perf: autobump bio/gridss/setupreference (#848)

Automatic update of bio/gridss/setupreference. --------- Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Co-authored-by: Filipe G. Vieira <1151762+fgvieira@users.noreply.github.com>
snakemake · Mar 21, 2023 · c2f9766 · c2f9766
1 parent ae2a295
commit c2f9766
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Showing 12 changed files with 11 additions and 37 deletions.
diff --git a/bio/gridss/setupreference/environment.yaml b/bio/gridss/setupreference/environment.yaml
@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - gridss ==2.9.4
+  - gridss =2.13.2
diff --git a/bio/gridss/setupreference/meta.yaml b/bio/gridss/setupreference/meta.yaml
@@ -5,6 +5,6 @@ description: >
     ``setupreference`` is a once-off setup generating additional files in the same directory as the reference.
     WARNING multiple instances of GRIDSS attempting to perform setupreference at the same time will result in file corruption.
     Make sure these files are generated before running parallel GRIDSS jobs.
-    Documentation at: https://github.com/PapenfussLab/gridss
+url: https://github.com/PapenfussLab/gridss
 authors:
   - Christopher Schröder
diff --git a/bio/gridss/setupreference/test/Snakefile b/bio/gridss/setupreference/test/Snakefile
@@ -1,10 +1,8 @@
 rule gridss_setupreference:
     input:
         reference="reference/genome.fasta",
-        dictionary="reference/genome.dict",
-        indices=multiext("reference/genome.fasta", ".amb", ".ann", ".bwt", ".pac", ".sa")
     output:
-        multiext("reference/genome.fasta", ".gridsscache", ".img")
+        idx=multiext("reference/genome.fasta", ".amb", ".ann", ".bwt", ".dict", ".fai", ".pac", ".sa")
     params:
         extra="--jvmheap 1g"
     log:

diff --git a/bio/gridss/setupreference/test/reference/genome.dict b/bio/gridss/setupreference/test/reference/genome.dict
diff --git a/bio/gridss/setupreference/test/reference/genome.fasta.amb b/bio/gridss/setupreference/test/reference/genome.fasta.amb
diff --git a/bio/gridss/setupreference/test/reference/genome.fasta.ann b/bio/gridss/setupreference/test/reference/genome.fasta.ann
diff --git a/bio/gridss/setupreference/test/reference/genome.fasta.bwt b/bio/gridss/setupreference/test/reference/genome.fasta.bwt
diff --git a/bio/gridss/setupreference/test/reference/genome.fasta.fai b/bio/gridss/setupreference/test/reference/genome.fasta.fai
diff --git a/bio/gridss/setupreference/test/reference/genome.fasta.pac b/bio/gridss/setupreference/test/reference/genome.fasta.pac
diff --git a/bio/gridss/setupreference/test/reference/genome.fasta.sa b/bio/gridss/setupreference/test/reference/genome.fasta.sa
diff --git a/bio/gridss/setupreference/wrapper.py b/bio/gridss/setupreference/wrapper.py
@@ -14,30 +14,8 @@
 # Placeholder for optional parameters
 extra = snakemake.params.get("extra", "")
 
-# Check inputs/arguments.
-reference = snakemake.input.get("reference", None)
-
-if not snakemake.input.reference:
-    raise ValueError("A reference genome has to be provided!")
-
-for ending in (".amb", ".ann", ".bwt", ".pac", ".sa"):
-    if not path.exists("{}{}".format(reference, ending)):
-        raise ValueError(
-            "{reference}{ending} missing. Please make sure the reference was properly indexed by bwa.".format(
-                reference=reference, ending=ending
-            )
-        )
-
-dictionary = path.splitext(reference)[0] + ".dict"
-if not path.exists(dictionary):
-    raise ValueError(
-        "{dictionary}.dict missing. Please make sure the reference dictionary was properly created. This can be accomplished for example by CreateSequenceDictionary.jar from Picard".format(
-            dictionary=dictionary
-        )
-    )
-
 shell(
     "(gridss -s setupreference "  # Tool
-    "--reference {reference} "  # Reference
+    "--reference {snakemake.input.reference} "  # Reference
     "{extra}) {log}"
 )
diff --git a/test.py b/test.py
@@ -854,8 +854,13 @@ def test_gridss_setupreference():
             "1",
             "--use-conda",
             "--show-failed-logs",
-            "reference/genome.fasta.gridsscache",
-            "reference/genome.fasta.img",
+            "reference/genome.fasta.amb",
+            "reference/genome.fasta.ann",
+            "reference/genome.fasta.bwt",
+            "reference/genome.fasta.dict",
+            "reference/genome.fasta.fai",
+            "reference/genome.fasta.pac",
+            "reference/genome.fasta.sa",
         ],
     )