From 79d0c26acc5a4363d1d80867c26871bbf6afa4d6 Mon Sep 17 00:00:00 2001
From: Madeline Scyphers <madelinescyphers@gmail.com>
Date: Mon, 4 Nov 2024 14:09:37 -0700
Subject: [PATCH] Paths as string concetation bugfix (issue #379)

---
 main.nf | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/main.nf b/main.nf
index d438da45..22c09559 100644
--- a/main.nf
+++ b/main.nf
@@ -122,10 +122,8 @@ params.make_product_pkg = "dram_viz"
 // Move to nextflow.config when ready
 params.trees = 0
 params.add_trees = 0
-params.trees = 0
 params.trees_list = "dmso"
 //trees_list = "nar_nxr;dsr;mcra;amoa_pmoa;hydrogenase"
-params.add_trees = ""
 params.tree_data_files = "${projectDir}/assets/trees/"
 params.trees_scripts = "${projectDir}/assets"
 
@@ -635,7 +633,7 @@ if( params.rename || params.call ){
     // If calling genes, then create a channel called ch_input_fastas.
     if ( params.input_fasta != "" ) {
         ch_input_fastas = Channel
-            .fromPath(params.input_fasta + params.fasta_fmt, checkIfExists: true)
+            .fromPath(file(params.input_fasta) / params.fasta_fmt, checkIfExists: true)
             .ifEmpty { exit 1, "Cannot find any fasta files matching: ${params.input_fasta}\nNB: Path needs to follow pattern: path/to/directory/" }
     } else {
         ch_input_fastas = Channel
@@ -664,7 +662,7 @@ if( params.annotate ){
     if( params.call == 0 ){
         // Set ch_input_genes
         ch_called_proteins = Channel
-            .fromPath(params.input_genes + params.genes_fmt, checkIfExists: true)
+            .fromPath(file(params.input_genes) / params.genes_fmt, checkIfExists: true)
             .ifEmpty { exit 1, "If you specify --annotate without --call, you must provide a fasta file of called genes using --input_genes. Cannot find any called gene fasta files matching: ${params.input_genes}\nNB: Path needs to follow pattern: path/to/directory/" }
             .map {
                 sampleName = it.getName().replaceAll(/\.[^.]+$/, '').replaceAll(/\./, '-')
@@ -775,7 +773,7 @@ if( params.trees ) {
             .ifEmpty { exit 1, "If you specify --distill_<topic|ecosystem|custom> without --annotate, you must provide an annotations TSV file (--annotations <path>) with approprite formatting. Cannot find any called gene fasta files matching: ${params.annotations}\nNB: Path needs to follow pattern: path/to/directory/" }
 
         ch_collected_faa = Channel
-            .fromPath(params.input_genes + params.genes_fmt, checkIfExists: true)
+            .fromPath(file(params.input_genes) / params.genes_fmt, checkIfExists: true)
             .ifEmpty { exit 1, "If you specify --annotations without --input_genes, with the desire to run trees, you must provide a fasta file of called genes using --input_genes. Cannot find any called gene fasta files matching: ${params.input_genes}\nNB: Path needs to follow pattern: path/to/directory/" }
             .collect()
     }