TranscriptomeAssembly-wf.single-end

ID	Name	Description	Type
end_mode	read -end mode format	Read -end mode format to be specify to Trimmomatic	#trimmomatic-end_mode.yaml/end_mode
forward_reads	Paired-end read file 1	Read file 1 in FASTQ format	File
read_files	FASTQ read file(s)	FASTQ file of reverse reads in Paired End mode	array containing File
trimmomatic_phred	quality score format	Either PHRED "33" or "64" specifies the base quality encoding. Default: 64	#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	#trimmomatic-sliding_window.yaml/slidingWindow
trinity_cpu	number of CPUs allocated	number of CPUs to use, default: 2	int
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_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
evaluate_contigs	Evaluates the contig quality.	Provide the assembled contigs (FASTA file)
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)
generate_filtered_stats	Generates a QC for the filtered read file(s).	Provide filtered/trimmed read file(s)
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).
run_assembly	Runs the actual assembly	provide filtered/trimmed read file(s)

ID	Name	Description	Type
assembled_contigs	n/a	n/a	File
assembly_output_dir	n/a	n/a	Directory
filtered_html_report	n/a	n/a	array containing File
filtered_qc_report	n/a	n/a	array containing File
forward_reads_paired	n/a	n/a	File
forward_reads_unpaired	n/a	n/a	File
raw_html_report	n/a	n/a	array containing File
raw_qc_report	n/a	n/a	array containing File
transrate_output_dir	n/a	n/a	Directory
trimmomatic_log_file	n/a	n/a	File

TranscriptomeAssembly-wf.single-end
Version 1