diff nf/ui.nf @ 0:d9c5c5b87fec draft

planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nf/ui.nf	Sat Aug 03 11:16:53 2024 +0000
@@ -0,0 +1,88 @@
+#!/usr/bin/env nextflow
+// main nextflow script for EGAPx ui execution
+// prepare data channels and call main subworkflow
+
+nextflow.enable.dsl=2
+
+include { egapx } from './subworkflows/ncbi/main'
+include { only_gnomon } from './subworkflows/ncbi/only_gnomon'
+
+params.verbose = false
+
+
+process export {
+    publishDir "${params.output}", mode: 'copy', saveAs: { fn -> fn.substring(fn.lastIndexOf('/')+1) }
+    input:
+        path out_files
+        path annot_builder_output, stageAs: 'annot_builder_output/*'
+        // path locus
+    output:
+        path "*", includeInputs: true
+    script:
+    """
+    echo "export script"
+    """
+    stub:
+    """
+    echo "export stub"
+    """
+}
+
+
+workflow {
+    // Parse input parameters
+    def input_params = params.get('input', [:])
+    def genome = input_params.get('genome', [])
+    def proteins = input_params.get('proteins', [])
+    def reads_query = input_params.get('reads_query', [])
+    def reads_ids = input_params.get('reads_ids', [])
+    def reads = input_params.get('reads', [])
+    def reads_metadata = input_params.get('reads_metadata', [])
+    def organelles = input_params.get('organelles', []) ?: []
+    def tax_id = input_params.get('taxid', [])
+    def hmm_params = input_params.get('hmm', []) ?: []
+    def hmm_taxid = input_params.get('hmm_taxid', []) ?: []
+    def softmask = input_params.get('softmask', []) ?: []
+    def max_intron = input_params.get('max_intron', [])
+    def genome_size_threshold = input_params.get('genome_size_threshold', [])
+    def rnaseq_alignments = input_params.get('rnaseq_alignments', []) ?: []
+    def protein_alignments = input_params.get('protein_alignments', []) ?: []
+    def task_params = params.get('tasks', [:])
+    def func_name = params.get('func_name', '')
+    if (params.verbose) {
+        println("input params:\ngenome ${genome}")
+        println("proteins ${proteins}")
+        println("reads_query ${reads_query}")
+        println("reads_ids ${reads_ids}")
+        println("reads ${reads}")
+        println("reads_metadata ${reads_metadata}")
+        println("organelles ${organelles}")
+        println("tax_id ${tax_id}")
+        println("hmm_params ${hmm_params}")
+        println("hmm_taxid ${hmm_taxid}")
+        println("softmask ${softmask}")
+        println("max_intron ${max_intron}")
+        println("genome_size_threshold ${genome_size_threshold}")
+        println("rnaseq_alignments ${rnaseq_alignments}")
+        println("protein_alignments ${protein_alignments}")
+        println("func_name ${func_name}")
+        // Keep it last as it is large
+        println("task_params ${task_params}")
+    }
+    
+    if(func_name == 'only_gnomon') {
+        if (params.verbose) {
+            print('in gnomon block')
+        }
+        only_gnomon(genome, proteins, rnaseq_alignments, protein_alignments, organelles, tax_id, hmm_params, hmm_taxid, softmask, task_params)
+        export(only_gnomon.out.out_files, only_gnomon.out.evidence)
+    }
+    else {
+        if (params.verbose) {
+            print('in egapx block')
+        }
+        egapx(genome, proteins, reads_query, reads_ids, reads, reads_metadata, organelles, tax_id, hmm_params, hmm_taxid, softmask, max_intron, genome_size_threshold, task_params)
+        // export(egapx.out.out_files, egapx.out.annot_builder_output, egapx.out.locus)
+        export(egapx.out.out_files, egapx.out.annot_builder_output)
+    }
+}