diff --git a/main.nf b/main.nf index 69acadb..3d4bf6a 100755 --- a/main.nf +++ b/main.nf @@ -1,5 +1,6 @@ #!/usr/bin/env nextflow +include { EFETCH } from './modules/efetch' include { HAPLINK_VARIANTS } from './modules/haplink/variants' include { VIQUAS } from './modules/viquas' @@ -68,27 +69,6 @@ workflow { ) } -process EFETCH { - cpus 1 - memory '256.MB' - container 'quay.io/biocontainers/entrez-direct:16.2--he881be0_1' - - publishDir "results", mode: 'copy' - - output: - path 'idv4.fasta' - - script: - """ - esearch \\ - -db nucleotide \\ - -query "NC_036618.1" \\ - | efetch \\ - -format fasta \\ - > idv4.fasta - """ -} - process NANOFILT { cpus 1 memory '8.GB' diff --git a/modules/efetch/main.nf b/modules/efetch/main.nf new file mode 100644 index 0000000..00ec585 --- /dev/null +++ b/modules/efetch/main.nf @@ -0,0 +1,20 @@ +process EFETCH { + cpus 1 + memory '256.MB' + container 'quay.io/biocontainers/entrez-direct:16.2--he881be0_1' + + publishDir "results", mode: 'copy' + + output: + path 'idv4.fasta' + + script: + """ + esearch \\ + -db nucleotide \\ + -query "NC_036618.1" \\ + | efetch \\ + -format fasta \\ + > idv4.fasta + """ +}