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Local genome files
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‎CHANGELOG‎

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2021/09/16
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* Added default "--resume" option in run_viralrecon.sh
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* New script "publish_results.sh" added.
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2021/09/15
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* Nexstrain results dir now goes inside results dir.

‎TODO‎

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2021/21/09
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* Implementar corrida local, es decir que no se requiera conexion para bajar genomas, GFFs y BEDs. Esta porción de codigo deberia sevir de guia:
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#--------------------------------------------------------------------
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# RUN IT
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#--------------------------------------------------------------------
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echo ""
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saythis "STARTING VIRALRECON ${vReconRelease}" "msg"
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echo ""
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sudo ${nfBin} run nf-core/viralrecon -r ${vReconRelease} \
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--input ${sampleSheet} \
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--platform nanopore \
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--fasta ${VIGILANTHOME}/viralrecon/GCA_009858895.3_ASM985889v3_genomic.200409.fna.gz \
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--gff ${VIGILANTHOME}/viralrecon/GCA_009858895.3_ASM985889v3_genomic.200409.gff \
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--primer_bed ${VIGILANTHOME}/viralrecon/primer.bed \
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--artic_scheme 'nCoV-2019' \
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--skip_nanoplot \
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--primer_set_version 3 \
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--fastq_dir ${fastqDir} \
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--artic_minion_caller medaka \
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--artic_minion_medaka_model ${medakaModel} \
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-profile docker \
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-c ${customConfig} \
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--sequencing_summary ${sequencingSummary} \
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--outdir ${outDir} \
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-resume
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Acá estan todos los genomas de referencia usados por viralrecon:
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https://github.com/nf-core/configs/blob/master/conf/pipeline/viralrecon/genomes.config
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*Chequear si el -resume por defecto funciona bien o no.
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* Post-procesamiento: renombrar los archivos multi_qc para que tengan como prefijo el ID de la corrida.
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* Capturar estadisticas de corrida. Ej, Librerias de entrada vs. librerias efectivamente analizadas.
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* Copiar todos los resultados a un lugar para su descarga. Se debn copiar los TSVs y los HTMLs de multiqc.

‎publish.sh‎

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#!/bin/bash
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# This script gets useful files reported by nf-core/viralrecon
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# and other scripts and makes them available for revision.
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# This was necessary since it is important to check results several times
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# in each run and it is quite boring going through different directories copying etc.
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#
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# USE:
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# publish.sh path_to_results_dir
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#
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#Import common library
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tp=$(dirname ${0})
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source $tp/vigilant.env
