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stats.cwl
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stats.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
inputs:
sequences:
type: File
reads:
type: File[]
output_dest:
type: string
min_contig_length:
type: int
assembler:
type: string
outputs:
bwa_index_output:
type: File
outputSource: bwa_index/output
bwa_mem_output:
type: File
outputSource: bwa_mem/output
samtools_view_output:
type: File
outputSource: samtools_view/output
samtools_sort_output:
type: File
outputSource: samtools_sort/sorted
samtools_index_output:
type: File
outputSource: samtools_index/alignments_with_index
metabat_coverage_output:
type: File
outputSource: metabat_jgi/output
logfile:
type: File
outputSource: stats_report/logfile
steps:
readfq:
run: ./readfq.cwl
in:
raw_reads:
source: reads
out:
- id: base_count
bwa_index:
run: ./bwa-index.cwl
in:
sequences:
source: sequences
out:
- output
bwa_mem:
run: ./bwa-mem.cwl
in:
reads:
source:
- reads
reference:
source: bwa_index/output
out:
- output
samtools_view:
run: ./samtools-view.cwl
in:
input:
source: bwa_mem/output
uncompressed:
default: true
unselected_output_reads:
default: true
output_name:
default: "unsorted.bam"
out:
- output
samtools_sort:
run: ./samtools-sort.cwl
in:
input:
source: samtools_view/output
output_name:
default: "sorted.bam"
out:
- sorted
samtools_index:
run: ./samtools-index.cwl
in:
alignments:
source: samtools_sort/sorted
out:
- alignments_with_index
metabat_jgi:
run: ./metabat-jgi-summarise.cwl
in:
input:
source: samtools_index/alignments_with_index
outputDepth:
default: "coverage.tab"
out:
- output
stats_report:
run: ./stats-report.cwl
in:
assembler:
source: assembler
sequences:
source: sequences
output:
default: "output.json"
coverage_file:
source: metabat_jgi/output
base_count:
source: readfq/base_count
min_contig_length:
source: min_contig_length
out:
- logfile
$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"