Workflow: cpo-pipeline

Fetched 2019-10-20 17:02:49 GMT
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Workflow as SVG
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Inputs

ID Type Title Doc
reads2 File
reads1 File
refseq_genomes_k21_s1000_msh File

Steps

ID Runs Label Doc
head
https://raw.githubusercontent.com/dfornika/cwl-workspace/master/tools/head/head.cwl (CommandLineTool)
head
quast
https://raw.githubusercontent.com/dfornika/cwl-workspace/master/tools/quast/quast.cwl (CommandLineTool)
quast
mlst
https://raw.githubusercontent.com/dfornika/cwl-workspace/master/tools/mlst/mlst.cwl (CommandLineTool)
mlst
fastqc
https://raw.githubusercontent.com/dfornika/cwl-workspace/master/tools/fastqc/fastqc.cwl (CommandLineTool)
fastqc
shovill
https://raw.githubusercontent.com/dfornika/cwl-workspace/master/tools/shovill/shovill.cwl (CommandLineTool)
shovill
fastqc_1
https://raw.githubusercontent.com/dfornika/cwl-workspace/master/tools/fastqc/fastqc.cwl (CommandLineTool)
fastqc
sort
https://raw.githubusercontent.com/dfornika/cwl-workspace/master/tools/sort/sort.cwl (CommandLineTool)
sort
mash_sketch
https://raw.githubusercontent.com/dfornika/cwl-workspace/master/tools/mash/mash_sketch/mash_sketch.cwl (CommandLineTool)
mash_sketch
mash_dist
https://raw.githubusercontent.com/dfornika/cwl-workspace/master/tools/mash/mash_dist/mash_dist.cwl (CommandLineTool)
mash_dist

Outputs

ID Type Label Doc
mlst_output File (Optional)
fastqc_R1_output Directory (Optional)
mash_dist_output File (Optional)
quast_output Directory
fastqc_R2_output Directory (Optional)
Permalink: https://w3id.org/cwl/view/git/55c70792643d65c0c2d0942d3941549e812d5d17/workflows/cpo-pipeline/cpo-pipeline.cwl