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This project proposes to contribute to fill the knowledge gap about Covid-19SARS-CoV-2 in Brazil and with the global knowledge about the pathogen. The scientific community and governments of other countries are looking for actions along these lines. The United Kingdom recently established a research network for genomic studies of SARS-CoV-2Covid-19 with a contribution of GBP 20 million (https://www.gov.uk/government/news/uk-launches-whole- genome-sequence-alliance-to-map-spread-of-coronavirus).

Dockerfile 6.49% Shell 39.42% R 52.56% Python 1.52%
covid19 genomics bioinformatics-pipeline bioinformatics-analysis bioinformatics-scripts

pipecov's Issues

Erro no Rscript

Olá Ronnie, tudo bem?

O pipeline de montagem está funcionando normalmente?
Porque eu implementei ele na Fiocruz e estava dando um erro, que ao "debugar" o script percebi que era na linha 175 do script com as funções para gerar o consenso (https://github.com/alvesrco/covid19_itvds/blob/master/dockerfiles/R/wgs_functions.R). A linha está escrita assim:
"poor_cov<-which(colSums(cm)<0);"

Olhando o script original (https://github.com/proychou/ViralWGS/blob/master/wgs_functions.R), percebi que ao invés do '0', seria '10'.
"poor_cov<-which(colSums(cm)<10);"

Foi intencional essa modificação? E não gerou um erro para vocês?

Um abraço,
Daniel Moreira

cp: can't stat 'usher_lineage_report.csv': No such file or directory error during assembly

Hi, I'm experiencing the error given below during the assembly process

Using UShER as inference engine.
****
Pangolin running in usher mode.
****
Maximum ambiguity allowed is 0.3.
****
Query file:	/output/home/thermite/setu_test/pipecov/11-pangolin_lineages/../test1_closedgap.fasta
****
Data files found:
usher_pb:	/opt/conda/envs/pangolin/lib/python3.10/site-packages/pangolin_data/data/lineageTree.pb
****
****
Output file written to: /output/home/thermite/setu_test/pipecov/11-pangolin_lineages/lineage_report.csv
****
Output alignment written to: /output/home/thermite/setu_test/pipecov/11-pangolin_lineages/alignment.fasta
cp: can't stat 'usher_lineage_report.csv': No such file or directory

Any help is greatly appreciated!

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