Workflow: 01-qc-se.cwl

Fetched 2021-04-11 15:53:52 GMT

ATAC-seq 01 QC - reads: SE

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Inputs

ID Type Title Doc
nthreads Integer

Number of threads.

default_adapters_file File

Adapters file

input_fastq_files File[]

Input fastq files

Steps

ID Runs Label Doc
extract_basename
../utils/basename.cwl (ExpressionTool)
extract_fastqc_data
../qc/extract_fastqc_data.cwl (CommandLineTool)

Unzips a zipped fastqc report and returns the fastqc_data.txt file. Unzips the file to pipe and uses redirection

overrepresented_sequence_extract
../qc/overrepresented_sequence_extract.cwl (CommandLineTool)
fastqc
../qc/fastqc.cwl (CommandLineTool)
compare_read_counts
../qc/diff.cwl (CommandLineTool)

Compares 2 files

count_raw_reads
../utils/count-fastq-reads.cwl (CommandLineTool)

Counts reads in a fastq file

count_fastqc_reads
../qc/count-fastqc-reads.cwl (CommandLineTool)

Extracts read count from fastqc_data.txt

Outputs

ID Type Label Doc
output_count_raw_reads File[]
output_fastqc_data_files File[]

FastQC data files

output_fastqc_report_files File[]

FastQC reports in zip format

output_diff_counts File[]
output_custom_adapters File[]
Permalink: https://w3id.org/cwl/view/git/8d02684ae0ff27e641f3704686e3bc8b1979b854/v1.0/ATAC-seq_pipeline/01-qc-se.cwl