From df8910de4e8ac0477bdfcd6c9164441e1bda35e5 Mon Sep 17 00:00:00 2001
From: Anthony Underwood <au3@sanger.ac.uk>
Date: Mon, 12 Apr 2021 17:01:26 +0100
Subject: [PATCH] Iqtree (#435)

* Resolve suggests after PR review

* add newline to functions

* need variable interpolation using double quotes; remove unnecessary tag

* add a more resilient link to raw github files

* remove trailing slash

* Update software/iqtree/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 software/iqtree/main.nf       | 4 ++--
 tests/config/test_data.config | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/software/iqtree/main.nf b/software/iqtree/main.nf
index 390cd4b3..1eeb3a2a 100644
--- a/software/iqtree/main.nf
+++ b/software/iqtree/main.nf
@@ -5,7 +5,7 @@ params.options = [:]
 options        = initOptions(params.options)
 
 process IQTREE {
-    tag "$variant_alignment"
+    tag "$alignment"
     label 'process_medium'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
@@ -28,7 +28,7 @@ process IQTREE {
 
     script:
     def software    = getSoftwareName(task.process)
-    def fconst_args = constant_sites ? '-fconst $constant_sites' : ''
+    def fconst_args = constant_sites ? "-fconst $constant_sites" : ''
     def memory      = task.memory.toString().replaceAll(' ', '')
     """
     iqtree \\
diff --git a/tests/config/test_data.config b/tests/config/test_data.config
index 18f453b2..f0267fb0 100644
--- a/tests/config/test_data.config
+++ b/tests/config/test_data.config
@@ -1,5 +1,5 @@
 // Base directory for test data
-def test_data_dir = "https://github.com/nf-core/test-datasets/raw/modules/data/"
+def test_data_dir = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data"
 
 params {
     test_data {