From 275d31d994c77dc3e1fadeadd25103fc3036acb4 Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Mon, 2 Dec 2024 17:01:25 +0100
Subject: [PATCH] Fix input truth vcf usage

---
 main.nf                       | 7 -------
 workflows/phaseimpute/main.nf | 7 +++++--
 2 files changed, 5 insertions(+), 9 deletions(-)

diff --git a/main.nf b/main.nf
index 0c3f01ec..b31db4b1 100644
--- a/main.nf
+++ b/main.nf
@@ -80,13 +80,6 @@ workflow NFCORE_PHASEIMPUTE {
         ch_input_validate = ch_input
     }
 
-    if (params.steps.split(',').contains("all")) {
-        ch_input_truth.map{
-            error "Cannot run all steps with --input-truth"
-        }
-        ch_input_truth = ch_input
-    }
-
     //
     // WORKFLOW: Run pipeline
     //
diff --git a/workflows/phaseimpute/main.nf b/workflows/phaseimpute/main.nf
index 1e914b56..47724cc4 100644
--- a/workflows/phaseimpute/main.nf
+++ b/workflows/phaseimpute/main.nf
@@ -118,7 +118,10 @@ workflow PHASEIMPUTE {
         }
 
         // Use input for simulation as truth for validation step
-        ch_input_truth = ch_input_sim
+        // if no truth is provided
+        if (!params.input_truth) {
+            ch_input_truth = ch_input_sim
+        }
 
         // Program to filter chromosomes
         filter_chr_program = ch_region
@@ -491,7 +494,7 @@ workflow PHASEIMPUTE {
             [[],[]],
             [[],[]],
             [[],[]],
-            ch_fasta.map{ [it[0], it[1]] }
+            [[],[]] //ch_fasta.map{ [it[0], it[1]] }
         )
         ch_versions = ch_versions.mix(BCFTOOLS_STATS_TRUTH.out.versions)
         ch_multiqc_files = ch_multiqc_files.mix(BCFTOOLS_STATS_TRUTH.out.stats.map{ [it[1]] })