small modfiy

Author: ShujiaHuang

scripts/create_pipeline.py

@@ -82,14 +82,14 @@ def creat_basetype_pipe():
             if opt.pop_group:
                 print(f'time {exe_prog} -t {opt.n_thread} -f {opt.reference} -L {opt.infilelist} '
                       f'-G {opt.pop_group} -r {reg} --min-af={opt.min_af} -q {opt.mapq} -Q {opt.min_bq} '
-                      f'--output-vcf {opt.outdir}/{outfile_prefix}.vcf.gz '
-                      f'--smart-rerun > {opt.outdir}/{outfile_prefix}.log && '
+                      f'--output-vcf {opt.outdir}/{outfile_prefix}.vcf.gz --smart-rerun '
+                      f'> {opt.outdir}/{outfile_prefix}.log && '
                       f'echo "** {outfile_prefix} done **"')
             else:    
                 print(f'time {exe_prog} -t {opt.n_thread} -f {opt.reference} -L {opt.infilelist} '
                       f'-r {reg} --min-af={opt.min_af} -q {opt.mapq} -Q {opt.min_bq} '
-                      f'--output-vcf {opt.outdir}/{outfile_prefix}.vcf.gz '
-                      f'--smart-rerun > {opt.outdir}/{outfile_prefix}.log && '
+                      f'--output-vcf {opt.outdir}/{outfile_prefix}.vcf.gz --smart-rerun '
+                      f'> {opt.outdir}/{outfile_prefix}.log && '
                       f'echo "** {outfile_prefix} done **"')
 
 

scripts/example.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
-python create_pipeline.py -R human_reference.fa --ref_fai human_reference.fa.fai -c chr1 --delta 5000000 -t 20 -L input_bamfile.list -o output_directory/ > run_chr1_basevar_shell.sh
+python create_pipeline.py -f human_reference.fa --ref_fai human_reference.fa.fai -c chr1 --delta 5000000 -t 24 -L input_bamfile.list -o output_directory/ > run_chr1_basevar_shell.sh
 
 # Add population groups
-python create_pipeline.py -R human_reference.fa --ref_fai human_reference.fa.fai -c chr1 --delta 5000000 -t 20 -L input_bamfile.list -G pop_group.list -o output_chr1_directory/ > run_basevar.sh
+python create_pipeline.py -f human_reference.fa --ref_fai human_reference.fa.fai -c chr1 --delta 5000000 -t 24 -L input_bamfile.list -G pop_group.list -o output_chr1_directory/ > run_basevar.sh