update UMI tests

Author: maxulysse

tests/preprocessing_umi.nf.test

@@ -9,7 +9,7 @@ nextflow_pipeline {
 
     def test_scenario = [
         [
-            name: "-profile test --input tests/csv/3.0/fastq_umi.csv --umi_read_structure '+T 7M1S+T' ",
+            name: "-profile test --input tests/csv/3.0/fastq_umi.csv --umi_read_structure '+T 7M1S+T'",
             params: [
                 input: "${projectDir}/tests/csv/3.0/fastq_umi.csv",
                 tools: null,

tests/preprocessing_umi.nf.test.snap

@@ -1,5 +1,5 @@
 {
-    "-profile test --input tests/csv/3.0/fastq_umi.csv --umi_read_structure '+T 7M1S+T' ": {
+    "-profile test --input tests/csv/3.0/fastq_umi.csv --umi_read_structure '+T 7M1S+T'": {
         "content": [
             30,
             {
@@ -14,7 +14,7 @@
                     "samtools": 1.21
                 },
                 "CALLUMICONSENSUS": {
-                    "fgbio": "2.4.0"
+                    "fgbio": "2.5.21"
                 },
                 "CAT_FASTQ": {
                     "cat": 9.5
@@ -32,7 +32,7 @@
                     "fastqc": "0.12.1"
                 },
                 "FASTQTOBAM": {
-                    "fgbio": "2.4.0"
+                    "fgbio": "2.5.21"
                 },
                 "GATK4_APPLYBQSR": {
                     "gatk4": "4.6.1.0"
@@ -48,7 +48,7 @@
                     "samtools": 1.21
                 },
                 "GROUPREADSBYUMI": {
-                    "fgbio": "2.4.0"
+                    "fgbio": "2.5.21"
                 },
                 "INDEX_CRAM": {
                     "samtools": 1.21
@@ -252,7 +252,8 @@
                 "reports/samtools/test/test.md.cram.stats",
                 "reports/samtools/test/test.recal.cram.stats",
                 "reports/umi",
-                "reports/umi/test-test_L1_umi-grouped_histogram.txt"
+                "reports/umi/test-test_L1_umi-grouped_histogram.txt",
+                "reports/umi/test-test_L1_umi-grouped_read-metrics.txt"
             ],
             [
                 "fastqc-status-check-heatmap.txt:md5,92fcedba625d8394492d1ef6e2eb64f0",
@@ -266,41 +267,42 @@
                 "fastqc_sequence_counts_plot.txt:md5,1a4aab87f1bd4fd9f69cabef40f5e5ed",
                 "fastqc_sequence_duplication_levels_plot.txt:md5,72e6366160d000a2990b2bbd321300a7",
                 "fastqc_sequence_length_distribution_plot.txt:md5,7c07faf0c0b90613cdc82a9f09bc1f19",
-                "mosdepth-coverage-per-contig-single.txt:md5,800ad271050c46d24bf53c0f8bdf7b6e",
-                "mosdepth-cumcoverage-dist-id.txt:md5,3c526ec6da433233b419bdbdd19a1b56",
-                "mosdepth_perchrom.txt:md5,800ad271050c46d24bf53c0f8bdf7b6e",
+                "mosdepth-coverage-per-contig-single.txt:md5,fc8d90478e230b3cbad16ef68ede3a62",
+                "mosdepth-cumcoverage-dist-id.txt:md5,7985d3196b234be9907f6c417c4fe0df",
+                "mosdepth_perchrom.txt:md5,fc8d90478e230b3cbad16ef68ede3a62",
                 "multiqc_citations.txt:md5,7d0b4b866fa577272c48a1f3ad72e75d",
                 "multiqc_fastqc.txt:md5,0ca2cba4204d9076a1eb17596379d10c",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_QualityScoreDistribution_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "samtools-stats-dp.txt:md5,4d27768d75a69a61daf23bf5efe17687",
-                "samtools_alignment_plot.txt:md5,3c2a882852a7ffe06610c9027f0a312a",
-                "test.md.mosdepth.global.dist.txt:md5,09d22913aa50a0207f97a3f85b182c6e",
-                "test.md.mosdepth.region.dist.txt:md5,61676a4a3668c0e84eb0f56dc6bda1ae",
-                "test.md.mosdepth.summary.txt:md5,9bbea5e4d213a51f501c2aadff8d4526",
-                "test.md.regions.bed.gz:md5,e24c18ad56e54376c41fdaacec372f9e",
-                "test.md.regions.bed.gz.csi:md5,d0713716f63ac573f4a3385733e9a537",
-                "test.recal.mosdepth.global.dist.txt:md5,09d22913aa50a0207f97a3f85b182c6e",
-                "test.recal.mosdepth.region.dist.txt:md5,61676a4a3668c0e84eb0f56dc6bda1ae",
-                "test.recal.mosdepth.summary.txt:md5,9bbea5e4d213a51f501c2aadff8d4526",
-                "test.recal.regions.bed.gz:md5,e24c18ad56e54376c41fdaacec372f9e",
-                "test.recal.regions.bed.gz.csi:md5,d0713716f63ac573f4a3385733e9a537",
-                "test-test_L1_umi-grouped_histogram.txt:md5,85292e9acb83edf17110dce17be27f44"
+                "samtools-stats-dp.txt:md5,7409b0ac85933f622b30f6b53777e894",
+                "samtools_alignment_plot.txt:md5,60b8f1d48124a8f28b06dc0d15ca4d59",
+                "test.md.mosdepth.global.dist.txt:md5,34135a9f55bc3ed522c38fe0cce2d89a",
+                "test.md.mosdepth.region.dist.txt:md5,11dc4683f9038de1938b4874e02974d6",
+                "test.md.mosdepth.summary.txt:md5,d6cda5af0f2bf21973e256cf198aa47a",
+                "test.md.regions.bed.gz:md5,2e0526a15f549024c6a7d99232543642",
+                "test.md.regions.bed.gz.csi:md5,5c556fe6462be13681267bb28257b654",
+                "test.recal.mosdepth.global.dist.txt:md5,34135a9f55bc3ed522c38fe0cce2d89a",
+                "test.recal.mosdepth.region.dist.txt:md5,11dc4683f9038de1938b4874e02974d6",
+                "test.recal.mosdepth.summary.txt:md5,d6cda5af0f2bf21973e256cf198aa47a",
+                "test.recal.regions.bed.gz:md5,2e0526a15f549024c6a7d99232543642",
+                "test.recal.regions.bed.gz.csi:md5,5c556fe6462be13681267bb28257b654",
+                "test-test_L1_umi-grouped_histogram.txt:md5,85292e9acb83edf17110dce17be27f44",
+                "test-test_L1_umi-grouped_read-metrics.txt:md5,cb2aecfe82357aa06e091d69b4606b9e"
             ],
             [
-                "test-test_L1_umi-consensus.bam:md5,18d420720f72366289d3a324f4552522"
+                "test-test_L1_umi-consensus.bam:md5,f11107c297c012c78616d7de965a0255"
             ],
             [
-                "test.md.cram:md5,2d0c176fed158d84a061b69e1947994c",
-                "test.recal.cram:md5,6927569ca52dbba512d27f8742bc6aae"
+                "test.md.cram:md5,9287aa93e5575923930765531544150",
+                "test.recal.cram:md5,9287aa93e5575923930765531544150"
             ],
             "No VCF files"
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.3"
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-06-16T10:56:22.096321902"
+        "timestamp": "2025-08-18T11:54:00.612320399"
     }
 }