Workflow: 01-qc-se.cwl

Fetched 2021-04-11 07:59:44 GMT

RNA-seq 01 QC - reads: SE

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Inputs

ID Type Title Doc
input_fastq_read1_files File[]

Input read1 fastq files

nthreads Integer

Number of threads.

default_adapters_file File

Adapters file

Steps

ID Runs Label Doc
compare_read_counts_read1
../qc/diff.cwl (CommandLineTool)

Compares 2 files

count_raw_reads_read1
../utils/count-fastq-reads.cwl (CommandLineTool)

Counts reads in a fastq file

overrepresented_sequence_extract_read1
../qc/overrepresented_sequence_extract.cwl (CommandLineTool)
fastqc_read1
../qc/fastqc.cwl (CommandLineTool)
extract_basename_read1
../utils/basename.cwl (ExpressionTool)
extract_fastqc_data_read1
../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

count_fastqc_reads_read1
../qc/count-fastqc-reads.cwl (CommandLineTool)

Extracts read count from fastqc_data.txt

Outputs

ID Type Label Doc
output_diff_counts_read1 File[]
output_fastqc_report_files_read1 File[]

FastQC reports in zip format for paired read 1

output_custom_adapters_read1 File[]
output_fastqc_data_files_read1 File[]

FastQC data files for paired read 1

output_count_raw_reads_read1 File[]
Permalink: https://w3id.org/cwl/view/git/4e568335133405d28f4b73ae11e7f51f2900dfa3/v1.0/RNA-seq_pipeline/01-qc-se.cwl