Fix unsorted sniffles1 variants

genomic-medicine-sweden · Feb 25, 2025 · eea50ac · eea50ac
1 parent 6b1d91f
commit eea50ac
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Showing 6 changed files with 56 additions and 24 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -27,6 +27,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#558](https://github.com/genomic-medicine-sweden/nallo/pull/558) - Changed VEP to single-threaded by default, because of https://github.com/Ensembl/ensembl-vep/issues/1759
 - [#560](https://github.com/genomic-medicine-sweden/nallo/pull/560) - Updated template to nf-core/tools version 3.2.0
 - [#566](https://github.com/genomic-medicine-sweden/nallo/pull/566) - Replaced dipcall with `ALIGN_ASSEMBLIES`, mostly mimicing the alignment part of dipcall, while omitting the variant calling. Updated docs and output files.
+- [#](https://github.com/genomic-medicine-sweden/nallo/pull/) - Changed `CALL_SVS` to sort sniffles1 variants, which could be unsorted by default
 
 ### `Removed`
 

diff --git a/conf/modules/call_svs.config b/conf/modules/call_svs.config
@@ -38,6 +38,10 @@ process {
         ext.args = '--list-samples'
     }
 
+    withName: '.*:CALL_SVS:BCFTOOLS_SORT' {
+        ext.args = '--output-type z'
+    }
+
     withName: '.*:CALL_SVS:CREATE_SAMPLES_FILE' {
         ext.prefix = { "${meta.id}_samples_file" }
     }

diff --git a/subworkflows/local/call_svs/main.nf b/subworkflows/local/call_svs/main.nf
@@ -3,6 +3,7 @@ include { CLEAN_SNIFFLES                  } from '../../../modules/local/clean_s
 include { SVDB_MERGE                      } from '../../../modules/nf-core/svdb/merge/main'
 include { BCFTOOLS_QUERY                  } from '../../../modules/nf-core/bcftools/query/main'
 include { BCFTOOLS_REHEADER               } from '../../../modules/nf-core/bcftools/reheader/main'
+include { BCFTOOLS_SORT                   } from '../../../modules/nf-core/bcftools/sort/main'
 include { CREATE_SAMPLES_FILE             } from '../../../modules/local/create_samples_file/main'
 include { SEVERUS                         } from '../../../modules/nf-core/severus/main'
 include { SNIFFLES                        } from '../../../modules/nf-core/sniffles/main'
@@ -46,8 +47,14 @@ workflow CALL_SVS {
     )
     ch_versions = ch_versions.mix(CLEAN_SNIFFLES.out.versions)
 
-    ch_sv_calls = ch_sv_calls.mix(
+
+    BCFTOOLS_SORT (
         CLEAN_SNIFFLES.out.vcf
+    )
+    ch_versions = ch_versions.mix(BCFTOOLS_SORT.out.versions)
+
+    ch_sv_calls = ch_sv_calls.mix(
+        BCFTOOLS_SORT.out.vcf
         .map { meta , vcf -> [ meta + [ sv_caller: 'sniffles' ], vcf ] }
     )
 

