COVID-SC.md

-Pipeline do projeto COVID-SC, criado para identificar novas variantes da COVID-19 no estado. 
+Pipeline do projeto COVID-SC, criado para identificar novas variantes da COVID-19 no estado. O pipeline tem 18 etapas, conectadas por volumes nfs, onde a saída de uma etapa está conectada na entrada de sua etapa posterior.
 
 #### Links
 - [bbmap](https://codigos.ufsc.br/bioinfo/bbmap)
 - [bcftools](https://codigos.ufsc.br/bioinfo/bcftools)
 - [bwa](https://codigos.ufsc.br/bioinfo/bwa)
 - [ivar](https://codigos.ufsc.br/bioinfo/ivar)
+- [nextclade](https://codigos.ufsc.br/bioinfo/nextclade)
 - [pangolin](https://codigos.ufsc.br/bioinfo/pangolin)
 - [python](https://codigos.ufsc.br/bioinfo/python)
 - [samtools](https://codigos.ufsc.br/bioinfo/samtools)
 - [seqtk](https://codigos.ufsc.br/bioinfo/seqtk)
 - [trimmomatic](https://codigos.ufsc.br/bioinfo/trimmomatic)
 
+
 #### Diagrama do pipeline
 
 ![covid-pipeline-docker](uploads/d3da533bdd85e2c95233a1b30a2da956/covid-pipeline-docker.png)
@@ -210,154 +212,154 @@ volumes:
     driver: local
     driver_opts:
       type: nfs
-      o: addr=150.162.6.180,rw,async
+      o: addr=190.162.6.180,rw,async
       device: :/export/bioinfo/amostras 
 
   reference:
     driver: local
     driver_opts:
       type: nfs
-      o: addr=150.162.6.180,rw,async
+      o: addr=190.162.6.180,rw,async
       device: :/export/bioinfo/reference
 
   reference_covid:
     driver: local
     driver_opts:
       type: nfs
-      o: addr=150.162.6.180,rw,async
+      o: addr=190.162.6.180,rw,async
       device: :/export/bioinfo/reference_covid
 
   nextclade_ref_cov:
     driver: local
     driver_opts:
       type: nfs
-      o: addr=150.162.6.180,rw,async
+      o: addr=190.162.6.180,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
+      o: addr=190.162.6.180,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
+      o: addr=190.162.6.180,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
+      o: addr=190.162.6.180,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
+      o: addr=190.162.6.180,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
+      o: addr=190.162.6.180,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
+      o: addr=190.162.6.180,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
+      o: addr=190.162.6.180,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
+      o: addr=190.162.6.180,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
+      o: addr=190.162.6.180,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
+      o: addr=190.162.6.180,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
+      o: addr=190.162.6.180,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
+      o: addr=190.162.6.180,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
+      o: addr=190.162.6.180,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
+      o: addr=190.162.6.180,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
+      o: addr=190.162.6.180,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
+      o: addr=190.162.6.180,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
+      o: addr=190.162.6.180,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
+      o: addr=190.162.6.180,rw,async
       device: :/export/bioinfo/18_annotate_nextclade
 ```