fix: remove misleading kmer size parameter for kallisto index (#518)

snakemake · Jul 19, 2022 · 309b376 · 309b376
1 parent 6a6d28a
commit 309b376
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Showing 2 changed files with 9 additions and 9 deletions.
diff --git a/bio/kallisto/index/test/Snakefile b/bio/kallisto/index/test/Snakefile
@@ -1,12 +1,12 @@
 rule kallisto_index:
     input:
-        fasta = "{transcriptome}.fasta"
+        fasta="{transcriptome}.fasta",
     output:
-        index = "{transcriptome}.idx"
+        index="{transcriptome}.idx",
     params:
-        extra = "--kmer-size=5"
+        extra="",  # optional parameters
     log:
-        "logs/kallisto_index_{transcriptome}.log"
+        "logs/kallisto_index_{transcriptome}.log",
     threads: 1
     wrapper:
         "master/bio/kallisto/index"
diff --git a/bio/kallisto/quant/test/Snakefile b/bio/kallisto/quant/test/Snakefile
@@ -1,13 +1,13 @@
 rule kallisto_quant:
     input:
-        fastq = ["reads/{exp}_R1.fastq", "reads/{exp}_R2.fastq"],
-        index = "index/transcriptome.idx"
+        fastq=["reads/{exp}_R1.fastq", "reads/{exp}_R2.fastq"],
+        index="index/transcriptome.idx",
     output:
-        directory('quant_results_{exp}')
+        directory("quant_results_{exp}"),
     params:
-        extra = ""
+        extra="",
     log:
-        "logs/kallisto_quant_{exp}.log"
+        "logs/kallisto_quant_{exp}.log",
     threads: 1
     wrapper:
         "master/bio/kallisto/quant"