 @@ rule intersect_sexchr_repma_beds:
         "docker://nbisweden/generode-bedtools-2.29.2"
     shell:
         """
-        bedtools intersect -a {input.no_rep_bed_dir} -b {input.sexchr_bed} > {output.repma_sex_chr} 2> {log}
+        bedtools intersect -a {input.no_rep_bed} -b {input.sexchr_bed} > {output.repma_sex_chr} 2> {log}
         """
 
 
 rule intersect_autos_repma_beds:
     input:
-        no_rep_bed_dir=rules.make_no_repeats_bed.output.no_rep_bed_dir,
+        no_rep_bed=rules.make_no_repeats_bed.output.no_rep_bed,
         autosome_bed=rules.make_autosomes_bed.output,
     output:
         repma_autos="results/" + REF_NAME + ".repma.autos.bed",
@@ -83,7 +83,7 @@ rule intersect_autos_repma_beds:
         "docker://nbisweden/generode-bedtools-2.29.2"
     shell:
         """
-        bedtools intersect -a {input.no_rep_bed_dir} -b {input.autosome_bed} > {output.repma_autos} 2> {log}
+        bedtools intersect -a {input.no_rep_bed} -b {input.autosome_bed} > {output.repma_autos} 2> {log}
         """
 
 

diff --git a/workflow/rules/8.2_vcf_qual_repeat_filtering.smk b/workflow/rules/8.2_vcf_qual_repeat_filtering.smk
@@ -359,7 +359,7 @@ rule remove_repeats_vcf:
     """Remove repeats from vcf files"""
     input:
         vcf=rules.filtered_bcf2vcf.output.vcf,
-        bed=rules.make_no_repeats_bed.output.no_rep_bed_dir,
+        bed=rules.make_no_repeats_bed.output.no_rep_bed,
         genomefile=rules.genome_file.output.genomefile,
     output:
         filtered=temp("results/{dataset}/vcf/" + REF_NAME + "/{sample}.merged.rmdup.merged.{processed}.snps5.noIndel.QUAL30.dp.AB.repma.vcf.gz"),