refactor: Make reference genome an input for EFETCH
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2 changed files with 5 additions and 2 deletions
2
main.nf
2
main.nf
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@ -11,7 +11,7 @@ workflow {
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.map { file -> tuple(file.simpleName, file) }
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.map { file -> tuple(file.simpleName, file) }
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.set { ch_input }
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.set { ch_input }
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EFETCH()
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EFETCH('NC_036618.1')
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EFETCH
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EFETCH
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.out
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.out
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.set { ch_reference }
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.set { ch_reference }
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@ -3,6 +3,9 @@ process EFETCH {
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container 'quay.io/biocontainers/entrez-direct:16.2--he881be0_1'
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container 'quay.io/biocontainers/entrez-direct:16.2--he881be0_1'
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input:
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val(genome)
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publishDir "results", mode: 'copy'
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publishDir "results", mode: 'copy'
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output:
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output:
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@ -12,7 +15,7 @@ process EFETCH {
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"""
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"""
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esearch \\
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esearch \\
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-db nucleotide \\
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-db nucleotide \\
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-query "NC_036618.1" \\
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-query "${genome}" \\
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| efetch \\
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| efetch \\
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-format fasta \\
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-format fasta \\
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> idv4.fasta
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> idv4.fasta
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