Workflow: TAP
Fetched 2023-01-11 06:34:21 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| primer |
Euk primer |
||
| tidy_up | Boolean | ||
| indexDir | Directory (Optional) |
Directory containing bowtie indices. Must containe index files with 'genome' prefix. |
|
| mate_pair |
List of forward and reverse compressed fastq file records |
||
| ion_torrent | Boolean | ||
| reference_database | File [null] |
Reference database, e.g. UNITE or SILVA |
|
| reference_taxonomy | File |
Taxonomy mapping from accession to tax string |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| PHIX |
../Tools/bowtie2.tool.cwl
(CommandLineTool)
|
PHIX |
STAGE:0060 PHIX removal using bowtie2 with Illumina RTA genome and Illumina built indeces |
| prep |
../Tools/cutadapt.tool.cwl
(CommandLineTool)
|
cutadapt |
none |
| cluster |
../Tools/vsearch/Clustering.vsearch.cwl
(CommandLineTool)
|
Clustering |
Clustering |
| merging |
../Tools/vsearch.tool.cwl
(CommandLineTool)
|
vsearch |
vsearcg |
| cleanReads |
../Tools/vsearch/Searching.vsearch.cwl
(CommandLineTool)
|
Searching |
Searching |
| decompress |
decompress_mate_pair.workflow.cwl
(Workflow)
|
Decompress |
Decompress mate pair fastq files |
| dereplicate |
../Tools/vsearch/Dereplication_and_rereplication.vsearch.cwl
(CommandLineTool)
|
Dereplication_and_rereplication |
Dereplication and rereplication |
| convertToOTU |
../Tools/uc2otu.tool.cwl
(CommandLineTool)
|
uc2otu |
n/a |
| removePrimer |
../Tools/cutadapt.tool.cwl
(CommandLineTool)
|
cutadapt |
none |
| classification |
../Tools/mothur/classification.mothur.tool.cwl
(CommandLineTool)
|
mothur command line |
n/a |
| extractFeatures |
../Tools/ITSx.tool.cwl
(CommandLineTool)
|
ITSx |
n/a |
| removeCommentsAddBarcodeLabel |
../Tools/regexp.tool.cwl
(CommandLineTool)
|
sed |
n/a |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| raw | https://w3id.org/cwl/salad#Any | ||
| tmp | File | ||
| OTUs | File | ||
| merged | File | ||
| noPHIX | File | ||
| features | File[] | ||
| noPrimer | File | ||
| clustered | File | ||
| Classified | File | ||
| RegexpTool | File[] | ||
| cleanedReads | File[] | ||
| dereplicated | File |
Permalink:
https://w3id.org/cwl/view/git/735a989b6923e9207baace2702be4554d70c92d7/CWL/Workflows/tap.euk.workflow.cwl
