Workflow: qc-assembled.workflow.cwl

Fetched 2024-06-20 04:36:14 GMT
children parents
Workflow as SVG
  • Selected
  • Default Values
  • Nested Workflows
  • Tools
  • Inputs/Outputs

Inputs

ID Type Title Doc
jobid String
sequences File
kmerLength Integer[] (Optional)

Steps

ID Runs Label Doc
kmer
../Tools/kmer-tool.tool.cwl (CommandLineTool)
calcualate kmer bins

Script to use jellyfish to get kmer information Input:\ fasta/fastq file Output:\ kmer information, one of:\ 1. hash:\ binary hash of counts 2. stats:\ summary stats 3. dump:\ profile (kmer seq - count) 4. histo:\ histogram (count - abundance) 5. histo ranked:\ count, abundance, count*abundance, reverse-sum(abundance), reverse-sum(count*abundance), ratio-to-largest

coverage
../Tools/assembly_coverage.tool.cwl (CommandLineTool)
formatQcStats
../Tools/format_qc_stats.tool.cwl (CommandLineTool)
sequenceStats
../Tools/seq_length_stats.tool.cwl (CommandLineTool)
sequence statistics

Calculate statistics for fasta files. Output fields:\ bp_count sequence_count average_length standard_deviation_length length_min length_max average_gc_content standard_deviation_gc_content average_gc_ratio standard_deviation_gc_ratio ambig_char_count ambig_sequence_count average_ambig_chars sequence_type

formatSequenceStats
../Tools/format_seq_stats.tool.cwl (CommandLineTool)

Outputs

ID Type Label Doc
qcStatFile File
seqBinFile File
seqStatFile File
qcSummaryFile File
assemblyCoverage File
Permalink: https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/qc-assembled.workflow.cwl