Workflow: 01-qc-pe.cwl
Fetched 2024-11-23 19:19:27 GMT
Verified with cwltool version 3.1.20221201130942
RNA-seq 01 QC - reads: PE
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
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 |
|
| input_fastq_read2_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/basename.cwl
(ExpressionTool)
|
||
| extract_basename_read2 |
../utils/basename.cwl
(ExpressionTool)
|
||
| 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 2 |
|
| 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 2 |
Permalink:
https://w3id.org/cwl/view/git/1a0dd34d59ec983d1f7ad77bff35da2f016e3134/v1.0/RNA-seq_pipeline/01-qc-pe.cwl
