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emg-assembly.cwl
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emg-assembly.cwl
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cwlVersion: v1.0
class: Workflow
label: EMG assembly for paired end Illumina
requirements:
- class: StepInputExpressionRequirement
- class: SubworkflowFeatureRequirement
- class: SchemaDefRequirement
types:
- $import: ../tools/InterProScan-apps.yaml
- $import: ../tools/InterProScan-protein_formats.yaml
- $import: ../tools/esl-reformat-replace.yaml
inputs:
forward_reads:
type: File
format: edam:format_1930 # FASTQ
reverse_reads:
type: File
format: edam:format_1930 # FASTQ
covariance_model_database:
type: File
secondaryFiles:
- .i1f
- .i1i
- .i1m
- .i1p
fraggenescan_model: File
fraggenescan_prob_forward: File
fraggenescan_prob_backward: File
fraggenescan_prob_noncoding: File
fraggenescan_prob_start: File
fraggenescan_prob_stop: File
fraggenescan_prob_start1: File
fraggenescan_prob_stop1: File
fraggenescan_pwm_dist: File
assembly_mem_limit:
type: int
doc: in Gb
mapseq_ref:
type: File
format: edam:format_1929 # FASTA
secondaryFiles: .mscluster
mapseq_taxonomies: File[]
outputs:
SSUs:
type: File
outputSource: extract_SSUs/sequences
classifications:
type: File
outputSource: classify_SSUs/classifications
scaffolds:
type: File
outputSource: assembly/scaffolds
pCDS:
type: File
outputSource: fraggenescan/predictedCDS
annotations:
type: File
outputSource: interproscan/i5Annotations
steps:
assembly:
run: ../tools/metaspades.cwl
in:
forward_reads: forward_reads
reverse_reads: reverse_reads
memory_limit: assembly_mem_limit
out: [ scaffolds ]
cmscan:
run: ../tools/infernal-cmscan.cwl
in:
query_sequences: assembly/scaffolds
covariance_model_database: covariance_model_database
only_hmm: { default: true }
omit_alignment_section: { default: true }
out: [ matches ]
get_SSU_coords:
run: ../tools/SSU-from-tablehits.cwl
in:
table_hits: cmscan/matches
out: [ SSU_coordinates ]
index_scaffolds:
run: ../tools/esl-sfetch-index.cwl
in:
sequences: assembly/scaffolds
out: [ sequences_with_index ]
extract_SSUs:
run: ../tools/esl-sfetch-manyseqs.cwl
in:
indexed_sequences: index_scaffolds/sequences_with_index
names: get_SSU_coords/SSU_coordinates
names_contain_subseq_coords: { default: true }
out: [ sequences ]
classify_SSUs:
run: ../tools/mapseq.cwl
in:
sequences: extract_SSUs/sequences
database: mapseq_ref
taxonomies: mapseq_taxonomies
out: [ classifications ]
fraggenescan:
run: ../tools/FragGeneScan1_20.cwl
in:
sequence: assembly/scaffolds
completeSeq: { default: true }
model: fraggenescan_model
prob_forward: fraggenescan_prob_forward
prob_backward: fraggenescan_prob_backward
prob_noncoding: fraggenescan_prob_noncoding
prob_start: fraggenescan_prob_start
prob_stop: fraggenescan_prob_stop
prob_start1: fraggenescan_prob_start1
prob_stop1: fraggenescan_prob_stop1
pwm_dist: fraggenescan_pwm_dist
out: [ predictedCDS ]
remove_asterisks_and_reformat:
run: ../tools/esl-reformat.cwl
in:
sequences: fraggenescan/predictedCDS
replace: { default: { find: '*', replace: X } }
out: [ reformatted_sequences ]
interproscan:
run: ../tools/InterProScan5.21-60.cwl
in:
proteinFile: remove_asterisks_and_reformat/reformatted_sequences
applications:
default:
- Pfam
- TIGRFAM
- PRINTS
- ProSitePatterns
- Gene3D
# outputFileType:
# valueFrom: TSV
out: [i5Annotations]
$namespaces: { edam: "http://edamontology.org/" }
$schemas: [ "http://edamontology.org/EDAM_1.16.owl" ]