fix issue with trackhub

harvardinformatics · Jun 18, 2024 · 438547e · 438547e
1 parent 0464efd
commit 438547e
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Showing 2 changed files with 10 additions and 4 deletions.
diff --git a/workflow/modules/trackhub/Snakefile b/workflow/modules/trackhub/Snakefile
@@ -178,9 +178,14 @@ rule non_callable_sites:
         bb = "results/{refGenome}/trackhub/non_callable_sites.bb"
     conda:
         "envs/trackhub.yml"
+    shadow:
+        "minimal"
     shell:
         """
-        sort -k1,1 {input.chrom_sizes} > sorted.chrom.sizes
-        bedtools complement -i {input.callable_sites} -g sorted.chrom.sizes > {output.bed}
-        bedToBigBed {output.bed} {input.chrom_sizes} {output.bb}
+        sort -k1,1V {input.chrom_sizes} > sorted.chrom.sizes
+        sort -k1,1V -k2,2n {input.callable_sites} >  sorted_callable_sites.bed
+        bedtools complement -i sorted_callable_sites.bed -g sorted.chrom.sizes > {output.bed}
+
+        bedSort {output.bed} bedsort_non_callable_sites.bed
+        bedToBigBed bedsort_non_callable_sites.bed sorted.chrom.sizes {output.bb}
         """
diff --git a/workflow/modules/trackhub/envs/trackhub.yml b/workflow/modules/trackhub/envs/trackhub.yml
@@ -7,4 +7,5 @@ dependencies:
   - bcftools==1.12
   - vcftools==0.1.16
   - ucsc-bedgraphtobigwig==377
-  - ucsc-bedtobigbed==377
+  - ucsc-bedtobigbed==377
+  - ucsc-bedsort==466