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source ${VIGILANTHOME}/lib/fp.sh
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#Check argument 2 is passed if not then die
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resultsDir=${2}
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#if publish dir is not defined as third argument create one in the same dir.
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#Get Multiqc report in resultsDir/multiqc/medaka
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‎run_viralrecon.sh‎

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-c ${customConfig} \
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--sequencing_summary ${sequencingSummary} \
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--outdir ${outDir} \
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-resume
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‎viralrecon/GCA_009858895.3_ASM985889v3_genomic.200409.fna.gz‎

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‎viralrecon/GCA_009858895.3_ASM985889v3_genomic.200409.gff‎

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##gff-version 3
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#!gff-spec-version 1.21
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#!processor NCBI annotwriter
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#!genome-build ASM985889v3
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#!genome-build-accession NCBI_Assembly:GCA_009858895.3
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##sequence-region MN908947.3 1 29903
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##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2697049
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MN908947.3 Genbank region 1 29903 . + . ID=MN908947.3:1..29903;Dbxref=taxon:2697049;collection-date=Dec-2019;country=China;gb-acronym=SARS-CoV-2;gbkey=Src;genome=genomic;isolate=Wuhan-Hu-1;mol_type=genomic RNA;nat-host=Homo sapiens;old-name=Wuhan seafood market pneumonia virus
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MN908947.3 Genbank five_prime_UTR 1 265 . + . ID=id-MN908947.3:1..265;gbkey=5'UTR
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MN908947.3 Genbank gene 266 21555 . + . ID=gene-orf1ab;Name=orf1ab;gbkey=Gene;gene=orf1ab;gene_biotype=protein_coding
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MN908947.3 Genbank CDS 266 13468 . + 0 ID=cds-QHD43415.1;Parent=gene-orf1ab;Dbxref=NCBI_GP:QHD43415.1;Name=QHD43415.1;Note=translated by -1 ribosomal frameshift;exception=ribosomal slippage;gbkey=CDS;gene=orf1ab;product=orf1ab polyprotein;protein_id=QHD43415.1
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MN908947.3 Genbank CDS 13468 21555 . + 0 ID=cds-QHD43415.1;Parent=gene-orf1ab;Dbxref=NCBI_GP:QHD43415.1;Name=QHD43415.1;Note=translated by -1 ribosomal frameshift;exception=ribosomal slippage;gbkey=CDS;gene=orf1ab;product=orf1ab polyprotein;protein_id=QHD43415.1
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MN908947.3 Genbank gene 21563 25384 . + . ID=gene-S;Name=S;gbkey=Gene;gene=S;gene_biotype=protein_coding
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MN908947.3 Genbank CDS 21563 25384 . + 0 ID=cds-QHD43416.1;Parent=gene-S;Dbxref=NCBI_GP:QHD43416.1;Name=QHD43416.1;Note=structural protein;gbkey=CDS;gene=S;product=surface glycoprotein;protein_id=QHD43416.1
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MN908947.3 Genbank gene 25393 26220 . + . ID=gene-ORF3a;Name=ORF3a;gbkey=Gene;gene=ORF3a;gene_biotype=protein_coding
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MN908947.3 Genbank CDS 25393 26220 . + 0 ID=cds-QHD43417.1;Parent=gene-ORF3a;Dbxref=NCBI_GP:QHD43417.1;Name=QHD43417.1;gbkey=CDS;gene=ORF3a;product=ORF3a protein;protein_id=QHD43417.1
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MN908947.3 Genbank gene 26245 26472 . + . ID=gene-E;Name=E;gbkey=Gene;gene=E;gene_biotype=protein_coding
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MN908947.3 Genbank CDS 26245 26472 . + 0 ID=cds-QHD43418.1;Parent=gene-E;Dbxref=NCBI_GP:QHD43418.1;Name=QHD43418.1;Note=structural protein%3B E protein;gbkey=CDS;gene=E;product=envelope protein;protein_id=QHD43418.1
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MN908947.3 Genbank gene 26523 27191 . + . ID=gene-M;Name=M;gbkey=Gene;gene=M;gene_biotype=protein_coding
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MN908947.3 Genbank CDS 26523 27191 . + 0 ID=cds-QHD43419.1;Parent=gene-M;Dbxref=NCBI_GP:QHD43419.1;Name=QHD43419.1;Note=structural protein;gbkey=CDS;gene=M;product=membrane glycoprotein;protein_id=QHD43419.1
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MN908947.3 Genbank gene 27202 27387 . + . ID=gene-ORF6;Name=ORF6;gbkey=Gene;gene=ORF6;gene_biotype=protein_coding
