Update version counts in QUALIMAP test blocks

pinin4fjords · claude · pinin4fjords · commit 3bd27e8dc895 · 2025-11-14T17:16:45.000Z
Increment version counts by 5 in test blocks that run qualimap to account for the additional SAMTOOLS_SORT_QUALIMAP process. Only test blocks containing QUALIMAP_RNASEQ are updated. 🤖 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
@@ -1,7 +1,7 @@
 {
     "BAM input for Salmon": {
         "content": [
-            139,
+            144,
             {
                 "BBMAP_BBSPLIT": {
                     "bbmap": 39.18
@@ -961,7 +961,7 @@
     },
     "BAM input for RSEM": {
         "content": [
-            138,
+            143,
             {
                 "BBMAP_BBSPLIT": {
                     "bbmap": 39.18
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
@@ -102,7 +102,7 @@
     },
     "Params: default": {
         "content": [
-            209,
+            214,
             {
                 "BBMAP_BBSPLIT": {
                     "bbmap": 39.18
diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap
@@ -102,7 +102,7 @@
     },
     "Params: --featurecounts_group_type false": {
         "content": [
-            199,
+            204,
             {
                 "BBMAP_BBSPLIT": {
                     "bbmap": 39.18
diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap
@@ -103,7 +103,7 @@
     },
     "Params: --aligner hisat2": {
         "content": [
-            200,
+            205,
             {
                 "BBMAP_BBSPLIT": {
                     "bbmap": 39.18
diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "Params: --min_mapped_reads 90": {
         "content": [
-            163,
+            168,
             {
                 "BBMAP_BBSPLIT": {
                     "bbmap": 39.18
diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "Params: --remove_ribo_rna": {
         "content": [
-            220,
+            225,
             {
                 "BBMAP_BBSPLIT": {
                     "bbmap": 39.18
diff --git a/tests/sentieon_default.nf.test.snap b/tests/sentieon_default.nf.test.snap
@@ -102,7 +102,7 @@
     },
     "Params: default --use_sentieon_star": {
         "content": [
-            209,
+            214,
             {
                 "BBMAP_BBSPLIT": {
                     "bbmap": 39.18
diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "Params: --skip_trimming": {
         "content": [
-            199,
+            204,
             {
                 "BBMAP_BBSPLIT": {
                     "bbmap": 39.18
diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "Params: --aligner star_rsem": {
         "content": [
-            207,
+            212,
             {
                 "BBMAP_BBSPLIT": {
                     "bbmap": 39.18
diff --git a/tests/umi.nf.test.snap b/tests/umi.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "--umi_dedup_tool 'umitools'": {
         "content": [
-            261,
+            266,
             {
                 "BEDTOOLS_GENOMECOV_FW": {
                     "bedtools": "2.31.1"
@@ -1510,7 +1510,7 @@
     },
     "Params: --aligner hisat2 --umi_dedup_tool 'umicollapse'": {
         "content": [
-            194,
+            199,
             {
                 "BEDTOOLS_GENOMECOV_FW": {
                     "bedtools": "2.31.1"

Original file line number	Diff line number	Diff line change
`@@ -1,7 +1,7 @@`
`1`	`1`	`{`
`2`	`2`	`"BAM input for Salmon": {`
`3`	`3`	`"content": [`
`4`		`- 139,`
	`4`	`+ 144,`
`5`	`5`	`{`
`6`	`6`	`"BBMAP_BBSPLIT": {`
`7`	`7`	`"bbmap": 39.18`
`@@ -961,7 +961,7 @@`
`961`	`961`	`},`
`962`	`962`	`"BAM input for RSEM": {`
`963`	`963`	`"content": [`
`964`		`- 138,`
	`964`	`+ 143,`
`965`	`965`	`{`
`966`	`966`	`"BBMAP_BBSPLIT": {`
`967`	`967`	`"bbmap": 39.18`
Original file line number	Diff line number	Diff line change
`@@ -102,7 +102,7 @@`
`102`	`102`	`},`
`103`	`103`	`"Params: default": {`
`104`	`104`	`"content": [`
`105`		`- 209,`
	`105`	`+ 214,`
`106`	`106`	`{`
`107`	`107`	`"BBMAP_BBSPLIT": {`
`108`	`108`	`"bbmap": 39.18`
Original file line number	Diff line number	Diff line change
`@@ -103,7 +103,7 @@`
`103`	`103`	`},`
`104`	`104`	`"Params: --aligner hisat2": {`
`105`	`105`	`"content": [`
`106`		`- 200,`
	`106`	`+ 205,`
`107`	`107`	`{`
`108`	`108`	`"BBMAP_BBSPLIT": {`
`109`	`109`	`"bbmap": 39.18`
Original file line number	Diff line number	Diff line change
`@@ -1,7 +1,7 @@`
`1`	`1`	`{`
`2`	`2`	`"Params: --min_mapped_reads 90": {`
`3`	`3`	`"content": [`
`4`		`- 163,`
	`4`	`+ 168,`
`5`	`5`	`{`
`6`	`6`	`"BBMAP_BBSPLIT": {`
`7`	`7`	`"bbmap": 39.18`
Original file line number	Diff line number	Diff line change
`@@ -1,7 +1,7 @@`
`1`	`1`	`{`
`2`	`2`	`"Params: --remove_ribo_rna": {`
`3`	`3`	`"content": [`
`4`		`- 220,`
	`4`	`+ 225,`
`5`	`5`	`{`
`6`	`6`	`"BBMAP_BBSPLIT": {`
`7`	`7`	`"bbmap": 39.18`
Original file line number	Diff line number	Diff line change
`@@ -1,7 +1,7 @@`
`1`	`1`	`{`
`2`	`2`	`"Params: --skip_trimming": {`
`3`	`3`	`"content": [`
`4`		`- 199,`
	`4`	`+ 204,`
`5`	`5`	`{`
`6`	`6`	`"BBMAP_BBSPLIT": {`
`7`	`7`	`"bbmap": 39.18`
Original file line number	Diff line number	Diff line change
`@@ -1,7 +1,7 @@`
`1`	`1`	`{`
`2`	`2`	`"Params: --aligner star_rsem": {`
`3`	`3`	`"content": [`
`4`		`- 207,`
	`4`	`+ 212,`
`5`	`5`	`{`
`6`	`6`	`"BBMAP_BBSPLIT": {`
`7`	`7`	`"bbmap": 39.18`
Original file line number	Diff line number	Diff line change
`@@ -1,7 +1,7 @@`
`1`	`1`	`{`
`2`	`2`	`"--umi_dedup_tool 'umitools'": {`
`3`	`3`	`"content": [`
`4`		`- 261,`
	`4`	`+ 266,`
`5`	`5`	`{`
`6`	`6`	`"BEDTOOLS_GENOMECOV_FW": {`
`7`	`7`	`"bedtools": "2.31.1"`
`@@ -1510,7 +1510,7 @@`
`1510`	`1510`	`},`
`1511`	`1511`	`"Params: --aligner hisat2 --umi_dedup_tool 'umicollapse'": {`
`1512`	`1512`	`"content": [`
`1513`		`- 194,`
	`1513`	`+ 199,`
`1514`	`1514`	`{`
`1515`	`1515`	`"BEDTOOLS_GENOMECOV_FW": {`
`1516`	`1516`	`"bedtools": "2.31.1"`