fix: use container for cutadapt

CCBR · Apr 12, 2024 · 9fcb3ee · 9fcb3ee
1 parent dbf0dc5
commit 9fcb3ee
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/config/config.yaml b/config/config.yaml
@@ -119,6 +119,7 @@ containers:
   bowtie1: "docker://nciccbr/charlie_bowtie1:v0.1.0"
   circexplorer: 'docker://nciccbr/ccbr_circexplorer:v1.0'
   clear: "docker://nciccbr/ccbr_clear:latest"
+  cutadapt: 'nciccbr/ncigb_cutadapt_v1.18:latest'
   dcc: "docker://nciccbr/charlie_dcc:v0.1.0"
   mapsplice: "docker://cgrlab/mapsplice2:latest"
   nclscan: "docker://nciccbr/charlie_nclscan:v0.1.0"

diff --git a/workflow/rules/preprocessing.smk b/workflow/rules/preprocessing.smk
@@ -31,8 +31,7 @@ rule cutadapt:
         cutadapt_q=config["cutadapt_q"],
         adapters=join(RESOURCES_DIR, "TruSeq_and_nextera_adapters.consolidated.fa"),
         randomstr=str(uuid.uuid4()),
-    envmodules:
-        TOOLS["cutadapt"]["version"],
+    container: config['containers']['cutadapt']
     threads: getthreads("cutadapt")
     shell:
         """