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- Inputs/Outputs
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source repository.
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 |
drisee |
../Tools/drisee.tool.cwl
(CommandLineTool)
|
||
consensus |
../Tools/consensus.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 |
Permalink:
https://w3id.org/cwl/view/git/932da3abed7166bd5a962871386ba2c31d47b85c/CWL/Workflows/qc-basic.workflow.cwl