TranscriptomeAssembly-wf.single-end
Version 1

Transcriptome assembly workflow (single-end version)

SEEK ID: https://dev.workflowhub.eu/workflows/30?version=1

Inputs

ID	Name	Description	Type
read_files	FASTQ read file(s)	FASTQ file of reverse reads in Paired End mode	File[]
forward_reads	Paired-end read file 1	Read file 1 in FASTQ format	File
end_mode	read -end mode format	Read -end mode format to be specify to Trimmomatic	../tools/Trimmomatic/trimmomatic-end_mode.yaml#end_mode
trimmomatic_phred	quality score format	Either PHRED "33" or "64" specifies the base quality encoding. Default: 64	../tools/Trimmomatic/trimmomatic-phred.yaml#phred
trimmomatic_slidingWindow	read filtering sliding window	Perform a sliding window trimming, cutting once the average quality within the window falls below a threshold. By considering multiple bases, a single poor quality base will not cause the removal of high quality data later in the read. specifies the number of bases to average across specifies the average quality required	../tools/Trimmomatic/trimmomatic-sliding_window.yaml#slidingWindow
trinity_max_mem	maximum memory allocated to Trinity	Suggested max memory to use by Trinity where limiting can be enabled. (jellyfish, sorting, etc) provided in Gb of RAM, ie. --max_memory 10G	string
trinity_cpu	number of CPUs allocated	number of CPUs to use, default: 2	int?
trinity_seq_type	read file(s) format	type of reads: (fa or fq)	string
trinity_ss_lib_type	Strand-specific RNA-Seq read orientation	Strand-specific RNA-Seq read orientation. if paired: RF or FR, if single: F or R. (dUTP method = RF). See web documentation	string

ID	Name	Description
generate_raw_stats	Generates a QC for the provided read file(s).	Provide reverse and forward read files for paired-end (PE) or a single read file for single-end (SE).
filter_reads	Filtering and trimmming read file(s)	Low quality trimming (low quality ends and sequences with < quality scores less than 15 over a 4 nucleotide wide window are removed)
run_assembly	Runs the actual assembly	provide filtered/trimmed read file(s)
generate_filtered_stats	Generates a QC for the filtered read file(s).	Provide filtered/trimmed read file(s)
evaluate_contigs	Evaluates the contig quality.	Provide the assembled contigs (FASTA file)

ID	Name	Description	Type
raw_qc_report	n/a	n/a	File[]
raw_html_report	n/a	n/a	File[]
filtered_qc_report	n/a	n/a	File[]
filtered_html_report	n/a	n/a	File[]
trimmomatic_log_file	n/a	n/a	File?
forward_reads_paired	n/a	n/a	File
forward_reads_unpaired	n/a	n/a	File?
assembly_output_dir	n/a	n/a	Directory
assembled_contigs	n/a	n/a	File
transrate_output_dir	n/a	n/a	Directory

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Views: 257 Downloads: 8

Created: 25th Feb 2020 at 13:18

Last updated: 25th Feb 2020 at 15:17

Last used: 17th Jan 2021 at 20:32

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