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Update COVID SC authored by Bruno da Silva Castilho's avatar Bruno da Silva Castilho
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COVID-SC.md
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......@@ -16,5 +16,349 @@ Pipeline do projeto COVID-SC, criado para identificar novas variantes da COVID-1
![covid-pipeline-docker](uploads/d3da533bdd85e2c95233a1b30a2da956/covid-pipeline-docker.png)
#### Configurações
##### Volumes
##### Stack
```yaml
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
```