Workflow: 01-qc-pe.cwl

Fetched 2023-01-09 00:44:44 GMT

ChIP-seq 01 QC - reads: PE

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workflow cluster_inputs Workflow Inputs cluster_outputs Workflow Outputs input_read1_fastq_files input_read1_fastq_files fastqc_read1 fastqc_read1 input_read1_fastq_files->fastqc_read1 input_fastq_file extract_basename_read1 extract_basename_read1 input_read1_fastq_files->extract_basename_read1 input_file count_raw_reads_read1 count_raw_reads_read1 input_read1_fastq_files->count_raw_reads_read1 input_fastq_file input_read2_fastq_files input_read2_fastq_files fastqc_read2 fastqc_read2 input_read2_fastq_files->fastqc_read2 input_fastq_file extract_basename_read2 extract_basename_read2 input_read2_fastq_files->extract_basename_read2 input_file count_raw_reads_read2 count_raw_reads_read2 input_read2_fastq_files->count_raw_reads_read2 input_fastq_file default_adapters_file default_adapters_file overrepresented_sequence_extract_read1 overrepresented_sequence_extract_read1 default_adapters_file->overrepresented_sequence_extract_read1 default_adapters_file overrepresented_sequence_extract_read2 overrepresented_sequence_extract_read2 default_adapters_file->overrepresented_sequence_extract_read2 default_adapters_file nthreads nthreads nthreads->fastqc_read1 threads nthreads->fastqc_read2 threads output_count_raw_reads_read2 output_count_raw_reads_read2 output_diff_counts_read1 output_diff_counts_read1 output_fastqc_report_files_read1 output_fastqc_report_files_read1 output_fastqc_data_files_read1 output_fastqc_data_files_read1 output_custom_adapters_read1 output_custom_adapters_read1 output_diff_counts_read2 output_diff_counts_read2 output_fastqc_report_files_read2 output_fastqc_report_files_read2 output_count_raw_reads_read1 output_count_raw_reads_read1 output_fastqc_data_files_read2 output_fastqc_data_files_read2 output_custom_adapters_read2 output_custom_adapters_read2 fastqc_read1->output_fastqc_report_files_read1 extract_fastqc_data_read1 extract_fastqc_data_read1 fastqc_read1->extract_fastqc_data_read1 input_qc_report_file overrepresented_sequence_extract_read1->output_custom_adapters_read1 extract_basename_read1->overrepresented_sequence_extract_read1 input_basename extract_basename_read1->extract_fastqc_data_read1 input_basename extract_basename_read1->count_raw_reads_read1 input_basename count_fastqc_reads_read1 count_fastqc_reads_read1 extract_basename_read1->count_fastqc_reads_read1 input_basename extract_fastqc_data_read1->output_fastqc_data_files_read1 extract_fastqc_data_read1->overrepresented_sequence_extract_read1 input_fastqc_data extract_fastqc_data_read1->count_fastqc_reads_read1 input_fastqc_data count_raw_reads_read1->output_count_raw_reads_read1 compare_read_counts_read1 compare_read_counts_read1 count_raw_reads_read1->compare_read_counts_read1 file1 compare_read_counts_read2 compare_read_counts_read2 compare_read_counts_read2->output_diff_counts_read2 count_fastqc_reads_read2 count_fastqc_reads_read2 count_fastqc_reads_read2->compare_read_counts_read2 file2 fastqc_read2->output_fastqc_report_files_read2 extract_fastqc_data_read2 extract_fastqc_data_read2 fastqc_read2->extract_fastqc_data_read2 input_qc_report_file overrepresented_sequence_extract_read2->output_custom_adapters_read2 extract_basename_read2->count_fastqc_reads_read2 input_basename extract_basename_read2->overrepresented_sequence_extract_read2 input_basename extract_basename_read2->extract_fastqc_data_read2 input_basename extract_basename_read2->count_raw_reads_read2 input_basename extract_fastqc_data_read2->output_fastqc_data_files_read2 extract_fastqc_data_read2->count_fastqc_reads_read2 input_fastqc_data extract_fastqc_data_read2->overrepresented_sequence_extract_read2 input_fastqc_data count_raw_reads_read2->output_count_raw_reads_read2 count_raw_reads_read2->compare_read_counts_read2 file1 compare_read_counts_read1->output_diff_counts_read1 count_fastqc_reads_read1->compare_read_counts_read1 file2
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Inputs

ID Type Title Doc
nthreads Integer

Number of threads.

default_adapters_file File

Adapters file

input_read1_fastq_files File[]

Input read1 fastq files

input_read2_fastq_files File[]

Input read2 fastq files

Steps

ID Runs Label Doc
fastqc_read1
../qc/fastqc.cwl (CommandLineTool)
fastqc_read2
../qc/fastqc.cwl (CommandLineTool)
count_raw_reads_read1
../utils/count-fastq-reads.cwl (CommandLineTool)

Counts reads in a fastq file

count_raw_reads_read2
../utils/count-fastq-reads.cwl (CommandLineTool)

Counts reads in a fastq file

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

Extracts the base name of a file

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

Extracts the base name of a 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_read1
../qc/diff.cwl (CommandLineTool)

Compares 2 files

compare_read_counts_read2
../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

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

overrepresented_sequence_extract_read1
../qc/overrepresented_sequence_extract.cwl (CommandLineTool)
overrepresented_sequence_extract_read2
../qc/overrepresented_sequence_extract.cwl (CommandLineTool)

Outputs

ID Type Label Doc
output_diff_counts_read1 File[]
output_diff_counts_read2 File[]
output_count_raw_reads_read1 File[]
output_count_raw_reads_read2 File[]
output_custom_adapters_read1 File[]
output_custom_adapters_read2 File[]
output_fastqc_data_files_read1 File[]

FastQC data files for paired read 1

output_fastqc_data_files_read2 File[]

FastQC data files for paired read 1

output_fastqc_report_files_read1 File[]

FastQC reports in zip format for paired read 1

output_fastqc_report_files_read2 File[]

FastQC reports in zip format for paired read 1

Permalink: https://w3id.org/cwl/view/git/6da8cef69f3a585fc3e2f4f2f730d361cbe2e978/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl