Workflow: screen out taxa

Fetched 2023-01-20 14:58:54 GMT

Remove sequences which align against a reference set using bowtie2. The references are preformatted (index files)

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Inputs

ID Type Title Doc
jobid String
indexDir Directory
indexName String (Optional)
sequences File

Steps

ID Runs Label Doc
screen
../Tools/bowtie2.tool.cwl (CommandLineTool)
organism screening

Remove sequences from specified host organism using bowtie2: >bowtie2 -f --reorder -p $proc --un $unalignedSequences -x $indexDir/$indexName -U $sequences > /dev/null\"

truncate
../Tools/seqUtil.tool.cwl (CommandLineTool)
seqUtil

Utility tool for various sequence file transformations.

sortInput
../Tools/seqUtil.tool.cwl (CommandLineTool)
seqUtil

Utility tool for various sequence file transformations.

sortScreenID
../Tools/seqUtil.tool.cwl (CommandLineTool)
seqUtil

Utility tool for various sequence file transformations.

untruncateScreen
../Tools/seqUtil.tool.cwl (CommandLineTool)
seqUtil

Utility tool for various sequence file transformations.

Outputs

ID Type Label Doc
passed File
Permalink: https://w3id.org/cwl/view/git/4e4d2e674bde612f98f2b0370445f8b2a47587df/CWL/Workflows/organism-screening.workflow.cwl