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pipeline.xml
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<?xml version="1.0" encoding="UTF-8"?>
<pipeline xmlns="http://www.sing-group.org/compi/pipeline-1.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<version>1.0.1</version>
<params>
<param name="workingDirectory" shortName="wd" global="true"></param>
<param name="input" shortName="i" global="true" defaultValue="input"></param>
<param name="output" shortName="o" global="true" defaultValue="output"></param>
<param name="paramsDir" shortName="pd" global="true" defaultValue="params"></param>
<param name="batchSize_rename_ncbi_1" shortName="bsrn1" defaultValue="2"></param>
<param name="batchSize_rename_ncbi_2" shortName="bsrn2" defaultValue="2"></param>
<param name="batchSize_blast_1" shortName="bsb1" defaultValue="2"></param>
<param name="batchSize_blast_2" shortName="bsb2" defaultValue="2"></param>
<param name="script_pipeline_runner" shortName="spr" global="true" defaultValue="pipeline-runner.sh"></param>
<param name="sedaCli" shortName="sc" global="true" defaultValue="run-cli.sh"></param>
<param name="script_create_batches" shortName="scb" global="true" defaultValue="create_batches"></param>
</params>
<tasks>
<task id="rename-ncbi_1" params="batchSize_rename_ncbi_1"/>
<task id="rename-ncbi_2" params="batchSize_rename_ncbi_2"/>
<task id="check-genome-contaminants_1" after="rename-ncbi_1" src="task-scripts/check-genome-contaminants.sh"/>
<task id="check-genome-contaminants_2" after="rename-ncbi_2" src="task-scripts/check-genome-contaminants.sh"/>
<task id="blast_1" after="check-genome-contaminants_1" params="batchSize_blast_1"/>
<task id="blast_2" after="check-genome-contaminants_2" params="batchSize_blast_2"/>
<task id="rename-ncbi_3" after="blast_1"/>
<task id="rename-ncbi_4" after="blast_2"/>
<task id="merge_1" after="rename-ncbi_3"/>
<task id="merge_2" after="rename-ncbi_4"/>
<task id="rename-header-replace-interval_1" after="merge_1"/>
<task id="rename-header-replace-interval_2" after="merge_2"/>
<task id="rename-header-replace-word_1" after="rename-header-replace-interval_1"/>
<task id="rename-header-replace-interval_3" after="rename-header-replace-interval_2"/>
<task id="rename-header-replace-word_2" after="rename-header-replace-word_1"/>
<task id="rename-header-replace-word_3" after="rename-header-replace-interval_3"/>
<task id="merge_3" after="rename-header-replace-word_2 rename-header-replace-word_3"/>
<task id="pattern-filtering_1" after="merge_3"/>
<task id="pattern-filtering_2" after="pattern-filtering_1"/>
<task id="remove-redundant" after="pattern-filtering_2"/>
<task id="filtering_1" after="remove-redundant"/>
<task id="reallocate" after="filtering_1"/>
<task id="filtering_2" after="reallocate"/>
<task id="remove-isoforms" after="filtering_2"/>
</tasks>
<metadata>
<task-description id="rename-ncbi_1">GenBank</task-description>
<task-description id="rename-ncbi_2">RefSeq</task-description>
<task-description id="check-genome-contaminants_1">GenBank</task-description>
<task-description id="check-genome-contaminants_2">RefSeq</task-description>
<task-description id="blast_1">GenBank</task-description>
<task-description id="blast_2">RefSeq</task-description>
<task-description id="rename-ncbi_3">GenBank</task-description>
<task-description id="rename-ncbi_4">RefSeq</task-description>
<task-description id="merge_1">GenBank</task-description>
<task-description id="merge_2">RefSeq</task-description>
<task-description id="rename-header-replace-interval_1">GenBank</task-description>
<task-description id="rename-header-replace-interval_2">RefSeq</task-description>
<task-description id="rename-header-replace-word_1">GenBank</task-description>
<task-description id="rename-header-replace-interval_3">RefSeq</task-description>
<task-description id="rename-header-replace-word_2">GenBank</task-description>
<task-description id="rename-header-replace-word_3">RefSeq</task-description>
<task-description id="merge_3">GenBank, RefSeq</task-description>
<task-description id="pattern-filtering_1">GenBank, RefSeq</task-description>
<task-description id="remove-redundant">GenBank, RefSeq</task-description>
<task-description id="filtering_1">GenBank, RefSeq</task-description>
<task-description id="reallocate">GenBank, RefSeq</task-description>
<task-description id="filtering_2">GenBank, RefSeq</task-description>
<task-description id="remove-isoforms">GenBank, RefSeq</task-description>
</metadata>
</pipeline>