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MN908947.3 Genbank CDS 27202 27387 . + 0 ID=cds-QHD43420.1;Parent=gene-ORF6;Dbxref=NCBI_GP:QHD43420.1;Name=QHD43420.1;gbkey=CDS;gene=ORF6;product=ORF6 protein;protein_id=QHD43420.1
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MN908947.3 Genbank gene 27394 27759 . + . ID=gene-ORF7a;Name=ORF7a;gbkey=Gene;gene=ORF7a;gene_biotype=protein_coding
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MN908947.3 Genbank CDS 27394 27759 . + 0 ID=cds-QHD43421.1;Parent=gene-ORF7a;Dbxref=NCBI_GP:QHD43421.1;Name=QHD43421.1;gbkey=CDS;gene=ORF7a;product=ORF7a protein;protein_id=QHD43421.1
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MN908947.3 Genbank gene 27894 28259 . + . ID=gene-ORF8;Name=ORF8;gbkey=Gene;gene=ORF8;gene_biotype=protein_coding
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MN908947.3 Genbank CDS 27894 28259 . + 0 ID=cds-QHD43422.1;Parent=gene-ORF8;Dbxref=NCBI_GP:QHD43422.1;Name=QHD43422.1;gbkey=CDS;gene=ORF8;product=ORF8 protein;protein_id=QHD43422.1
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MN908947.3 Genbank gene 28274 29533 . + . ID=gene-N;Name=N;gbkey=Gene;gene=N;gene_biotype=protein_coding
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MN908947.3 Genbank CDS 28274 29533 . + 0 ID=cds-QHD43423.2;Parent=gene-N;Dbxref=NCBI_GP:QHD43423.2;Name=QHD43423.2;Note=structural protein;gbkey=CDS;gene=N;product=nucleocapsid phosphoprotein;protein_id=QHD43423.2
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MN908947.3 Genbank gene 29558 29674 . + . ID=gene-ORF10;Name=ORF10;gbkey=Gene;gene=ORF10;gene_biotype=protein_coding
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MN908947.3 Genbank CDS 29558 29674 . + 0 ID=cds-QHI42199.1;Parent=gene-ORF10;Dbxref=NCBI_GP:QHI42199.1;Name=QHI42199.1;gbkey=CDS;gene=ORF10;product=ORF10 protein;protein_id=QHI42199.1
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MN908947.3 Genbank three_prime_UTR 29675 29903 . + . ID=id-MN908947.3:29675..29903;gbkey=3'UTR
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###

‎viralrecon/primer.bed‎

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MN908947.3 30 54 nCoV-2019_1_LEFT 1 +
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MN908947.3 385 410 nCoV-2019_1_RIGHT 1 -
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MN908947.3 320 342 nCoV-2019_2_LEFT 2 +
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MN908947.3 704 726 nCoV-2019_2_RIGHT 2 -
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MN908947.3 642 664 nCoV-2019_3_LEFT 1 +
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MN908947.3 1004 1028 nCoV-2019_3_RIGHT 1 -
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MN908947.3 943 965 nCoV-2019_4_LEFT 2 +
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MN908947.3 1312 1337 nCoV-2019_4_RIGHT 2 -
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MN908947.3 1242 1264 nCoV-2019_5_LEFT 1 +
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MN908947.3 1623 1651 nCoV-2019_5_RIGHT 1 -
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MN908947.3 1573 1595 nCoV-2019_6_LEFT 2 +
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MN908947.3 1942 1964 nCoV-2019_6_RIGHT 2 -
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MN908947.3 1875 1897 nCoV-2019_7_LEFT 1 +
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MN908947.3 1868 1890 nCoV-2019_7_LEFT_alt0 1 +
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MN908947.3 2247 2269 nCoV-2019_7_RIGHT 1 -
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MN908947.3 2242 2264 nCoV-2019_7_RIGHT_alt5 1 -
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MN908947.3 2181 2205 nCoV-2019_8_LEFT 2 +
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MN908947.3 2568 2592 nCoV-2019_8_RIGHT 2 -
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MN908947.3 2505 2529 nCoV-2019_9_LEFT 1 +
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MN908947.3 2504 2528 nCoV-2019_9_LEFT_alt4 1 +
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MN908947.3 2882 2904 nCoV-2019_9_RIGHT 1 -
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MN908947.3 2880 2902 nCoV-2019_9_RIGHT_alt2 1 -
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MN908947.3 2826 2850 nCoV-2019_10_LEFT 2 +
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MN908947.3 3183 3210 nCoV-2019_10_RIGHT 2 -
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MN908947.3 3144 3166 nCoV-2019_11_LEFT 1 +
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MN908947.3 3507 3531 nCoV-2019_11_RIGHT 1 -
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MN908947.3 3460 3482 nCoV-2019_12_LEFT 2 +
