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cwlVersion: v1.0
class: Workflow
label: EMG QC workflow, (paired end version). Benchmarking with MG-RAST expt.
requirements:
- class: SubworkflowFeatureRequirement
- class: SchemaDefRequirement
types:
- $import: ../tools/FragGeneScan-model.yaml
- $import: ../tools/trimmomatic-sliding_window.yaml
- $import: ../tools/trimmomatic-end_mode.yaml
- $import: ../tools/trimmomatic-phred.yaml
inputs:
forward_reads:
type: File
format: edam:format_1930 # FASTQ
reverse_reads:
type: File
format: edam:format_1930 # FASTQ
outputs:
processed_sequences:
type: File
outputSource: clean_fasta_headers/sequences_with_cleaned_headers
steps:
overlap_reads:
label: Paired-end overlapping reads are merged
run: ../tools/seqprep.cwl
in:
forward_reads: forward_reads
reverse_reads: reverse_reads
out: [ merged_reads, forward_unmerged_reads, reverse_unmerged_reads ]
combine_overlaped_and_unmerged_reads:
run: ../tools/seqprep-merge.cwl
in:
merged_reads: overlap_reads/merged_reads
forward_unmerged_reads: overlap_reads/forward_unmerged_reads
reverse_unmerged_reads: overlap_reads/reverse_unmerged_reads
out: [ merged_with_unmerged_reads ]
trim_quality_control:
doc: |
Low quality trimming (low quality ends and sequences with < quality scores
less than 15 over a 4 nucleotide wide window are removed)
run: ../tools/trimmomatic.cwl
in:
reads1: combine_overlaped_and_unmerged_reads/merged_with_unmerged_reads
phred: { default: '33' }
leading: { default: 3 }
trailing: { default: 3 }
end_mode: { default: SE }
minlen: { default: 100 }
slidingwindow:
default:
windowSize: 4
requiredQuality: 15
out: [reads1_trimmed]
convert_trimmed-reads_to_fasta:
run: ../tools/fastq_to_fasta.cwl
in:
fastq: trim_quality_control/reads1_trimmed
out: [ fasta ]
clean_fasta_headers:
run: ../tools/clean_fasta_headers.cwl
in:
sequences: convert_trimmed-reads_to_fasta/fasta
out: [ sequences_with_cleaned_headers ]
$namespaces:
edam: http://edamontology.org/
s: http://schema.org/
$schemas:
- http://edamontology.org/EDAM_1.16.owl
- https://schema.org/docs/schema_org_rdfa.html
s:license: "https://www.apache.org/licenses/LICENSE-2.0"
s:copyrightHolder: "EMBL - European Bioinformatics Institute"
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