From ada3208cc7fa08c2ddcf9a678147d1aecdd88778 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 29 Jan 2025 13:43:32 +0100
Subject: [PATCH] rescue more tests

---
 tests/alignment_to_fastq.nf.test.snap | 19 +++++++++++++------
 tests/tumor-normal-pair.nf.test.snap  | 17 ++++++++++++-----
 2 files changed, 25 insertions(+), 11 deletions(-)

diff --git a/tests/alignment_to_fastq.nf.test.snap b/tests/alignment_to_fastq.nf.test.snap
index 0bf19803d..ea54d4938 100644
--- a/tests/alignment_to_fastq.nf.test.snap
+++ b/tests/alignment_to_fastq.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "Run with profile test,alignment_to_fastq": {
         "content": [
-            27,
+            25,
             {
                 "BCFTOOLS_STATS": {
                     "bcftools": 1.2
@@ -223,6 +223,10 @@
                 "preprocessing/recalibrated/test/test.recal.bam",
                 "preprocessing/recalibrated/test/test.recal.bam.bai",
                 "reference",
+                "reference/intervals",
+                "reference/intervals/GRCh38_chr22.bed.gz",
+                "reference/intervals/chr22_1-40001.bed",
+                "reference/intervals/chr22_1-40001.bed.gz",
                 "reports",
                 "reports/bcftools",
                 "reports/bcftools/strelka",
@@ -306,6 +310,9 @@
                 "samtools-stats-dp.txt:md5,c94f4d3ffa3f510552f90e173fdd9f9d",
                 "samtools_alignment_plot.txt:md5,717f499a3543e7ee4c7a8454bf80aeca",
                 "vcftools_tstv_by_count.txt:md5,50efc5214fe2c39f21efb66a710d2ed6",
+                "GRCh38_chr22.bed.gz:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
+                "chr22_1-40001.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
+                "chr22_1-40001.bed.gz:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
                 "test.strelka.variants.bcftools_stats.txt:md5,86bd4938eed920d36f3f5937102a2967",
                 "test.md.mosdepth.global.dist.txt:md5,b61e1acee11a6ddf7ce3232a5948a6a0",
                 "test.md.mosdepth.region.dist.txt:md5,1a382f98d488d2ae3df83a0d87caafc1",
@@ -323,13 +330,13 @@
                 "test.strelka.variants.TsTv.count:md5,fa27f678965b7cba6a92efcd039f802a"
             ],
             [
-
+                
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-11-09T17:49:40.35031"
+        "timestamp": "2025-01-29T13:43:14.341569664"
     }
-}
+}
\ No newline at end of file
diff --git a/tests/tumor-normal-pair.nf.test.snap b/tests/tumor-normal-pair.nf.test.snap
index e4810e5fe..f6a8df5c1 100644
--- a/tests/tumor-normal-pair.nf.test.snap
+++ b/tests/tumor-normal-pair.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "Run with profile test | --input tests/csv/3.0/fastq_pair.csv": {
         "content": [
-            40,
+            38,
             {
                 "BCFTOOLS_STATS": {
                     "bcftools": 1.2
@@ -217,6 +217,10 @@
                 "preprocessing/recalibrated/test2/test2.recal.cram",
                 "preprocessing/recalibrated/test2/test2.recal.cram.crai",
                 "reference",
+                "reference/intervals",
+                "reference/intervals/GRCh38_chr22.bed.gz",
+                "reference/intervals/chr22_1-40001.bed",
+                "reference/intervals/chr22_1-40001.bed.gz",
                 "reports",
                 "reports/bcftools",
                 "reports/bcftools/strelka",
@@ -331,6 +335,9 @@
                 "samtools-stats-dp.txt:md5,d81e84864ecb732951a137e88d87a263",
                 "samtools_alignment_plot.txt:md5,e757696d1f7107df2bd4ad92f607272e",
                 "vcftools_tstv_by_count.txt:md5,9d3f23467779f62d81573894f71ba0d4",
+                "GRCh38_chr22.bed.gz:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
+                "chr22_1-40001.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
+                "chr22_1-40001.bed.gz:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
                 "test.strelka.variants.bcftools_stats.txt:md5,550430d0b8336ac650b7e50bdfdc914c",
                 "test2_vs_test.strelka.somatic_indels.bcftools_stats.txt:md5,2ce8bffbfbb88c4da6a5239b11dc2f44",
                 "test2_vs_test.strelka.somatic_snvs.bcftools_stats.txt:md5,869e2d3a46760e2bea9b2e027002848d",
@@ -385,9 +392,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-11-09T18:22:56.125003"
+        "timestamp": "2025-01-29T13:40:39.382455748"
     }
-}
+}
\ No newline at end of file