diff --git a/main.nf b/main.nf index 3d4bf6a..54ff5e4 100755 --- a/main.nf +++ b/main.nf @@ -11,7 +11,7 @@ workflow { .map { file -> tuple(file.simpleName, file) } .set { ch_input } - EFETCH() + EFETCH('NC_036618.1') EFETCH .out .set { ch_reference } diff --git a/modules/efetch/main.nf b/modules/efetch/main.nf index 2041d45..66272fd 100644 --- a/modules/efetch/main.nf +++ b/modules/efetch/main.nf @@ -3,6 +3,9 @@ process EFETCH { container 'quay.io/biocontainers/entrez-direct:16.2--he881be0_1' + input: + val(genome) + publishDir "results", mode: 'copy' output: @@ -12,7 +15,7 @@ process EFETCH { """ esearch \\ -db nucleotide \\ - -query "NC_036618.1" \\ + -query "${genome}" \\ | efetch \\ -format fasta \\ > idv4.fasta