Workflow: FASTQ Vector Removal

Fetched 2024-02-28 21:50:03 GMT

This workflow clean up vectros from fastq files

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Inputs

ID Type Title Doc
fastq1 File
fastq2 File (Optional)
tax_id Integer
threads Integer
blastdir Directory
tax_pickle File

Steps

ID Runs Label Doc
fastqc1
../../tools/fastqc/fastqc.cwl (CommandLineTool)
FastQC

BASH echo command

fastqc2
../../tools/fastqc/fastqc.cwl (CommandLineTool)
FastQC

BASH echo command

contaminated_reads
../../tools/python/filter-blastout-query.cwl (CommandLineTool)
contamination_detection

This tools remove contamination using a Blast TSV file

create_clean_fastq
../../tools/bbmap/filterbyname.cwl (CommandLineTool)
filterbyname

Filterbyname

Outputs

ID Type Label Doc
fastqc1_zip File[]
fastqc2_zip File[] (Optional)
fastqc1_html File[]
fastqc2_html File[] (Optional)
fastq1_output File
fastq2_output File (Optional)
Permalink: https://w3id.org/cwl/view/git/1b1cb5bbbe53a2dd5d7de7cdbff19c1bdbe23a49/workflows/File-formats/remove-fastq-reads-from-blast.cwl