--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/resfinder/scripts/resfinder_asm.nf	Mon Jan 10 20:06:07 2022 +0000
@@ -0,0 +1,52 @@
+#!/usr/bin/env nextflow
+
+python3 = "python3"
+resfinder = "/home/projects/cge/apps/resfinder/resfinder/run_resfinder.py"
+
+params.input = './*.fa'
+// params.indir = './'
+// params.ext = '.fa'
+params.outdir = '.'
+params.species = 'other'
+
+println("Search pattern: $params.input")
+
+infile_ch = Channel
+              .fromPath("$params.input", followLinks: true)
+              .map{ file -> tuple(file.baseName, file) }
+
+process resfinder{
+
+    cpus 1
+    time '30m'
+    memory '1 GB'
+    clusterOptions '-V -W group_list=cge -A cge'
+    executor "PBS"
+
+    input:
+    set sampleID, file(datasetFile) from infile_ch
+
+    output:
+    stdout result
+
+    """
+    set +u
+    module unload mgmapper metabat fastqc
+    module unload ncbi-blast perl
+    source /home/projects/cge/apps/env/rf4_env/bin/activate
+    module load perl
+    module load ncbi-blast/2.8.1+
+    if [ $params.species = 'other' ]
+    then
+        $python3 $resfinder -acq -ifa $datasetFile -o '$params.outdir/$sampleID' -s '$params.species'
+    else
+        $python3 $resfinder -acq -ifa $datasetFile -o '$params.outdir/$sampleID' -s '$params.species' --point
+    fi
+    """
+}
+
+/*
+result.subscribe {
+    println it
+}
+*/