Workflow: 02-trim-pe.cwl

Fetched 2021-01-09 03:44:29 GMT

STARR-seq 02 trimming - reads: PE

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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

Permalink: https://w3id.org/cwl/view/git/4e568335133405d28f4b73ae11e7f51f2900dfa3/v1.0/STARR-seq_pipeline/02-trim-pe.cwl