Workflow: 01-qc-se.cwl

Fetched 2024-06-20 02:53:52 GMT

RNA-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_read1_files File[]

Input read1 fastq files

Steps

ID Runs Label Doc
fastqc_read1
../qc/fastqc.cwl (CommandLineTool)
count_raw_reads_read1
../utils/count-fastq-reads.cwl (CommandLineTool)

Counts reads in a fastq file

extract_basename_read1
../utils/basename.cwl (ExpressionTool)
count_fastqc_reads_read1
../qc/count-fastqc-reads.cwl (CommandLineTool)

Extracts read count from fastqc_data.txt

compare_read_counts_read1
../qc/diff.cwl (CommandLineTool)

Compares 2 files

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

overrepresented_sequence_extract_read1
../qc/overrepresented_sequence_extract.cwl (CommandLineTool)

Outputs

ID Type Label Doc
output_diff_counts_read1 File[]
output_count_raw_reads_read1 File[]
output_custom_adapters_read1 File[]
output_fastqc_data_files_read1 File[]

FastQC data files for paired read 1

output_fastqc_report_files_read1 File[]

FastQC reports in zip format for paired read 1

Permalink: https://w3id.org/cwl/view/git/487af88ef0b971f76ecd1a215639bb47e3ee94e1/v1.0/RNA-seq_pipeline/01-qc-se.cwl