Mercurial > repos > bgruening > bismark
comparison bismark_wrapper.py @ 35:a81701137fa0 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 02087ce2966cf8b4aac9197a41171e7f986c11d1"
author | bgruening |
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date | Tue, 01 Oct 2019 12:43:21 -0400 |
parents | e5105f7e7b0d |
children | b2d0e92f81c2 |
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34:e5105f7e7b0d | 35:a81701137fa0 |
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165 cmd.append('--fastq') | 165 cmd.append('--fastq') |
166 | 166 |
167 # alignment options | 167 # alignment options |
168 if args.num_threads > 2: | 168 if args.num_threads > 2: |
169 # divide num_threads by 2 here since bismark will spawn 2 jobs with -p threads each | 169 # divide num_threads by 2 here since bismark will spawn 2 jobs with -p threads each |
170 cmd.extend(['-p', str(math.ceil(args.num_threads / 2))]) | 170 cmd.extend(['-p', str(int(math.floor(args.num_threads / 2)))]) |
171 if args.seed_mismatches: | 171 if args.seed_mismatches: |
172 cmd.extend(['-N', str(args.seed_mismatches)]) | 172 cmd.extend(['-N', str(args.seed_mismatches)]) |
173 if args.seed_len: | 173 if args.seed_len: |
174 cmd.extend(['-L', str(args.seed_len)]) | 174 cmd.extend(['-L', str(args.seed_len)]) |
175 if args.seed_extention_attempts: | 175 if args.seed_extention_attempts: |