Workflow: post_assembly.cwl

Fetched 2020-07-14 15:59:14 GMT
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Inputs

ID Type Title Doc
assembly_log File
assembly File
reads File[]
assembler String
min_contig_length Integer

Steps

ID Runs Label Doc
write_stats_output
post_assembly.cwl#write_stats_output/organise (ExpressionTool)
stats_report
stats/stats.cwl (Workflow)
fasta_processing
fasta_trimming/fasta-trimming.cwl (CommandLineTool)

usage: trim_fasta.py [-h] fasta min_contig_length contig_filename

Remove contigs of length < min_contig_length from a fasta file.

positional arguments: fasta Path to fasta file to trim min_contig_length Minimum contig length, set to 0 for no trimming contig_filename Filename (without ANY extension) to give to contig files

optional arguments: -h, --help show this help message and exit

Outputs

ID Type Label Doc
stats_output Directory
Permalink: https://w3id.org/cwl/view/git/202e51ac4bfe78d68af50af5ec9ae37bf380c7a7/cwl/post_assembly.cwl