Merge pull request #11 from fmaguire/master

Primer params renamed to forward and reverse
jaleezyy · Apr 16, 2020 · 276dfbb · 276dfbb
2 parents cf0ad27 + 21b866c
commit 276dfbb
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Showing 2 changed files with 5 additions and 5 deletions.
diff --git a/pipeline/Snakefile.master b/pipeline/Snakefile.master
@@ -86,11 +86,11 @@ rule run_cutadapt:
     log:
         'fastq_primers_removed/cutadapt.log'
     params:
-        primer_R1 = config['primer_R1'],
-        primer_R2 = config['primer_R2']
+        primer_fw = config['primer_fw'],
+        primer_rc = config['primer_rc']
     shell:
         'cutadapt -j {threads}'
-	' -a file:{params.primer_R1} -A file:{params.primer_R2}'   # primers
+	' -a file:{params.primer_fw} -A file:{params.primer_rc}'   # primers
 	' -o {output[0]} -p {output[1]}'     # output files
 	' {input}'                           # input files
         ' >{log}'                            # log file

diff --git a/pipeline/example_config.yaml b/pipeline/example_config.yaml
@@ -4,8 +4,8 @@
 # It is ingested by the Snakefile, and also intended to be human-readable.
 
 # Used as -a,-A arguments to 'cutadapt'
-primer_R1: '/home/kmsmith/data/wuhan_primers_28.01.20_trim_RC.fa'
-primer_R2: '/home/kmsmith/data/wuhan_primers_28.01.20_trim_FW.fa'
+primer_fw: '/home/kmsmith/data/wuhan_primers_28.01.20_trim_RC.fa'
+primer_rc: '/home/kmsmith/data/wuhan_primers_28.01.20_trim_FW.fa'
 
 # Last arguments on 'trimmomatic' command line (after input, output files)
 trimmomatic_args: 'ILLUMINACLIP:/home/kmsmith/data/NexteraPE-PE.fa:2:30:10 SLIDINGWINDOW:4:20'