Commit b6186f78 authored by Nijsse, Bart's avatar Nijsse, Bart
Browse files

label and naming

parent 1f80c11c
......@@ -17,13 +17,14 @@ doc: |
- Flye (de novo assembly)
- Medaka (assembly polishing)
- metaQUAST (assembly quality reports)
When Illumina reads are provided:
- Assembly polishing with Pilon
- Metabat2 binning
- CheckM
- BUSCO
- GTDB-Tk
Binnning:
- Metabat2
- CheckM
- BUSCO
- GTDB-Tk
outputs:
nanopore_quality_output:
......@@ -137,7 +138,7 @@ steps:
#############################################
#### Quality Nanopore
workflow_quality_nanopore:
label: Nanopore quality and filtering
label: Nanopore quality and filtering workflow
doc: Quality and filtering workflow for nanopore reads
run: workflow_nanopore_quality.cwl
in:
......@@ -172,8 +173,8 @@ steps:
#############################################
#### Taxonomic classification of with Kraken2
nanopore_kraken2:
label: Taxonomic classification with Kraken2
doc: Taxonomic classification of FASTQ reads
label: Kraken2 Nanopore
doc: Taxonomic classification of Nanopore reads
run: ../kraken2/kraken2.cwl
in:
tmp_id: identifier
......@@ -185,7 +186,7 @@ steps:
out: [standard_report, sample_report]
illumina_kraken2:
label: Taxonomic classification with Kraken2
label: Kraken2 Illumina
doc: Taxonomic classification of FASTQ reads
when: $(inputs.binning)
run: ../kraken2/kraken2.cwl
......@@ -257,7 +258,7 @@ steps:
#############################################
#### Workflow Pilon assembly polishing
workflow_pilon:
label: Pilon
label: Pilon worklow
doc: Illumina reads assembly polishing with Pilon
when: $(inputs.binning)
run: workflow_pilon_mapping.cwl
......
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