Update test snapshots for SAMTOOLS_SORT_QUALIMAP

pinin4fjords · claude · pinin4fjords · commit e481c5a978c3 · 2025-11-14T16:21:30.000Z
Add SAMTOOLS_SORT_QUALIMAP version entry to all test snapshots that run qualimap, reflecting the new samtools sort step added for performance optimization. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
diff --git a/tests/bam_input.nf.test.snap b/tests/bam_input.nf.test.snap
@@ -79,6 +79,9 @@
                 "SAMTOOLS_INDEX": {
                     "samtools": 1.21
                 },
+                "SAMTOOLS_SORT_QUALIMAP": {
+                    "samtools": 1.21
+                },
                 "SAMTOOLS_STATS": {
                     "samtools": 1.21
                 },
@@ -1041,6 +1044,9 @@
                 "SAMTOOLS_INDEX": {
                     "samtools": 1.21
                 },
+                "SAMTOOLS_SORT_QUALIMAP": {
+                    "samtools": 1.21
+                },
                 "SAMTOOLS_STATS": {
                     "samtools": 1.21
                 },
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
@@ -199,6 +199,9 @@
                 "SAMTOOLS_SORT": {
                     "samtools": 1.21
                 },
+                "SAMTOOLS_SORT_QUALIMAP": {
+                    "samtools": 1.21
+                },
                 "SAMTOOLS_STATS": {
                     "samtools": 1.21
                 },
diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap
@@ -196,6 +196,9 @@
                 "SAMTOOLS_SORT": {
                     "samtools": 1.21
                 },
+                "SAMTOOLS_SORT_QUALIMAP": {
+                    "samtools": 1.21
+                },
                 "SAMTOOLS_STATS": {
                     "samtools": 1.21
                 },
diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap
@@ -203,6 +203,9 @@
                 "SAMTOOLS_SORT": {
                     "samtools": 1.21
                 },
+                "SAMTOOLS_SORT_QUALIMAP": {
+                    "samtools": 1.21
+                },
                 "SAMTOOLS_STATS": {
                     "samtools": 1.21
                 },
diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap
@@ -98,6 +98,9 @@
                 "SAMTOOLS_SORT": {
                     "samtools": 1.21
                 },
+                "SAMTOOLS_SORT_QUALIMAP": {
+                    "samtools": 1.21
+                },
                 "SAMTOOLS_STATS": {
                     "samtools": 1.21
                 },
diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap
@@ -98,6 +98,9 @@
                 "SAMTOOLS_SORT": {
                     "samtools": 1.21
                 },
+                "SAMTOOLS_SORT_QUALIMAP": {
+                    "samtools": 1.21
+                },
                 "SAMTOOLS_STATS": {
                     "samtools": 1.21
                 },
diff --git a/tests/sentieon_default.nf.test.snap b/tests/sentieon_default.nf.test.snap
@@ -199,6 +199,9 @@
                 "SAMTOOLS_SORT": {
                     "samtools": 1.21
                 },
+                "SAMTOOLS_SORT_QUALIMAP": {
+                    "samtools": 1.21
+                },
                 "SAMTOOLS_STATS": {
                     "samtools": 1.21
                 },
diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap
@@ -98,6 +98,9 @@
                 "SAMTOOLS_SORT": {
                     "samtools": 1.21
                 },
+                "SAMTOOLS_SORT_QUALIMAP": {
+                    "samtools": 1.21
+                },
                 "SAMTOOLS_STATS": {
                     "samtools": 1.21
                 },
diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap
@@ -109,6 +109,9 @@
                 "SAMTOOLS_SORT": {
                     "samtools": 1.21
                 },
+                "SAMTOOLS_SORT_QUALIMAP": {
+                    "samtools": 1.21
+                },
                 "SAMTOOLS_STATS": {
                     "samtools": 1.21
                 },
diff --git a/tests/umi.nf.test.snap b/tests/umi.nf.test.snap
@@ -92,6 +92,9 @@
                 "SAMTOOLS_SORT": {
                     "samtools": 1.21
                 },
+                "SAMTOOLS_SORT_QUALIMAP": {
+                    "samtools": 1.21
+                },
                 "SAMTOOLS_STATS": {
                     "samtools": 1.21
                 },
