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tt_ani_top_n.cwl
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tt_ani_top_n.cwl
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cwlVersion: v1.0
label: "ani_top_n"
# file: task_types/tt_ani_top_n.cwl
class: Workflow # task type
hints:
DockerRequirement:
dockerPull: ncbi/gpdev:latest
inputs:
gencoll_asn: File
blast_align: File
ANI_cutoff: File
asn_cache: Directory
ref_assembly_taxid: int
outputs:
top:
type: File
outputSource: ani_top_identification/top
annot:
type: File
outputSource: ani_top_identification/annot
#/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2018-03-13.build2663/bin/ani_top_identification \
# -ANI_cutoff \
# /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2018-03-13.build2663/third-party/data/BacterialPipeline/ANI_cutoff/ANI_cutoff.xml \
# -N \
# 25 \
# -asn-cache \
# /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/data56/Mycoplasma_genitalium_G37/Mycoplasma_genitalium_External_PGAP.4585524/sequence_cache,/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe_id_cache/full_id_cache \
# -input-manifest \
# /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/data56/Mycoplasma_genitalium_G37/Mycoplasma_genitalium_External_PGAP.4585524/4829637/ani_top_n.455674852/inp/assm_aligns.mft \
# -min-gap \
# 10000 \
# -min-region \
# 1000 \
# -o \
# /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/data56/Mycoplasma_genitalium_G37/Mycoplasma_genitalium_External_PGAP.4585524/4829637/ani_top_n.455674852/out/ani-tax-report.xml \
# -o-annot \
# /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/data56/Mycoplasma_genitalium_G37/Mycoplasma_genitalium_External_PGAP.4585524/4829637/ani_top_n.455674852/out/annot.asn \
# -query-assembly \
# /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/data56/Mycoplasma_genitalium_G37/Mycoplasma_genitalium_External_PGAP.4585524/4829637/gc_create_from_sequences.455674892/out/gencoll.asn \
# -ref-assembly-id \
# 0 \
# -ref-assembly-taxid \
# 243273
steps:
ani_top_identification:
run: ../progs/ani_top_identification.cwl
in:
ANI_cutoff: ANI_cutoff
N:
default: 25
asn_cache: asn_cache
input: blast_align
min_gap:
default: 10000
min_region:
default: 1000
query_assembly: gencoll_asn
ref_assembly_id:
default: 0
ref_assembly_taxid: ref_assembly_taxid
out: [annot, top]