perf: update to fasterq-dump wrapper v1.23.5

* added fasterq-dump params
akcorut · Mar 16, 2023 · 373b406 · 373b406
1 parent 35d5690
commit 373b406
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Showing 3 changed files with 28 additions and 6 deletions.
diff --git a/.test/config_ecoli/config.yaml b/.test/config_ecoli/config.yaml
@@ -101,6 +101,16 @@ resources:
 
 params:
 
+  # ----------------------------------------------------------------------
+  #     fasterq-dump Params
+  # ----------------------------------------------------------------------
+
+  fasterq_dump:
+    # Number of threads for fasterq-dump
+    threads: 6
+    # Additional parameters for fasterq-dump
+    extra: "--skip-technical"
+
   # ----------------------------------------------------------------------
   #     FastQC Params
   # ----------------------------------------------------------------------

diff --git a/config/config.yaml b/config/config.yaml
@@ -101,6 +101,16 @@ resources:
 
 params:
 
+  # ----------------------------------------------------------------------
+  #     fasterq-dump Params
+  # ----------------------------------------------------------------------
+
+  fasterq_dump:
+    # Number of threads for fasterq-dump
+    threads: 6
+    # Additional parameters for fasterq-dump
+    extra: "--skip-technical"
+
   # ----------------------------------------------------------------------
   #     FastQC Params
   # ----------------------------------------------------------------------

diff --git a/workflow/rules/ref.smk b/workflow/rules/ref.smk
@@ -78,20 +78,22 @@ rule sra_get_fastq_pe:
         "resources/ref/sra-pe-reads/{accession}_1.fastq",
         "resources/ref/sra-pe-reads/{accession}_2.fastq"
     params:
-        extra="--skip-technical --progress --temp resources/ref/sra-pe-reads"
-    threads: 6
+        extra= config["params"]["fasterq_dump"]["extra"]
+    threads: 
+        config["params"]["fasterq_dump"]["threads"]
     log:
         "logs/ref/sra-pe-reads/{accession}.log"
     wrapper:
-        "v1.12.2/bio/sra-tools/fasterq-dump"
+        "v1.23.5/bio/sra-tools/fasterq-dump"
 
 rule sra_get_fastq_se:
     output:
         "resources/ref/sra-se-reads/{accession}.fastq"
     params:
-        extra="--skip-technical --progress --temp resources/ref/sra-pe-reads"
-    threads: 6
+        extra= config["params"]["fasterq_dump"]["extra"]
+    threads: 
+        config["params"]["fasterq_dump"]["threads"]
     log:
         "logs/ref/sra-pe-reads/{accession}.log"
     wrapper:
-        "v1.12.2/bio/sra-tools/fasterq-dump"
+        "v1.23.5/bio/sra-tools/fasterq-dump"