Workflow: 01-qc-pe.cwl

Fetched 2020-06-02 17:48:38 GMT

RNA-seq 01 QC - reads: PE

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Inputs

ID Type Title Doc
input_fastq_read2_files File[]

Input read2 fastq files

input_fastq_read1_files File[]

Input read1 fastq files

default_adapters_file File

Adapters file

nthreads Integer

Number of threads.

Steps

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

Compares 2 files

overrepresented_sequence_extract_read1
../qc/overrepresented_sequence_extract.cwl (CommandLineTool)
fastqc_read2
../qc/fastqc.cwl (CommandLineTool)
overrepresented_sequence_extract_read2
../qc/overrepresented_sequence_extract.cwl (CommandLineTool)
fastqc_read1
../qc/fastqc.cwl (CommandLineTool)
extract_fastqc_data_read2
../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

extract_basename_read2
../utils/extract-basename.cwl (CommandLineTool)

Extracts the base name of a file

extract_basename_read1
../utils/extract-basename.cwl (CommandLineTool)

Extracts the base name of a file

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_raw_reads_read2
../utils/count-fastq-reads.cwl (CommandLineTool)

Counts reads in a fastq file

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

Counts reads in a fastq file

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

Extracts read count from fastqc_data.txt

count_fastqc_reads_read2
../qc/count-fastqc-reads.cwl (CommandLineTool)

Extracts read count from fastqc_data.txt

compare_read_counts_read2
../qc/diff.cwl (CommandLineTool)

Compares 2 files

Outputs

ID Type Label Doc
output_diff_counts_read1 File[]
output_diff_counts_read2 File[]
output_fastqc_report_files_read2 File[]

FastQC reports in zip format for paired read 2

output_fastqc_report_files_read1 File[]

FastQC reports in zip format for paired read 1

output_custom_adapters_read2 File[]
output_custom_adapters_read1 File[]
output_fastqc_data_files_read2 File[]

FastQC data files for paired read 2

output_count_raw_reads_read2 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/517487e59d240c197fc91f08d20dadca97a9e121/v1.0/RNA-seq_pipeline/01-qc-pe.cwl