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MN908947.3 3826 3853 nCoV-2019_12_RIGHT 2 -
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MN908947.3 3771 3795 nCoV-2019_13_LEFT 1 +
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MN908947.3 4142 4164 nCoV-2019_13_RIGHT 1 -
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MN908947.3 4054 4077 nCoV-2019_14_LEFT 2 +
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MN908947.3 4044 4068 nCoV-2019_14_LEFT_alt4 2 +
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MN908947.3 4428 4450 nCoV-2019_14_RIGHT 2 -
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MN908947.3 4402 4424 nCoV-2019_14_RIGHT_alt2 2 -
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MN908947.3 4294 4321 nCoV-2019_15_LEFT 1 +
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MN908947.3 4296 4322 nCoV-2019_15_LEFT_alt1 1 +
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MN908947.3 4674 4696 nCoV-2019_15_RIGHT 1 -
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MN908947.3 4666 4689 nCoV-2019_15_RIGHT_alt3 1 -
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MN908947.3 4636 4658 nCoV-2019_16_LEFT 2 +
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MN908947.3 4995 5017 nCoV-2019_16_RIGHT 2 -
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MN908947.3 4939 4966 nCoV-2019_17_LEFT 1 +
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MN908947.3 5296 5321 nCoV-2019_17_RIGHT 1 -
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MN908947.3 5230 5259 nCoV-2019_18_LEFT 2 +
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MN908947.3 5257 5287 nCoV-2019_18_LEFT_alt2 2 +
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MN908947.3 5620 5644 nCoV-2019_18_RIGHT 2 -
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MN908947.3 5620 5643 nCoV-2019_18_RIGHT_alt1 2 -
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MN908947.3 5563 5586 nCoV-2019_19_LEFT 1 +
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MN908947.3 5932 5957 nCoV-2019_19_RIGHT 1 -
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MN908947.3 5867 5894 nCoV-2019_20_LEFT 2 +
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MN908947.3 6247 6272 nCoV-2019_20_RIGHT 2 -
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MN908947.3 6167 6196 nCoV-2019_21_LEFT 1 +
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MN908947.3 6168 6197 nCoV-2019_21_LEFT_alt2 1 +
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MN908947.3 6528 6550 nCoV-2019_21_RIGHT 1 -
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MN908947.3 6526 6548 nCoV-2019_21_RIGHT_alt0 1 -
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MN908947.3 6466 6495 nCoV-2019_22_LEFT 2 +
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MN908947.3 6846 6873 nCoV-2019_22_RIGHT 2 -
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MN908947.3 6718 6745 nCoV-2019_23_LEFT 1 +
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MN908947.3 7092 7117 nCoV-2019_23_RIGHT 1 -
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MN908947.3 7035 7058 nCoV-2019_24_LEFT 2 +
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MN908947.3 7389 7415 nCoV-2019_24_RIGHT 2 -
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MN908947.3 7305 7332 nCoV-2019_25_LEFT 1 +
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MN908947.3 7671 7694 nCoV-2019_25_RIGHT 1 -
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MN908947.3 7626 7651 nCoV-2019_26_LEFT 2 +
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MN908947.3 7997 8019 nCoV-2019_26_RIGHT 2 -
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MN908947.3 7943 7968 nCoV-2019_27_LEFT 1 +
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MN908947.3 8319 8341 nCoV-2019_27_RIGHT 1 -
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MN908947.3 8249 8275 nCoV-2019_28_LEFT 2 +
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MN908947.3 8635 8661 nCoV-2019_28_RIGHT 2 -
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MN908947.3 8595 8619 nCoV-2019_29_LEFT 1 +
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MN908947.3 8954 8983 nCoV-2019_29_RIGHT 1 -
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MN908947.3 8888 8913 nCoV-2019_30_LEFT 2 +
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MN908947.3 9245 9271 nCoV-2019_30_RIGHT 2 -
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MN908947.3 9204 9226 nCoV-2019_31_LEFT 1 +
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MN908947.3 9557 9585 nCoV-2019_31_RIGHT 1 -
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MN908947.3 9477 9502 nCoV-2019_32_LEFT 2 +
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MN908947.3 9834 9858 nCoV-2019_32_RIGHT 2 -
