From 375e45ef2fb49e75a78c1c177e59dfc1c5cd0b7a Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Fri, 15 Sep 2023 14:10:40 +0200
Subject: [PATCH 1/2] fix bin_size

---
 conf/modules.config  | 3 ++-
 conf/test.config     | 2 +-
 nextflow.config      | 2 +-
 nextflow_schema.json | 2 +-
 tests/main.nf.test   | 4 ++--
 5 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 238e210..9325b91 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -17,7 +17,8 @@ process {
     ]
 
     withName: WISECONDORX_NEWREF {
-        ext.prefix = {"${meta.id}.${meta.bin_size}kbp"}
+        ext.prefix = {"${meta.id}_${meta.bin_size as Integer > 1000 ? meta.bin_size as Integer/1000 : meta.bin_size}${meta.bin_size as Integer > 1000 ? "k" : ""}bp"}
+        ext.args = { "--binsize ${meta.bin_size}" }
         publishDir = [
             enabled: true,
             path: { "${params.outdir}" },
diff --git a/conf/test.config b/conf/test.config
index 295741a..2adb674 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -21,7 +21,7 @@ params {
 
     genomes_ignore = true
 
-    bin_sizes       = "10,5"
+    bin_sizes       = "10000,5"
 
     fasta           = params.test_data["homo_sapiens"]["genome"]["genome_fasta"]
     fai             = null //params.test_data["homo_sapiens"]["genome"]["genome_fasta_fai"]
diff --git a/nextflow.config b/nextflow.config
index 18e5bce..4d25b17 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -15,7 +15,7 @@ params {
 
     // Other options
     no_metrics                 = false
-    bin_sizes                  = "1000,500,50,30,15,10,5,1"
+    bin_sizes                  = "1000000,500000,50000,30000,15000,10000,5000,1000"
 
     // References
     genome                     = "GRCh38"
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 2fa2094..f61d761 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -60,7 +60,7 @@
                 "bin_sizes": {
                     "type": "string",
                     "description": "A comma-delimited list of bin sizes to use for the analysis",
-                    "default": "1000,500,50,30,15,10,5,1"
+                    "default": "1000000,500000,50000,30000,15000,10000,5000,1000"
                 }
             }
         },
diff --git a/tests/main.nf.test b/tests/main.nf.test
index 694db1a..7a83b6f 100644
--- a/tests/main.nf.test
+++ b/tests/main.nf.test
@@ -9,14 +9,14 @@ nextflow_pipeline {
         when {
             params {
                 prefix = "test_reference"
-                bin_sizes = "10,5"
+                bin_sizes = "10000,5"
             }
         }
 
         then {
             assert workflow.success
             assert file("${outputDir}/test_reference.10kbp.npz").exists()
-            assert file("${outputDir}/test_reference.5kbp.npz").exists()
+            assert file("${outputDir}/test_reference.5bp.npz").exists()
             assert file("${outputDir}/metrics.txt").exists()
             assert file("${outputDir}/multiqc_reports/multiqc_report.html").exists()
         }

From 344d965e2f27e7a71012fef3ecaacf5f2b2712f7 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Fri, 15 Sep 2023 14:42:28 +0200
Subject: [PATCH 2/2] fix tests

---
 tests/main.nf.test | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/main.nf.test b/tests/main.nf.test
index 7a83b6f..02eba75 100644
--- a/tests/main.nf.test
+++ b/tests/main.nf.test
@@ -15,8 +15,8 @@ nextflow_pipeline {
 
         then {
             assert workflow.success
-            assert file("${outputDir}/test_reference.10kbp.npz").exists()
-            assert file("${outputDir}/test_reference.5bp.npz").exists()
+            assert file("${outputDir}/test_reference_10kbp.npz").exists()
+            assert file("${outputDir}/test_reference_5bp.npz").exists()
             assert file("${outputDir}/metrics.txt").exists()
             assert file("${outputDir}/multiqc_reports/multiqc_report.html").exists()
         }