diff --git a/subworkflows/local/call_svs/tests/main.nf.test.snap b/subworkflows/local/call_svs/tests/main.nf.test.snap
@@ -17,6 +17,7 @@
                 "versions.yml:md5,9b9842e144dad4e4b6e619ef00583694",
                 "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
                 "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                "versions.yml:md5,c7cbcd9fc24aa7580029e7b4d6411fcc",
                 "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
                 "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
                 "versions.yml:md5,d6665112b721f1651ae340c644f9a27c",
@@ -27,7 +28,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-02-12T15:52:24.963416028"
+        "timestamp": "2025-02-25T09:20:32.572227776"
     },
     "1 sample - [bam, bai], 'severus', [] -stub": {
         "content": [
@@ -80,6 +81,7 @@
                     "versions.yml:md5,9b9842e144dad4e4b6e619ef00583694",
                     "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
                     "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                    "versions.yml:md5,c7cbcd9fc24aa7580029e7b4d6411fcc",
                     "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
                     "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
                     "versions.yml:md5,d6665112b721f1651ae340c644f9a27c",
@@ -133,6 +135,7 @@
                     "versions.yml:md5,9b9842e144dad4e4b6e619ef00583694",
                     "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
                     "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                    "versions.yml:md5,c7cbcd9fc24aa7580029e7b4d6411fcc",
                     "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
                     "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
                     "versions.yml:md5,d6665112b721f1651ae340c644f9a27c",
@@ -144,7 +147,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-02-12T15:54:56.496246671"
+        "timestamp": "2025-02-25T09:23:35.493390557"
     },
     "1 sample - [bam, bai], 'sniffles', bed -stub": {
         "content": [
@@ -197,6 +200,7 @@
                     "versions.yml:md5,9b9842e144dad4e4b6e619ef00583694",
                     "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
                     "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                    "versions.yml:md5,c7cbcd9fc24aa7580029e7b4d6411fcc",
                     "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
                     "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
                     "versions.yml:md5,d6665112b721f1651ae340c644f9a27c",
@@ -250,6 +254,7 @@
                     "versions.yml:md5,9b9842e144dad4e4b6e619ef00583694",
                     "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
                     "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                    "versions.yml:md5,c7cbcd9fc24aa7580029e7b4d6411fcc",
                     "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
                     "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
                     "versions.yml:md5,d6665112b721f1651ae340c644f9a27c",
@@ -261,7 +266,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-02-12T15:54:21.880099608"
+        "timestamp": "2025-02-25T09:22:52.646657985"
     },
     "2 samples - [bam, bai], 'sniffles', []": {
         "content": [
@@ -593,6 +598,8 @@
                 "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
                 "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
                 "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                "versions.yml:md5,c7cbcd9fc24aa7580029e7b4d6411fcc",
+                "versions.yml:md5,c7cbcd9fc24aa7580029e7b4d6411fcc",
                 "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
                 "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
                 "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
@@ -605,7 +612,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-02-12T15:52:06.545796192"
+        "timestamp": "2025-02-25T09:20:10.640467285"
     },
     "2 samples - [bam, bai], 'severus', []": {
         "content": [
@@ -636,6 +643,8 @@
                 "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
                 "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
                 "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                "versions.yml:md5,c7cbcd9fc24aa7580029e7b4d6411fcc",
+                "versions.yml:md5,c7cbcd9fc24aa7580029e7b4d6411fcc",
                 "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
                 "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
                 "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
@@ -648,7 +657,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-02-12T15:53:48.055925418"
+        "timestamp": "2025-02-25T09:22:13.152680523"
     },
     "2 samples - [bam, bai], 'severus', [] -stub": {
         "content": [
@@ -708,6 +717,8 @@
                 "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
                 "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
                 "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                "versions.yml:md5,c7cbcd9fc24aa7580029e7b4d6411fcc",
+                "versions.yml:md5,c7cbcd9fc24aa7580029e7b4d6411fcc",
                 "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
                 "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
                 "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
@@ -720,7 +731,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-02-12T15:55:31.136525568"
+        "timestamp": "2025-02-25T09:24:18.087423468"
     },
     "1 sample - [bam, bai], 'severus', bed -stub": {
         "content": [
@@ -773,6 +784,7 @@
                     "versions.yml:md5,9b9842e144dad4e4b6e619ef00583694",
                     "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
                     "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                    "versions.yml:md5,c7cbcd9fc24aa7580029e7b4d6411fcc",
                     "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
                     "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
                     "versions.yml:md5,d6665112b721f1651ae340c644f9a27c",
@@ -826,6 +838,7 @@
                     "versions.yml:md5,9b9842e144dad4e4b6e619ef00583694",
                     "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
                     "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                    "versions.yml:md5,c7cbcd9fc24aa7580029e7b4d6411fcc",
                     "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
                     "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
                     "versions.yml:md5,d6665112b721f1651ae340c644f9a27c",
@@ -837,7 +850,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-02-12T15:55:13.008041118"
+        "timestamp": "2025-02-25T09:23:55.351889305"
     },
     "1 sample - [bam, bai], 'sniffles', [] -stub": {
         "content": [
@@ -890,6 +903,7 @@
                     "versions.yml:md5,9b9842e144dad4e4b6e619ef00583694",
                     "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
                     "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                    "versions.yml:md5,c7cbcd9fc24aa7580029e7b4d6411fcc",
                     "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
                     "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
                     "versions.yml:md5,d6665112b721f1651ae340c644f9a27c",
@@ -943,6 +957,7 @@
                     "versions.yml:md5,9b9842e144dad4e4b6e619ef00583694",
                     "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
                     "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                    "versions.yml:md5,c7cbcd9fc24aa7580029e7b4d6411fcc",
                     "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
                     "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
                     "versions.yml:md5,d6665112b721f1651ae340c644f9a27c",
@@ -954,7 +969,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-02-12T15:54:05.025782157"
+        "timestamp": "2025-02-25T09:22:33.533615379"
     },
     "1 sample - [bam, bai], 'sniffles', bed": {
         "content": [
@@ -974,6 +989,7 @@
                 "versions.yml:md5,9b9842e144dad4e4b6e619ef00583694",
                 "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
                 "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                "versions.yml:md5,c7cbcd9fc24aa7580029e7b4d6411fcc",
                 "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
                 "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
                 "versions.yml:md5,d6665112b721f1651ae340c644f9a27c",
@@ -984,7 +1000,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-02-12T15:51:01.485884248"
+        "timestamp": "2025-02-25T09:18:52.356990713"
     },
     "1 sample - [bam, bai], 'severus', bed": {
         "content": [
@@ -1004,6 +1020,7 @@
                 "versions.yml:md5,9b9842e144dad4e4b6e619ef00583694",
                 "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
                 "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                "versions.yml:md5,c7cbcd9fc24aa7580029e7b4d6411fcc",
                 "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
                 "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
                 "versions.yml:md5,d6665112b721f1651ae340c644f9a27c",
@@ -1014,7 +1031,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-02-12T15:52:44.406653449"
+        "timestamp": "2025-02-25T09:20:55.908723365"
     },
     "1 sample - [bam, bai], 'sniffles', []": {
         "content": [
@@ -1032,6 +1049,7 @@
                 "versions.yml:md5,9b9842e144dad4e4b6e619ef00583694",
                 "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
                 "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                "versions.yml:md5,c7cbcd9fc24aa7580029e7b4d6411fcc",
                 "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
                 "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
                 "versions.yml:md5,d6665112b721f1651ae340c644f9a27c",
@@ -1042,7 +1060,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-02-12T15:50:41.053715921"
+        "timestamp": "2025-02-25T09:18:27.590446344"
     },
     "2 samples - [bam, bai], 'sniffles', [] -stub": {
         "content": [
@@ -1102,6 +1120,8 @@
                 "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
                 "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
                 "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                "versions.yml:md5,c7cbcd9fc24aa7580029e7b4d6411fcc",
+                "versions.yml:md5,c7cbcd9fc24aa7580029e7b4d6411fcc",
                 "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
                 "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
                 "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
@@ -1114,6 +1134,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-02-12T15:54:40.015041254"
+        "timestamp": "2025-02-25T09:23:15.633543248"
     }
 }
diff --git a/tests/samplesheet_multisample_ont_bam.nf.test b/tests/samplesheet_multisample_ont_bam.nf.test
@@ -9,15 +9,15 @@ nextflow_pipeline {
 
