Workflow: viralrecon.nanopore.single.cwl
Fetched 2024-05-17 22:10:47 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
Apache License 2.0
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| SAMPLE_NAME | String | ||
| BARCODE_NAME | String | ||
| SNPEFF_CONFIG | File | ||
| SNPEFF_DATADIR | Directory | ||
| FAST5_DIRECTORY | Directory | ||
| FASTQ_DIRECTORY | Directory | ||
| SCHEME_DIRECTORY | Directory | ||
| NEXTCLADE_DATASET | Directory | ||
| SEQUENCING_SUMMARY | File | ||
| REFERENCE_GENOME_PREFIX | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| pigz |
../tool/artic/pigz.cwl
(CommandLineTool)
|
||
| tabix |
../tool/tabix/tabix.cwl
(CommandLineTool)
|
||
| snpeff |
../tool/snpeff/snpeff.cwl
(CommandLineTool)
|
||
| snpsift |
../tool/snpsift/snpsift.cwl
(CommandLineTool)
|
||
| vcfuniq |
../tool/vcfuniq/vcfuniq.cwl
(CommandLineTool)
|
||
| nanoplot |
../tool/nanoplot/nanoplot.cwl
(CommandLineTool)
|
||
| pangolin |
../tool/pangolin/pangolin.cwl
(CommandLineTool)
|
||
| nextclade |
../tool/nextclade/nextclade.cwl
(CommandLineTool)
|
||
| artic.minion |
../tool/artic/artic.minion.cwl
(CommandLineTool)
|
||
| samtools.view |
../tool/samtools/samtools.view.cwl
(CommandLineTool)
|
||
| bcftools.stats |
../tool/bcftools/bcftools.stats.cwl
(CommandLineTool)
|
||
| artic.guppyplex |
../tool/artic/artic.guppyplex.cwl
(CommandLineTool)
|
||
| mosdepth.genome |
../tool/mosdepth/mosdepth.genome.cwl
(CommandLineTool)
|
||
| mosdepth.amplicon |
../tool/mosdepth/mosdepth.amplicon.cwl
(CommandLineTool)
|
||
| to_vcf_with_index |
viralrecon.nanopore.single.cwl#to_vcf_with_index/58f1e4d3-f34f-4e2c-99ba-327e4b2b489d
(CommandLineTool)
|
||
| extract_primer_bed |
viralrecon.nanopore.single.cwl#extract_primer_bed/8bd97e9a-7451-49bf-9e17-32a833c052b0
(CommandLineTool)
|
||
| collapse_primer_bed |
../tool/collapse_primer_bed/collapse_primer_bed.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| snpsift.out | File | ||
| nanoplot.all | Directory[] | ||
| pangolin.csv | File | ||
| nextclade.out | Directory | ||
| consensus_fasta | File | ||
| bcftoos.stats.txt | File | ||
| mosdepth.genome.all | Directory[] | ||
| mosdepth.amplicon.all | Directory[] |
Permalink:
https://w3id.org/cwl/view/git/344088271e5f85632f2f8fdeae78af56089904a9/nanopore/workflow/viralrecon.nanopore.single.cwl
