Add index files.

snakemake · Feb 19, 2017 · a6ff13c · a6ff13c
1 parent 0bba853
commit a6ff13c
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Showing 7 changed files with 2 additions and 2 deletions.
diff --git a/bio/bowtie2/align/test/Snakefile b/bio/bowtie2/align/test/Snakefile
@@ -1,13 +1,13 @@
 rule bowtie2:
     input:
-        ref="genome.fasta",
         sample=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"]
     output:
         "mapped/{sample}.bam"
     log:
         "logs/bowtie2/{sample}.log"
     params:
-        ""  # optional parameters
+        index="index/genome",  # prefix of reference genome index (built with bowtie2-build)
+        extra=""  # optional parameters
     threads: 8
     wrapper:
         "master/bio/bowtie2/align"
diff --git a/bio/bowtie2/align/test/index/genome.1.bt2 b/bio/bowtie2/align/test/index/genome.1.bt2
diff --git a/bio/bowtie2/align/test/index/genome.2.bt2 b/bio/bowtie2/align/test/index/genome.2.bt2
diff --git a/bio/bowtie2/align/test/index/genome.3.bt2 b/bio/bowtie2/align/test/index/genome.3.bt2
diff --git a/bio/bowtie2/align/test/index/genome.4.bt2 b/bio/bowtie2/align/test/index/genome.4.bt2
diff --git a/bio/bowtie2/align/test/index/genome.rev.1.bt2 b/bio/bowtie2/align/test/index/genome.rev.1.bt2
diff --git a/bio/bowtie2/align/test/index/genome.rev.2.bt2 b/bio/bowtie2/align/test/index/genome.rev.2.bt2