perf: autobump bio/gridss/preprocess (#800)

Automatic update of bio/gridss/preprocess. --------- 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 · 71463ad · 71463ad
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Showing 6 changed files with 7 additions and 8 deletions.
diff --git a/bio/gridss/preprocess/environment.yaml b/bio/gridss/preprocess/environment.yaml
@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - gridss ==2.9.4
+  - gridss =2.13.2
diff --git a/bio/gridss/preprocess/meta.yaml b/bio/gridss/preprocess/meta.yaml
@@ -2,8 +2,7 @@ name: "gridss preprocess"
 description: >
     GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.
     It includes a genome-wide break-end assembler, as well as a structural variation caller for Illumina sequencing data.
-    ``preprocess`` pre-processes input BAM files.
-    Can be run per input file.
-    Documentation at: https://github.com/PapenfussLab/gridss
+    ``preprocess`` pre-processes input BAM files (can be run per file).
+url: https://github.com/PapenfussLab/gridss
 authors:
   - Christopher Schröder
diff --git a/bio/gridss/preprocess/test/Snakefile b/bio/gridss/preprocess/test/Snakefile
@@ -6,9 +6,9 @@ rule gridss_preprocess:
         bai="mapped/{sample}.bam.bai",
         reference="reference/genome.fasta",
         dictionary="reference/genome.dict",
-        refindex=multiext("reference/genome.fasta", ".amb", ".ann", ".bwt", ".pac", ".sa", ".gridsscache", ".img")
+        refindex=multiext("reference/genome.fasta", ".amb", ".ann", ".bwt", ".pac", ".sa")
     output:
-        multiext("{WORKING_DIR}/{sample}.bam.gridss.working/{sample}.bam", ".cigar_metrics", ".coverage.blacklist.bed", ".idsv_metrics", ".insert_size_histogram.pdf", ".insert_size_metrics", ".mapq_metrics", ".sv.bam", ".sv.bam.bai", ".sv_metrics", ".tag_metrics")
+        multiext("{WORKING_DIR}/{sample}.bam.gridss.working/{sample}.bam", ".cigar_metrics", ".computesamtags.changes.tsv", ".coverage.blacklist.bed", ".idsv_metrics", ".insert_size_histogram.pdf", ".insert_size_metrics", ".mapq_metrics", ".sv.bam", ".sv.bam.csi", ".tag_metrics")
     params:
         extra="--jvmheap 1g",
         workingdir=WORKING_DIR

diff --git a/bio/gridss/preprocess/test/reference/genome.fasta.gridsscache b/bio/gridss/preprocess/test/reference/genome.fasta.gridsscache
diff --git a/bio/gridss/preprocess/test/reference/genome.fasta.img b/bio/gridss/preprocess/test/reference/genome.fasta.img
diff --git a/test.py b/test.py
@@ -831,14 +831,14 @@ def test_gridss_preprocess():
             "--use-conda",
             "--show-failed-logs",
             "working_dir/A.bam.gridss.working/A.bam.cigar_metrics",
+            "working_dir/A.bam.gridss.working/A.bam.computesamtags.changes.tsv",
             "working_dir/A.bam.gridss.working/A.bam.coverage.blacklist.bed",
             "working_dir/A.bam.gridss.working/A.bam.idsv_metrics",
             "working_dir/A.bam.gridss.working/A.bam.insert_size_histogram.pdf",
             "working_dir/A.bam.gridss.working/A.bam.insert_size_metrics",
             "working_dir/A.bam.gridss.working/A.bam.mapq_metrics",
             "working_dir/A.bam.gridss.working/A.bam.sv.bam",
-            "working_dir/A.bam.gridss.working/A.bam.sv.bam.bai",
-            "working_dir/A.bam.gridss.working/A.bam.sv_metrics",
+            "working_dir/A.bam.gridss.working/A.bam.sv.bam.csi",
             "working_dir/A.bam.gridss.working/A.bam.tag_metrics",
         ],
     )