From 9b6ba7f08f964dc0222560c424ba8ed84a6debbf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Miguel=20=C3=81lvarez=20Herrera?=
 <m.alvarez.herrera@csic.es>
Date: Thu, 4 Jan 2024 18:24:37 +0100
Subject: [PATCH] Fix snakemake typo

---
 workflow/rules/fetch.smk | 23 +++++++++++++----------
 1 file changed, 13 insertions(+), 10 deletions(-)

diff --git a/workflow/rules/fetch.smk b/workflow/rules/fetch.smk
index f56d7ac..f594a3f 100644
--- a/workflow/rules/fetch.smk
+++ b/workflow/rules/fetch.smk
@@ -2,30 +2,33 @@ rule fetch_alignment_reference:
     threads: 1
     conda: "../envs/fetch.yaml"
     params:
-        ref = config["ALIGNMENT_REFERENCE"]
+        id = config["ALIGNMENT_REFERENCE"],
+        db = "nucleotide",
+        format = "fasta"
     output:
         fasta = OUTDIR/"reference.fasta"
     log:
         LOGDIR / "fetch_alignment_reference" / "log.txt"
-    shell:
-        "esearch -db nucleotide -query {params.ref} | efetch -format fasta > {output.fasta} 2> {log}"
+    wrapper:
+        "v3.3.3/bio/entrez/efetch"
 
 
 rule fetch_reference_gb:
     threads: 1
     conda: "../envs/fetch.yaml"
     params:
-        ref = config["ALIGNMENT_REFERENCE"]
+        id = config["ALIGNMENT_REFERENCE"],
+        db = "gb",
+        format = "fasta"
     output:
         fasta = OUTDIR/"reference.gb"
     log:
         LOGDIR / "fetch_reference_gb" / "log.txt"
-    shell:
-        "esearch -db nucleotide -query {params.ref} | efetch -format gb > {output.fasta} 2> {log}"
-
+    wrapper:
+        "v3.3.3/bio/entrez/efetch"
 
 
-rule fetch_mapping_references:
+rule fetch_mapping_references:  # TODO: use wrapper
     threads: 1
     conda: "../envs/fetch.yaml"
     input:
@@ -45,13 +48,13 @@ rule fetch_mapping_references:
 rule fetch_alignment_annotation:
     threads: 1
     params:
-        ref = config["ALIGNMENT_REFERENCE"]
+        id = config["ALIGNMENT_REFERENCE"]
     output:
         temp(OUTDIR/"reference.gff3")
     log:
         LOGDIR / "fetch_alignment_annotation" / "log.txt"
     shell:
-        "curl 'https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?db=nuccore&report=gff3&id={params.ref}' -o {output} -s 2>{log}"
+        "curl 'https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?db=nuccore&report=gff3&id={params.id}' -o {output} -s 2>{log}"
 
 
 rule fetch_problematic_vcf: