remove readgroup

1dayac · May 31, 2020 · 116cf5a · 116cf5a
1 parent 0e3e598
commit 116cf5a
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Showing 2 changed files with 1 addition and 3 deletions.
diff --git 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
@@ -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