feat: Delly automated conversion of output file (#468)

* Allowed for any output format

* Automated conversion of output file

* Updated wrapper-utils

bio/delly/environment.yaml

@@ -3,4 +3,6 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - delly ==0.9.1
+  - delly =1.1
+  - bcftools =1.15
+  - snakemake-wrapper-utils =0.5

bio/delly/meta.yaml

@@ -1,4 +1,15 @@
 name: delly
 description: Call variants with delly.
+url: https://github.com/dellytools/delly
 authors:
   - Johannes Köster
+  - Filipe G. Vieira
+input:
+  - BAM/CRAM file(s)
+  - reference genome
+  - BED file (optional)
+output:
+  - VCF/BCF with SVs.
+notes: |
+  * The `uncompressed_bcf` param sets output to uncompressed BCF (ignored if output is `vcf` or `vcf.gz`)
+  * The `extra` param allows for additional program arguments

bio/delly/test/Snakefile

@@ -1,15 +1,33 @@
-rule delly:
+rule delly_bcf:
     input:
         ref="genome.fasta",
-        samples=["mapped/a.bam"],
-        # optional exclude template (see https://github.com/dellytools/delly)
-        exclude="human.hg19.excl.tsv"
+        alns=["mapped/a.bam"],
+        # optional
+        exclude="human.hg19.excl.tsv",
     output:
-        "sv/calls.bcf"
+        "sv/calls.bcf",
     params:
-        extra=""  # optional parameters for delly (except -g, -x)
+        uncompressed_bcf=True,
+        extra="",  # optional parameters for delly (except -g, -x)
     log:
-        "logs/delly.log"
+        "logs/delly.log",
+    threads: 2  # It is best to use as many threads as samples
+    wrapper:
+        "master/bio/delly"
+
+
+rule delly_vcfgz:
+    input:
+        ref="genome.fasta",
+        alns=["mapped/a.bam"],
+        # optional
+        exclude="human.hg19.excl.tsv",
+    output:
+        "sv/calls.vcf.gz",
+    params:
+        extra="",  # optional parameters for delly (except -g, -x)
+    log:
+        "logs/delly.log",
     threads: 2  # It is best to use as many threads as samples
     wrapper:
         "master/bio/delly"

bio/delly/wrapper.py

@@ -5,19 +5,27 @@
 
 
 from snakemake.shell import shell
+from snakemake_wrapper_utils.bcftools import get_bcftools_opts
 
 
-exclude = (
-    "-x {}".format(snakemake.input.exclude)
-    if snakemake.input.get("exclude", "")
-    else ""
-)
-
+bcftools_opts = get_bcftools_opts(snakemake, parse_ref=False, parse_memory=False)
 extra = snakemake.params.get("extra", "")
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)
 
+
+exclude = snakemake.input.get("exclude", "")
+if exclude:
+    exclude = f"-x {exclude}"
+
+
 shell(
-    "OMP_NUM_THREADS={snakemake.threads} delly call {extra} "
-    "{exclude} -g {snakemake.input.ref} "
-    "-o {snakemake.output[0]} {snakemake.input.samples} {log}"
+    "(OMP_NUM_THREADS={snakemake.threads} delly call"
+    " -g {snakemake.input.ref}"
+    " {exclude}"
+    " {extra}"
+    " {snakemake.input.alns} | "
+    # Convert output to specified format
+    "bcftools view"
+    " {bcftools_opts}"
+    ") {log}"
 )

test.py

@@ -3330,6 +3330,11 @@ def test_delly():
     run("bio/delly", ["snakemake", "--cores", "1", "sv/calls.bcf", "--use-conda", "-F"])
 
 
+@skip_if_not_modified
+def test_delly():
+    run("bio/delly", ["snakemake", "--cores", "1", "sv/calls.vcf.gz", "--use-conda", "-F"])
+
+
 @skip_if_not_modified
 def test_manta():
     run(