diff resfinder/scripts/resfinder.nf @ 0:55051a9bc58d draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/resfinder/scripts/resfinder.nf	Mon Jan 10 20:06:07 2022 +0000
@@ -0,0 +1,51 @@
+#!/usr/bin/env nextflow
+
+python3 = "python3"
+resfinder = "/home/projects/cge/apps/resfinder/resfinder/run_resfinder.py"
+
+params.indir = './'
+params.ext = '.fq.gz'
+params.outdir = '.'
+params.species = 'other'
+
+println("Search pattern: $params.indir*{1,2}$params.ext")
+
+Channel
+    .fromFilePairs("$params.indir*{1,2}$params.ext", followLinks: true)
+    .set{ infile_ch }
+
+process resfinder{
+
+    cpus 5
+    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 -ifq $datasetFile -o '$params.outdir/$sampleID' -s '$params.species'
+    else
+        $python3 $resfinder -acq -ifq $datasetFile -o '$params.outdir/$sampleID' -s '$params.species' --point
+    fi
+    """
+}
+
+/*
+result.subscribe {
+    println it
+}
+*/