Pindel windows: place in a subdir, remove subdir after merge

snakecnv/svsnakemake_utils.py

@@ -71,7 +71,7 @@ class SnakemakeUtils:
     def get_pindel_chr_batches(self, wildcards):
         inputs = []
         for batch in self.chr_batches[wildcards.chrom]:
-            inputs.append("{batch}/pindel/{chrbatch}/pindel_{chrom}_{svtype}.gz".format(
+            inputs.append("{batch}/pindel/{chrom}/{chrbatch}/pindel_{chrom}_{svtype}.gz".format(
                 batch=wildcards.batch, chrom=wildcards.chrom, chrbatch="-".join(map(str, batch)),
                 svtype=wildcards.svtype
             ))

snakecnv/tools/pindel.snk

@@ -30,9 +30,9 @@ rule pindel:
         genome = REFERENCE,
         fai = REFERENCE + ".fai"
     output:
-        "{batch}/pindel/{chrbatch}/pindel_{chrom}_D.gz",
-        "{batch}/pindel/{chrbatch}/pindel_{chrom}_INV.gz",
-        "{batch}/pindel/{chrbatch}/pindel_{chrom}_TD.gz",
+        "{batch}/pindel/{chrom}/{chrbatch}/pindel_{chrom}_D.gz",
+        "{batch}/pindel/{chrom}/{chrbatch}/pindel_{chrom}_INV.gz",
+        "{batch}/pindel/{chrom}/{chrbatch}/pindel_{chrom}_TD.gz",
     threads:
         get_threads("pindel", 4)
     log:
@@ -50,7 +50,7 @@ rule pindel:
         """
         for svtype in D TD INV RP SI LI BP CloseEndMapped INT_final;
         do
-        gzip -f {wildcards.batch}/pindel/{wildcards.chrbatch}/pindel_{wildcards.chrom}_${{svtype}}
+        gzip -f {wildcards.batch}/pindel/{wildcards.chrom}/{wildcards.chrbatch}/pindel_{wildcards.chrom}_${{svtype}}
         done
         """
 
@@ -65,4 +65,5 @@ rule mergepindelbatches:
     threads:
         1
     shell:
-        "mergepindelbatches.py {output} {input} 1>{log.stdout} 2>{log.stderr}"
+        "mergepindelbatches.py {output} {input} 1>{log.stdout} 2>{log.stderr}; "
\ No newline at end of file
+        "rm -rf {wildcards.batch}/pindel/{wildcards.chrom}"
\ No newline at end of file