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version: "3.5"
services:
  01_prepare_reads:
    image: registry.codigos.ufsc.br/bioinfo/python
    environment:
      - INTERVALO=10
    volumes: 
      - amostras:/input
      - 01_prepare_reads:/output
    command: "/prepare_reads.py"
    
  02_filter_reads_trimmomatic:
    image: registry.codigos.ufsc.br/bioinfo/trimmomatic
    environment:
      - THREADS=12
      - INTERVALO=10
    volumes:
      - 01_prepare_reads:/input
      - 02_filter_reads_trimmomatic:/output
      
  03_contamination_bwa_mem:
    image: registry.codigos.ufsc.br/bioinfo/bwa
    environment:
      - THREADS=12
      - INTERVALO=60
      - FASTA=Human_Ref_v37.fasta
    volumes:
      - 02_filter_reads_trimmomatic:/input
      - reference:/reference
      - 03_contamination_bwa_mem:/output

  04_contamination_samtools_view_sort:
    image: registry.codigos.ufsc.br/bioinfo/samtools
    environment:
      - THREADS=12
      - INTERVALO=10
    volumes: 
      - 03_contamination_bwa_mem:/input
      - 04_contamination_samtools_view_sort:/output
    command: "04_contamination_samtools_view_sort"

  05_contamination_samtools_fastq:
    image: registry.codigos.ufsc.br/bioinfo/samtools
    environment:
      - THREADS=12
      - INTERVALO=10
    volumes: 
      - 04_contamination_samtools_view_sort:/input
      - 05_contamination_samtools_fastq:/output
    command: "05_contamination_samtools_fastq"

  06_map_reads_covid_bwa_mem:
    image: registry.codigos.ufsc.br/bioinfo/bwa
    environment:
      - THREADS=12
      - INTERVALO=60
      - FASTA=NC_045512_Ref_Genome.fasta
    volumes:
      - 05_contamination_samtools_fastq:/input
      - reference:/reference
      - 06_map_reads_covid_bwa_mem:/output

  07_map_reads_covid_samtools_sort:
    image: registry.codigos.ufsc.br/bioinfo/samtools
    environment:
      - THREADS=12
      - INTERVALO=10
    volumes: 
      - 06_map_reads_covid_bwa_mem:/input
      - 07_map_reads_covid_samtools_sort:/output
    command: "07_map_reads_covid_samtools_sort"

  08_statistics_bbmap:
    image: registry.codigos.ufsc.br/bioinfo/bbmap
    environment:
      - INTERVALO=10
    volumes: 
      - 07_map_reads_covid_samtools_sort:/input
      - 08_statistics_bbmap:/output 

  09_map_reads_covid_samtools_index:
    image: registry.codigos.ufsc.br/bioinfo/samtools
    environment:
      - THREADS=12
      - INTERVALO=10
    volumes: 
      - 07_map_reads_covid_samtools_sort:/input
      - 09_map_reads_covid_samtools_index:/output
    command: "09_map_reads_covid_samtools_index"

  10_variant_call_samtools_pileup:
    image: registry.codigos.ufsc.br/bioinfo/samtools
    environment:
      - THREADS=12
      - INTERVALO=10
    volumes: 
      - 09_map_reads_covid_samtools_index:/input
      - 10_variant_call_samtools_pileup:/output
    command: "10_variant_call_samtools_pileup"

  11_variant_call_ivar_variants:
    image: registry.codigos.ufsc.br/bioinfo/ivar
    environment:
      - INTERVALO=10
      - REFERENCE=primers_pcr.sorted.bed
    volumes: 
      - 10_variant_call_samtools_pileup:/input
      - reference_covid:/reference
      - 11_variant_call_ivar_variants:/output

    command: "11_variant_call_ivar_variants"

  12_primers_ivar_trim:
    image: registry.codigos.ufsc.br/bioinfo/ivar
    environment:
      - INTERVALO=10
      - REFERENCE=primers_pcr
    volumes: 
      - 09_map_reads_covid_samtools_index:/input
      - reference_covid:/reference
      - 12_primers_ivar_trim:/output
      
    command: "12_primers_ivar_trim"

  13_assembly_samtools_sort:
    image: registry.codigos.ufsc.br/bioinfo/samtools
    environment:
      - THREADS=12
      - INTERVALO=10
    volumes: 
      - 12_primers_ivar_trim:/input
      - 13_assembly_samtools_sort:/output
    command: "13_assembly_samtools_sort"


  14_assembly_samtools_mpileup:
    image: registry.codigos.ufsc.br/bioinfo/samtools
    environment:
      - THREADS=12
      - INTERVALO=10
    volumes: 
      - 13_assembly_samtools_sort:/input
      - 14_assembly_samtools_mpileup:/output
    command: "14_assembly_samtools_mpileup"

  15_assembly_ivar_consensus:
    image: registry.codigos.ufsc.br/bioinfo/ivar
    environment:
      - INTERVALO=10
    volumes: 
      - 14_assembly_samtools_mpileup:/input
      - 15_assembly_ivar_consensus:/output
      
    command: "15_assembly_ivar_consensus"

