Workflow: 02-trim-pe.cwl
Fetched 2024-11-26 16:09:30 GMT
Verified with cwltool version 3.1.20221201130942
ATAC-seq 02 trimming - reads: PE
- Selected
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- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| nthreads | Integer |
Number of threads |
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| quality_score | String | ||
| trimmomatic_jar_path | String |
Trimmomatic Java jar file |
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| trimmomatic_java_opts | String (Optional) |
JVM arguments should be a quoted, space separated list |
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| input_read1_fastq_files | File[] |
Input fastq files for paired_read1 |
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| input_read2_fastq_files | File[] |
Input fastq files for paired_read2 |
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| input_read1_adapters_files | File[] |
Input adapters files for paired_read1 |
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| input_read2_adapters_files | File[] |
Input adapters files for paired_read2 |
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). |
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| concat_adapters |
../utils/concat-files.cwl
(CommandLineTool)
|
Concat file1 and file2 into output_file. |
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| extract_basename_read1 |
../utils/basename.cwl
(ExpressionTool)
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| extract_basename_read2 |
../utils/basename.cwl
(ExpressionTool)
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| count_fastq_reads_read1 |
../utils/count-fastq-reads.cwl
(CommandLineTool)
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Counts reads in a fastq file |
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| 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_read1 |
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| output_data_fastq_read2_trimmed_files | File[] |
Trimmed fastq files for paired_read2 |
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| output_trimmed_read1_fastq_read_count | File[] |
Trimmed read counts of fastq files for paired_read1 |
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| output_trimmed_read2_fastq_read_count | File[] |
Trimmed read counts of fastq files for paired_read2 |
https://w3id.org/cwl/view/git/487af88ef0b971f76ecd1a215639bb47e3ee94e1/v1.0/ATAC-seq_pipeline/02-trim-pe.cwl
