| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolrepo.galaxytrakr.org/repos/jpayne/snp_pipeline/call_consensus/1.0.1 (this tool) |
| call_consensus |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| bzip2 | 1.0.6 | package |
| snp-pipeline | 2.0.2 | package |
| boto3 | 1.9.134 | package |
| python | 3.6.8 | package |
| Additional information about this tool |
export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
#set $identifier = $call_pileup.name.split(' ')[0]
python $__tool_directory__/snp-cache.py snp_consenus_calls
"\$(md5sum $snps $calls $call_pileup | cut -c -32 | md5sum | cut -c -32)"
-c "
mkdir -p ./$identifier/
&& cp $call_pileup ./$identifier/reads.all.pileup
&& cfsan_snp_pipeline call_consensus -v 4 -l $snps --vcfFileName "consensus.vcf" ./$identifier/reads.all.pileup 1>&2 && tar zcv ./consensus.vcf ./consensus.fasta
"
-l $cache_log
| tar zvx ./
&& cp ./consensus.fasta $calls_consensus_fa
&& cp ./consensus.vcf $calls_consensus_vcf
&& cat $cache_log
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
snps: snplist.txt call_pileup: samples/sample1/reads.all.pileup calls: samples/sample1/var.flt.vcf |
attributes: name attributes: name |
snplist.txt samples/sample1/var.flt.vcf samples/sample1/reads.all.pileup name |