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MN908947.3 9784 9806 nCoV-2019_33_LEFT 1 +
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MN908947.3 10146 10171 nCoV-2019_33_RIGHT 1 -
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MN908947.3 10076 10099 nCoV-2019_34_LEFT 2 +
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MN908947.3 10437 10459 nCoV-2019_34_RIGHT 2 -
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MN908947.3 10362 10384 nCoV-2019_35_LEFT 1 +
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MN908947.3 10737 10763 nCoV-2019_35_RIGHT 1 -
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MN908947.3 10666 10688 nCoV-2019_36_LEFT 2 +
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MN908947.3 11048 11074 nCoV-2019_36_RIGHT 2 -
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MN908947.3 10999 11022 nCoV-2019_37_LEFT 1 +
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MN908947.3 11372 11394 nCoV-2019_37_RIGHT 1 -
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MN908947.3 11306 11331 nCoV-2019_38_LEFT 2 +
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MN908947.3 11668 11693 nCoV-2019_38_RIGHT 2 -
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MN908947.3 11555 11584 nCoV-2019_39_LEFT 1 +
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MN908947.3 11927 11949 nCoV-2019_39_RIGHT 1 -
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MN908947.3 11863 11889 nCoV-2019_40_LEFT 2 +
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MN908947.3 12234 12256 nCoV-2019_40_RIGHT 2 -
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MN908947.3 12110 12133 nCoV-2019_41_LEFT 1 +
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MN908947.3 12465 12490 nCoV-2019_41_RIGHT 1 -
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MN908947.3 12417 12439 nCoV-2019_42_LEFT 2 +
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MN908947.3 12779 12802 nCoV-2019_42_RIGHT 2 -
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MN908947.3 12710 12732 nCoV-2019_43_LEFT 1 +
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MN908947.3 13074 13096 nCoV-2019_43_RIGHT 1 -
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MN908947.3 13005 13027 nCoV-2019_44_LEFT 2 +
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MN908947.3 13007 13029 nCoV-2019_44_LEFT_alt3 2 +
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MN908947.3 13378 13400 nCoV-2019_44_RIGHT 2 -
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MN908947.3 13363 13385 nCoV-2019_44_RIGHT_alt0 2 -
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MN908947.3 13319 13344 nCoV-2019_45_LEFT 1 +
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MN908947.3 13307 13336 nCoV-2019_45_LEFT_alt2 1 +
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MN908947.3 13669 13699 nCoV-2019_45_RIGHT 1 -
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MN908947.3 13660 13689 nCoV-2019_45_RIGHT_alt7 1 -
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MN908947.3 13599 13621 nCoV-2019_46_LEFT 2 +
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MN908947.3 13602 13625 nCoV-2019_46_LEFT_alt1 2 +
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MN908947.3 13962 13984 nCoV-2019_46_RIGHT 2 -
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MN908947.3 13961 13984 nCoV-2019_46_RIGHT_alt2 2 -
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MN908947.3 13918 13946 nCoV-2019_47_LEFT 1 +
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MN908947.3 14271 14299 nCoV-2019_47_RIGHT 1 -
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MN908947.3 14207 14232 nCoV-2019_48_LEFT 2 +
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MN908947.3 14579 14601 nCoV-2019_48_RIGHT 2 -
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MN908947.3 14545 14570 nCoV-2019_49_LEFT 1 +
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MN908947.3 14898 14926 nCoV-2019_49_RIGHT 1 -
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MN908947.3 14865 14895 nCoV-2019_50_LEFT 2 +
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MN908947.3 15224 15246 nCoV-2019_50_RIGHT 2 -
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MN908947.3 15171 15193 nCoV-2019_51_LEFT 1 +
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MN908947.3 15538 15560 nCoV-2019_51_RIGHT 1 -
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MN908947.3 15481 15503 nCoV-2019_52_LEFT 2 +
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MN908947.3 15861 15886 nCoV-2019_52_RIGHT 2 -
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MN908947.3 15827 15851 nCoV-2019_53_LEFT 1 +
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MN908947.3 16186 16209 nCoV-2019_53_RIGHT 1 -
