From 116cf5a667109d65969d5f8a4ede72afd8cb50f4 Mon Sep 17 00:00:00 2001
From: dmm2017 <meleshko.dmitrii@gmail.com>
Date: Sun, 31 May 2020 10:18:39 -0400
Subject: [PATCH] remove readgroup

---
 Snakefile  | 3 +--
 novel-x.py | 1 -
 2 files changed, 1 insertion(+), 3 deletions(-)

diff --git a/Snakefile b/Snakefile
index 10a9406..898fea3 100644
--- a/Snakefile
+++ b/Snakefile
@@ -5,7 +5,6 @@ configfile: "path_to_executables_config.json"
 SAMPLE=config["sample"]
 GIT_ROOT=config["root"]
 BLAST_DB=config["blast_db"]
-READGROUP=config["readgroup"]
 GENOME=config["genome"]
 SAMTOOLS=config["samtools"]
 VELVETH=config["velveth"]
@@ -100,7 +99,7 @@ rule align_unmapped_reads_to_the_contigs:
     shell:
         """
         {LONGRANGER} mkref {input.filtered_fasta}
-        {LONGRANGER} align --localcores={THREADS} --localmem={MEMORY} --id=temp_{wildcards.sample} --reference={output.refdata} --fastqs={input.temp_dir}/{READGROUP}
+        {LONGRANGER} align --localcores={THREADS} --localmem={MEMORY} --id=temp_{wildcards.sample} --reference={output.refdata} --fastqs={input.temp_dir}/
         {SAMTOOLS} view -b -F 12 temp_{wildcards.sample}/outs/possorted_bam.bam >{output.mapped_bam}
         """
 
diff --git a/novel-x.py b/novel-x.py
index 5c77f34..dbc4676 100644
--- a/novel-x.py
+++ b/novel-x.py
@@ -25,7 +25,6 @@ def create_config(bam, genome, nt, outdir, lr20, m, t):
     data['root'] = path.dirname(path.realpath(__file__))
     data['sample'] = path.basename(bam)[:-4]
     data['outdir'] = outdir
-    data['readgroup'] = get_read_group(bam)
     data['threads'] = int(t)
     data['memory'] = int(m)
     data['memory_per_thread'] = int(m/(2*t)) + 1