Workflow: 02-trim-se.cwl

Fetched 2019-03-19 00:35:49 GMT

ChIP-seq 02 trimming - reads: SE

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Inputs

ID Type Title Doc
input_read1_fastq_files File[]

Input fastq files

trimmomatic_java_opts String (Optional)

JVM arguments should be a quoted, space separated list

quality_score String
input_adapters_files File[]

Input adapters files

nthreads Integer

Number of threads

trimmomatic_jar_path String

Trimmomatic Java jar file

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).

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

Extracts the base name of a file

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

Counts reads in a fastq file

Outputs

ID Type Label Doc
output_trimmed_fastq_read_count File[]

Trimmed read counts of fastq files

output_data_fastq_trimmed_files File[]

Trimmed fastq files

Permalink: https://w3id.org/cwl/view/git/6d9457382f0b7cc2510e148d21383261280d17ed/v1.0/ChIP-seq_pipeline/02-trim-se.cwl