perf: autobump bio/bismark/deduplicate_bismark (#1141)

Automatic update of bio/bismark/deduplicate_bismark. --------- 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 · 45cd1a6 · 45cd1a6
1 parent d8c3faa
commit 45cd1a6
Show file tree

Hide file tree

Showing 6 changed files with 6 additions and 5 deletions.
diff --git a/bio/bismark/deduplicate_bismark/environment.yaml b/bio/bismark/deduplicate_bismark/environment.yaml
@@ -3,6 +3,6 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - bowtie2 =2.5.0
   - bismark =0.24.0
+  - bowtie2 =2.5.1
   - samtools =1.16.1
diff --git a/bio/bismark/deduplicate_bismark/meta.yaml b/bio/bismark/deduplicate_bismark/meta.yaml
@@ -1,6 +1,7 @@
 name: deduplicate_bismark
 description: |
-  Deduplicate Bismark Bam Files and saves as \*.bam file (see https://github.com/FelixKrueger/Bismark/blob/master/deduplicate_bismark).
+  Deduplicate Bismark Bam Files
+url: https://github.com/FelixKrueger/Bismark/
 authors:
   - Roman Cherniatchik
 input:

diff --git a/bio/bismark/deduplicate_bismark/test/Snakefile b/bio/bismark/deduplicate_bismark/test/Snakefile
@@ -1,5 +1,5 @@
 rule deduplicate_bismark:
-    input: "bams/a_genome_pe.bam"
+    input: "bams/{sample}.bam"
     output:
         bam="bams/{sample}.deduplicated.bam",
         report="bams/{sample}.deduplication_report.txt",

diff --git a/...plicate_bismark/test/bams/a_genome_pe.bam → ...rk/deduplicate_bismark/test/bams/a_pe.bam b/...plicate_bismark/test/bams/a_genome_pe.bam → ...rk/deduplicate_bismark/test/bams/a_pe.bam
diff --git a/...eduplicate_bismark/test/bams/b_genome.bam → ...smark/deduplicate_bismark/test/bams/b.bam b/...eduplicate_bismark/test/bams/b_genome.bam → ...smark/deduplicate_bismark/test/bams/b.bam
diff --git a/test.py b/test.py
@@ -4467,8 +4467,8 @@ def test_bismark_deduplicate_bismark():
             "snakemake",
             "--cores",
             "1",
-            "bams/a_genome_pe.deduplicated.bam",
-            "bams/b_genome.deduplicated.bam",
+            "bams/a_pe.deduplicated.bam",
+            "bams/b.deduplicated.bam",
             "--use-conda",
             "-F",
         ],