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MN908947.3 16118 16144 nCoV-2019_54_LEFT 2 +
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MN908947.3 16485 16510 nCoV-2019_54_RIGHT 2 -
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MN908947.3 16416 16444 nCoV-2019_55_LEFT 1 +
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MN908947.3 16804 16833 nCoV-2019_55_RIGHT 1 -
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MN908947.3 16748 16770 nCoV-2019_56_LEFT 2 +
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MN908947.3 17130 17152 nCoV-2019_56_RIGHT 2 -
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MN908947.3 17065 17087 nCoV-2019_57_LEFT 1 +
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MN908947.3 17430 17452 nCoV-2019_57_RIGHT 1 -
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MN908947.3 17381 17406 nCoV-2019_58_LEFT 2 +
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MN908947.3 17738 17761 nCoV-2019_58_RIGHT 2 -
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MN908947.3 17674 17697 nCoV-2019_59_LEFT 1 +
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MN908947.3 18036 18062 nCoV-2019_59_RIGHT 1 -
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MN908947.3 17966 17993 nCoV-2019_60_LEFT 2 +
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MN908947.3 18324 18348 nCoV-2019_60_RIGHT 2 -
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MN908947.3 18253 18275 nCoV-2019_61_LEFT 1 +
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MN908947.3 18650 18672 nCoV-2019_61_RIGHT 1 -
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MN908947.3 18596 18618 nCoV-2019_62_LEFT 2 +
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MN908947.3 18957 18979 nCoV-2019_62_RIGHT 2 -
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MN908947.3 18896 18918 nCoV-2019_63_LEFT 1 +
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MN908947.3 19275 19297 nCoV-2019_63_RIGHT 1 -
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MN908947.3 19204 19232 nCoV-2019_64_LEFT 2 +
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MN908947.3 19591 19616 nCoV-2019_64_RIGHT 2 -
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MN908947.3 19548 19570 nCoV-2019_65_LEFT 1 +
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MN908947.3 19911 19939 nCoV-2019_65_RIGHT 1 -
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MN908947.3 19844 19866 nCoV-2019_66_LEFT 2 +
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MN908947.3 20231 20255 nCoV-2019_66_RIGHT 2 -
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MN908947.3 20172 20200 nCoV-2019_67_LEFT 1 +
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MN908947.3 20542 20572 nCoV-2019_67_RIGHT 1 -
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MN908947.3 20472 20496 nCoV-2019_68_LEFT 2 +
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MN908947.3 20867 20890 nCoV-2019_68_RIGHT 2 -
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MN908947.3 20786 20813 nCoV-2019_69_LEFT 1 +
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MN908947.3 21146 21169 nCoV-2019_69_RIGHT 1 -
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MN908947.3 21075 21104 nCoV-2019_70_LEFT 2 +
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MN908947.3 21427 21455 nCoV-2019_70_RIGHT 2 -
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MN908947.3 21357 21386 nCoV-2019_71_LEFT 1 +
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MN908947.3 21716 21743 nCoV-2019_71_RIGHT 1 -
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MN908947.3 21658 21682 nCoV-2019_72_LEFT 2 +
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MN908947.3 22013 22038 nCoV-2019_72_RIGHT 2 -
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MN908947.3 21961 21990 nCoV-2019_73_LEFT 1 +
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MN908947.3 22324 22346 nCoV-2019_73_RIGHT 1 -
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MN908947.3 22262 22290 nCoV-2019_74_LEFT 2 +
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MN908947.3 22626 22650 nCoV-2019_74_RIGHT 2 -
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MN908947.3 22516 22542 nCoV-2019_75_LEFT 1 +
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MN908947.3 22877 22903 nCoV-2019_75_RIGHT 1 -
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MN908947.3 22797 22819 nCoV-2019_76_LEFT 2 +
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MN908947.3 22798 22821 nCoV-2019_76_LEFT_alt3 2 +
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MN908947.3 23192 23214 nCoV-2019_76_RIGHT 2 -
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MN908947.3 23189 23212 nCoV-2019_76_RIGHT_alt0 2 -
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