From bc9ab713f7c11b04bae296a27970aceeb12ab1ae Mon Sep 17 00:00:00 2001
From: David Laehnemann <david.laehnemann@hhu.de>
Date: Mon, 25 Mar 2024 17:54:03 +0100
Subject: [PATCH] perf: update all wrapper to latest v3.5.3 (#78)

---
 workflow/rules/align.smk |  2 +-
 workflow/rules/qc.smk    |  2 +-
 workflow/rules/ref.smk   | 10 +++++-----
 workflow/rules/trim.smk  |  6 +++---
 4 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/workflow/rules/align.smk b/workflow/rules/align.smk
index 24aa523..1fdc497 100644
--- a/workflow/rules/align.smk
+++ b/workflow/rules/align.smk
@@ -13,4 +13,4 @@ rule align:
         extra=lambda wc, input: f'--outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --sjdbGTFfile {input.gtf} {config["params"]["star"]}',
     threads: 24
     wrapper:
-        "v1.21.4/bio/star/align"
+        "v3.5.3/bio/star/align"
diff --git a/workflow/rules/qc.smk b/workflow/rules/qc.smk
index da62289..e41355a 100644
--- a/workflow/rules/qc.smk
+++ b/workflow/rules/qc.smk
@@ -193,4 +193,4 @@ rule multiqc:
     log:
         "logs/multiqc.log",
     wrapper:
-        "v2.7.0/bio/multiqc"
+        "v3.5.3/bio/multiqc"
diff --git a/workflow/rules/ref.smk b/workflow/rules/ref.smk
index 6e5d5ad..9be480b 100644
--- a/workflow/rules/ref.smk
+++ b/workflow/rules/ref.smk
@@ -10,7 +10,7 @@ rule get_genome:
         release=config["ref"]["release"],
     cache: True
     wrapper:
-        "v1.21.4/bio/reference/ensembl-sequence"
+        "v3.5.3/bio/reference/ensembl-sequence"
 
 
 rule get_annotation:
@@ -26,7 +26,7 @@ rule get_annotation:
     log:
         "logs/get_annotation.log",
     wrapper:
-        "v1.21.4/bio/reference/ensembl-annotation"
+        "v3.5.3/bio/reference/ensembl-annotation"
 
 
 rule genome_faidx:
@@ -38,7 +38,7 @@ rule genome_faidx:
         "logs/genome-faidx.log",
     cache: True
     wrapper:
-        "v1.21.4/bio/samtools/faidx"
+        "v3.5.3/bio/samtools/faidx"
 
 
 rule bwa_index:
@@ -52,7 +52,7 @@ rule bwa_index:
         mem_mb=369000,
     cache: True
     wrapper:
-        "v1.21.4/bio/bwa/index"
+        "v3.5.3/bio/bwa/index"
 
 
 rule star_index:
@@ -68,4 +68,4 @@ rule star_index:
         "logs/star_index_genome.log",
     cache: True
     wrapper:
-        "v1.21.4/bio/star/index"
+        "v3.5.3/bio/star/index"
diff --git a/workflow/rules/trim.smk b/workflow/rules/trim.smk
index 829e4d5..b6843fb 100644
--- a/workflow/rules/trim.smk
+++ b/workflow/rules/trim.smk
@@ -5,7 +5,7 @@ rule get_sra:
     log:
         "logs/get-sra/{accession}.log",
     wrapper:
-        "v1.21.4/bio/sra-tools/fasterq-dump"
+        "v3.5.3/bio/sra-tools/fasterq-dump"
 
 
 rule cutadapt_pipe:
@@ -36,7 +36,7 @@ rule cutadapt_pe:
         adapters=lambda w: str(units.loc[w.sample].loc[w.unit, "adapters"]),
     threads: 8
     wrapper:
-        "v1.21.4/bio/cutadapt/pe"
+        "v3.5.3/bio/cutadapt/pe"
 
 
 rule cutadapt_se:
@@ -52,4 +52,4 @@ rule cutadapt_se:
         adapters=lambda w: str(units.loc[w.sample].loc[w.unit, "adapters"]),
     threads: 8
     wrapper:
-        "v1.21.4/bio/cutadapt/se"
+        "v3.5.3/bio/cutadapt/se"