Workflow: contaminant_cleanup

Fetched 2022-10-02 15:23:06 GMT

This workflow detect and remove contamination from a DNA fasta file

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Inputs

ID Type Title Doc
threads Integer
trans_fsa File
min_length Integer
contaminant_fsa File

Steps

ID Runs Label Doc
collect_blastdb
../../tools/basic/files2dir.cwl (ExpressionTool)
files2dir

Group all input files in a directory

equal_seq_removal
../../tools/python/equal-removal.cwl (CommandLineTool)
equal_removal

This tools remove equal sequences

contaminant_blastn
../../tools/blast/blastn.cwl (CommandLineTool)
BlastN

NCBI BlastN Nucleotide-Nucleotide BLAST

contaminant_blastdb
../../tools/blast/makeblastdb.cwl (CommandLineTool)
makeblastdb

NCBI makeblastdb

contamination_removal
../../tools/python/contaminant-removal.cwl (CommandLineTool)
contaminant_removal

This tools detect contaminants from a Blast TSV file

Outputs

ID Type Label Doc
equal_seq_removal_fsa File
equal_seq_removal_tsv File
contaminant_blastn_tsv File
contamination_removal_cont File
Permalink: https://w3id.org/cwl/view/git/e1c19e64f6fc210f65472ee227786d33c9b4909a/workflows/Contamination/contaminant-cleanup.cwl