add initial script

main.nf

@@ -0,0 +1,34 @@
+#!/usr/bin/env nextflow
+
+params.in = "$baseDir/combined.fa"
+params.pangolin_options = ''
+params.outdir = 'out'
+
+process pangolin {
+    publishDir "${params.outdir}", mode: 'copy'
+    tag 'pangolin'
+
+    container 'staphb/pangolin:latest'
+
+    input:
+    file(fasta) from params.in
+
+    output:
+    file("${task.process}/lineage_report.csv") into pangolin_file
+    file("logs/${task.process}/${task.process}.${workflow.sessionId}.{log,err}")
+
+    shell:
+    '''
+      mkdir -p !{task.process} logs/!{task.process}
+      log_file=logs/!{task.process}/!{task.process}.!{workflow.sessionId}.log
+      err_file=logs/!{task.process}/!{task.process}.!{workflow.sessionId}.err
+      date | tee -a $log_file $err_file > /dev/null
+      pangolin --version >> $log_file
+      pangolin --pangoLEARN-version >> $log_file
+      cat !{fasta} > ultimate_consensus.fasta
+      pangolin !{params.pangolin_options} \
+        --outdir !{task.process} \
+        ultimate_consensus.fasta \
+        2>> $err_file >> $log_file
+    '''
+}