Workflow: 02-trim-pe.cwl
Fetched 2023-01-15 00:39:13 GMT
Verified with cwltool version 3.1.20221201130942
STARR-seq 02 trimming - reads: PE
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| nthreads | Integer |
Number of threads |
|
| quality_score | String | ||
| trimmomatic_jar_path | String |
Trimmomatic Java jar file |
|
| trimmomatic_java_opts | String (Optional) |
JVM arguments should be a quoted, space separated list |
|
| input_fastq_read1_files | File[] |
Input read 1 fastq files |
|
| input_fastq_read2_files | File[] |
Input read 2 fastq files |
|
| input_read1_adapters_files | File[] |
Input read 1 adapters files |
|
| input_read2_adapters_files | File[] |
Input read 2 adapters files |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| trimmomatic |
../trimmomatic/trimmomatic.cwl
(CommandLineTool)
|
Trimmomatic is a fast, multithreaded command line tool that can be used to trim and crop Illumina (FASTQ) data as well as to remove adapters. These adapters can pose a real problem depending on the library preparation and downstream application. There are two major modes of the program: Paired end mode and Single end mode. The paired end mode will maintain correspondence of read pairs and also use the additional information contained in paired reads to better find adapter or PCR primer fragments introduced by the library preparation process. Trimmomatic works with FASTQ files (using phred + 33 or phred + 64 quality scores, depending on the Illumina pipeline used). |
|
| concat_adapters |
../utils/concat-files.cwl
(CommandLineTool)
|
Concat file1 and file2 into output_file. |
|
| extract_basename_read1 |
../utils/basename.cwl
(ExpressionTool)
|
||
| extract_basename_read2 |
../utils/extract-basename.cwl
(CommandLineTool)
|
Extracts the base name of a file |
|
| count_fastq_reads_read1 |
../utils/count-fastq-reads.cwl
(CommandLineTool)
|
Counts reads in a fastq file |
|
| count_fastq_reads_read2 |
../utils/count-fastq-reads.cwl
(CommandLineTool)
|
Counts reads in a fastq file |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output_data_fastq_read1_trimmed_files | File[] |
Trimmed fastq files for paired read 1 |
|
| output_data_fastq_read2_trimmed_files | File[] |
Trimmed fastq files for paired read 2 |
|
| output_trimmed_read1_fastq_read_count | File[] |
Trimmed read counts of paired read 1 fastq files |
|
| output_trimmed_read2_fastq_read_count | File[] |
Trimmed read counts of paired read 2 fastq files |
https://w3id.org/cwl/view/git/4e568335133405d28f4b73ae11e7f51f2900dfa3/v1.0/STARR-seq_pipeline/02-trim-pe.cwl
