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1 <tool id="call_consensus" name="5. Call consensus SNPs" version="1.0.1" profile="16.10">
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2 <description>for a sample, or lookup cached consensus SNP calls</description>
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3 <requirements>
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4 <container type="docker">quay.io/staphb/cfsan-snp-pipeline</container>
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5 <!-- <requirement type="package" version="1.0.8">bzip2</requirement>
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6 <requirement type="package" version="2.2.1">snp-pipeline</requirement>
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7 <requirement type="package" version="1.9.134">boto3</requirement> -->
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8 <!-- <requirement type="package" version="3.6.8">python</requirement> -->
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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11 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
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12 #set $identifier = $call_pileup.name.split(' ')[0]
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13 python $__tool_directory__/snp-cache.py snp_consenus_calls
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14 "\$(md5sum $snps $calls $call_pileup | cut -c -32 | md5sum | cut -c -32)"
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15 -c "
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16 mkdir -p ./$identifier/
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17 && cp $call_pileup ./$identifier/reads.all.pileup
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18 && cfsan_snp_pipeline call_consensus -v 4 -l $snps --vcfFileName "consensus.vcf" ./$identifier/reads.all.pileup 1>&2 && tar zcv ./consensus.vcf ./consensus.fasta
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19 "
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20 -l $cache_log
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21 | tar zvx ./
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22 && cp ./consensus.fasta $calls_consensus_fa
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23 && cp ./consensus.vcf $calls_consensus_vcf
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24 && cat $cache_log
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25 ]]></command>
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26 <inputs>
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27 <param type="data" name="snps" format="txt" />
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28 <param type="data" name="calls" format="vcf" />
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29 <param type="data" name="call_pileup" format="pileup" />
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30 </inputs>
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31 <outputs>
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32 <data label="${calls.name.split(' ')[0]} consensus SNPs (VCF)" name="calls_consensus_vcf" format="vcf" />
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33 <data label="${calls.name.split(' ')[0]} consensus SNPs (FASTA)" name="calls_consensus_fa" format="fasta" hidden="true"/>
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34 <data label="S3 Cache log" name="cache_log" format="txt" hidden="true" />
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35 </outputs>
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36 <tests>
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37 <test>
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38 <param name="snps" value="snplist.txt" />
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39 <param name="calls" value="samples/sample1/var.flt.vcf" />
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40 <param name="call_pileup" value="samples/sample1/reads.all.pileup" />
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41 <output name="calls_consensus_vcf" value="samples/sample1/consensus.vcf" lines_diff="20" />
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42 <output name="calls_consensus_fa" value="samples/sample1/consensus.fasta" lines_diff="2" />
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43 </test>
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44 </tests>
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45 <help><![CDATA[
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46 <a href="http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html</a>
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47 ]]></help>
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48 <citations>
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49 <citation type="doi">10.7717/peerj-cs.20</citation>
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50 </citations>
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51 </tool> |