  16_concatenate_all_genomes:
    image: registry.codigos.ufsc.br/bioinfo/python
    environment:
      - INTERVALO=10
    volumes: 
      - 15_assembly_ivar_consensus:/15_assembly_ivar_consensus
      - 08_statistics_bbmap:/08_statistics_bbmap
      - 16_concatenate_all_genomes:/output

    command: "/parser_files_covgenomes.py"

  17_annotate_pangolin:
      image: registry.codigos.ufsc.br/bioinfo/pangolin
      environment:
        - INTERVALO=10
      volumes: 
        - 16_concatenate_all_genomes:/input
        - 17_annotate_pangolin:/output

  18_annotate_nextclade:
    image: registry.codigos.ufsc.br/bioinfo/nextclade
    environment:
      - INTERVALO=10
    volumes: 
      - 16_concatenate_all_genomes:/input
      - nextclade_ref_cov:/nextclade_ref_cov
      - 18_annotate_nextclade:/output 



volumes:
  amostras:
    driver: local
    driver_opts:
      type: nfs
      o: addr=150.162.6.180,rw,async
      device: :/export/bioinfo/amostras 

  reference:
    driver: local
    driver_opts:
      type: nfs
      o: addr=150.162.6.180,rw,async
      device: :/export/bioinfo/reference

  reference_covid:
    driver: local
    driver_opts:
      type: nfs
      o: addr=150.162.6.180,rw,async
      device: :/export/bioinfo/reference_covid

  nextclade_ref_cov:
    driver: local
    driver_opts:
      type: nfs
      o: addr=150.162.6.180,rw,async
      device: :/export/bioinfo/nextclade_ref_cov
      
  01_prepare_reads:
    driver: local
    driver_opts:
      type: nfs
      o: addr=150.162.6.180,rw,async
      device: :/export/bioinfo/01_prepare_reads
      
  02_filter_reads_trimmomatic:
    driver: local
    driver_opts:
      type: nfs
      o: addr=150.162.6.180,rw,async
      device: :/export/bioinfo/02_filter_reads_trimmomatic
       
  03_contamination_bwa_mem:
    driver: local
    driver_opts:
      type: nfs
      o: addr=150.162.6.180,rw,async
      device: :/export/bioinfo/03_contamination_bwa_mem

  04_contamination_samtools_view_sort:
    driver: local
    driver_opts:
      type: nfs
      o: addr=150.162.6.180,rw,async
      device: :/export/bioinfo/04_contamination_samtools_view_sort

  05_contamination_samtools_fastq:
    driver: local
    driver_opts:
      type: nfs
      o: addr=150.162.6.180,rw,async
      device: :/export/bioinfo/05_contamination_samtools_fastq

  06_map_reads_covid_bwa_mem:
    driver: local
    driver_opts:
      type: nfs
      o: addr=150.162.6.180,rw,async
      device: :/export/bioinfo/06_map_reads_covid_bwa_mem
   
  07_map_reads_covid_samtools_sort:
    driver: local
    driver_opts:
      type: nfs
      o: addr=150.162.6.180,rw,async
      device: :/export/bioinfo/07_map_reads_covid_samtools_sort
      
  08_statistics_bbmap:
    driver: local
    driver_opts:
      type: nfs
      o: addr=150.162.6.180,rw,async
      device: :/export/bioinfo/08_statistics_bbmap
      
  09_map_reads_covid_samtools_index:
    driver: local
    driver_opts:
      type: nfs
      o: addr=150.162.6.180,rw,async
      device: :/export/bioinfo/09_map_reads_covid_samtools_index
 
  10_variant_call_samtools_pileup:
    driver: local
    driver_opts:
      type: nfs
      o: addr=150.162.6.180,rw,async
      device: :/export/bioinfo/10_variant_call_samtools_pileup

  11_variant_call_ivar_variants:
    driver: local
    driver_opts:
      type: nfs
      o: addr=150.162.6.180,rw,async
      device: :/export/bioinfo/11_variant_call_ivar_variants

  12_primers_ivar_trim:
    driver: local
    driver_opts:
      type: nfs
      o: addr=150.162.6.180,rw,async
      device: :/export/bioinfo/12_primers_ivar_trim
      
  13_assembly_samtools_sort:
    driver: local
    driver_opts:
      type: nfs
      o: addr=150.162.6.180,rw,async
      device: :/export/bioinfo/13_assembly_samtools_sort
      
  14_assembly_samtools_mpileup:
    driver: local
    driver_opts:
      type: nfs
      o: addr=150.162.6.180,rw,async
      device: :/export/bioinfo/14_assembly_samtools_mpileup
      
  15_assembly_ivar_consensus:
    driver: local
    driver_opts:
      type: nfs
      o: addr=150.162.6.180,rw,async
      device: :/export/bioinfo/15_assembly_ivar_consensus
      
  16_concatenate_all_genomes:
    driver: local
    driver_opts:
      type: nfs
      o: addr=150.162.6.180,rw,async
      device: :/export/bioinfo/16_concatenate_all_genomes
      
  17_annotate_pangolin:
    driver: local
    driver_opts:
      type: nfs
      o: addr=150.162.6.180,rw,async
      device: :/export/bioinfo/17_annotate_pangolin
      
  18_annotate_nextclade:
    driver: local
    driver_opts:
      type: nfs
      o: addr=150.162.6.180,rw,async
      device: :/export/bioinfo/18_annotate_nextclade