diff --git a/lib/processes/cluster.nf b/lib/processes/cluster.nf index 1142ef5..303081e 100644 --- a/lib/processes/cluster.nf +++ b/lib/processes/cluster.nf @@ -2,7 +2,7 @@ consensus_fasta="consensus.fasta" vsearch_dir="vsearch_clusters" detected_umis_file_name="dected_umis.fastq" process CLUSTER { - publishDir "${params.output}/${sample}/clustering/${type}", pattern: "cluster*", mode: 'copy' + publishDir "${params.output}/${sample.baseName}/clustering/${type}", pattern: "cluster*", mode: 'copy' input: path sample diff --git a/lib/workflows/umi-pipeline.nf b/lib/workflows/umi-pipeline.nf index 86d8cdc..07b21c3 100644 --- a/lib/workflows/umi-pipeline.nf +++ b/lib/workflows/umi-pipeline.nf @@ -35,6 +35,8 @@ Channel.fromPath("${params.input}/*", type: 'dir') .filter( ~/.*barcode(([0-9][0-9]))/ ) .set { detected_umis_ch } +detected_umis_ch.view() + //////////////////// // BEGIN PIPELINE // ////////////////////