         when {
             params {
-                pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/630ff7c9bd62f3446070ebd685df380a53926366/'
-                input                        = params.pipelines_testdata_base_path + 'testdata/samplesheet_multisample_bam_ont.csv'
-                outdir                       = "$outputDir"
-                preset                       = 'ONT_R10'
-                alignment_processes          = 1
-                snv_calling_processes        = 1
-                phaser                       = "whatshap"
-                sv_caller                    = "sniffles"
-                publish_unannotated_family_svs    = true
+                pipelines_testdata_base_path   = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/630ff7c9bd62f3446070ebd685df380a53926366/'
+                input                          = params.pipelines_testdata_base_path + 'testdata/samplesheet_multisample_bam_ont.csv'
+                outdir                         = "$outputDir"
+                preset                         = 'ONT_R10'
+                alignment_processes            = 1
+                snv_calling_processes          = 1
+                phaser                         = "whatshap"
+                sv_caller                      = "sniffles"
+                publish_unannotated_family_svs = true
             }
         }
 

diff --git a/tests/samplesheet_multisample_ont_bam.nf.test.snap b/tests/samplesheet_multisample_ont_bam.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "samplesheet_multisample_ont_bam | --preset ONT_R10 --phaser whatshap --alignment_processes 1 --snv_calling_processes 1 --sv_caller sniffles --publish_unannotated_family_svs": {
         "content": [
-            156,
+            158,
             {
                 "ADD_FOUND_IN_TAG": {
                     "bcftools": 1.2,
@@ -743,6 +743,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-02-17T15:51:11.213948714"
+        "timestamp": "2025-02-25T09:42:23.566844965"
     }
 }