diff --git a/src/main.nf b/src/main.nf index 6a5799f4bad64aa7ad29790598a23ce424011046..7b3aadc4e1b91616e9945dbc1802d47ad613270d 100644 --- a/src/main.nf +++ b/src/main.nf @@ -22,10 +22,12 @@ Channel.fromPath( file(params.csv) ) } .set{ fastq } +Channel.fromPath("params.csv").set{params_csv} + workflow { SPLIT(fastq.r1.mix(fastq.r2)) FASTKMERS(SPLIT.out.fastq.transpose()) MERGEKMER(FASTKMERS.out.csv.groupTuple()) COLLATEKMER(MERGEKMER.out.csv.map{it -> [it[0].specie, it[1]] }.groupTuple()) - KMERCLUST(COLLATEKMER.out.csv) + KMERCLUST(COLLATEKMER.out.csv, params_csv.collect()) } diff --git a/src/modules/kmerclust.nf b/src/modules/kmerclust.nf index 74a5fbfeb0a776656436cb9b5477eec623097181..9a9e51a52cad7483930e4fe4fbde54546b0d9339 100644 --- a/src/modules/kmerclust.nf +++ b/src/modules/kmerclust.nf @@ -7,6 +7,7 @@ process KMERCLUST { input: tuple val(specie), path(csv) + path params_csv output: tuple val(specie), path("*.pdf"), emit: pdf @@ -16,7 +17,7 @@ process KMERCLUST { script: def args = task.ext.args ?: '' """ - Rscript ${projectDir}/bin/kmerclust.R ${params.csv} ${csv} ${specie} ${task.cpus} + Rscript ${projectDir}/bin/kmerclust.R ${params_csv} ${csv} ${specie} ${task.cpus} cat <<-END_VERSIONS > versions.yml "${task.process}":