Merge pull request #184 from nf-cmgg/fix/automap-updio-issues

Fix/automap updio issues
nf-cmgg · Aug 8, 2024 · 55a68ab · 55a68ab
2 parents 62ced4c + 7f36cda
commit 55a68ab
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## v1.7.0dev
 
+## Fixes
+
+1. Automap analysis should now give the correct output files for individuals.
+
 ## v1.6.0 - Offbeat Ostend - [April 29 2024]
 
 ### New features

diff --git a/conf/modules.config b/conf/modules.config
@@ -564,7 +564,7 @@ process {
             withName: "^.*VCF_ROH_AUTOMAP:AUTOMAP_AUTOMAP\$" {
                 ext.prefix = {"automap_${meta.caller}"}
                 ext.args = {[
-                    meta.family_count > 1 ? "--multivcf" : "",
+                    meta.family_count > 1 ? "--multivcf" : "--id ${meta.samples}",
                     params.automap_panel_name ? "--panelname ${params.automap_panel_name}" : ""
                 ].findAll { it != "" }.join(" ")}
                 publishDir = [

diff --git a/modules/local/automap/automap/main.nf b/modules/local/automap/automap/main.nf
@@ -29,7 +29,7 @@ process AUTOMAP_AUTOMAP {
     automap \\
         --vcf $vcf \\
         --genome $hg_genome \\
-        --out $prefix \\
+        --out $prefix/ \\
         --repeats $repeats \\
         $panel_file \\
         $args

diff --git a/subworkflows/local/cram_call_vardictjava/main.nf b/subworkflows/local/cram_call_vardictjava/main.nf
@@ -125,6 +125,10 @@ workflow CRAM_CALL_VARDICTJAVA {
 
         ch_filter_output
             .join(TABIX_TABIX.out.tbi, failOnDuplicate: true, failOnMismatch: true)
+            .map { meta, vcf, tbi ->
+                def new_meta = meta + [samples: meta.sample]
+                [ new_meta, vcf, tbi ]
+            }
             .set { ch_vcfs }
 
     emit:

diff --git a/subworkflows/local/gvcf_joint_genotype_gatk4/main.nf b/subworkflows/local/gvcf_joint_genotype_gatk4/main.nf
@@ -53,9 +53,13 @@ workflow GVCF_JOINT_GENOTYPE_GATK4 {
                 family_count:   meta.family_count,
                 caller:         meta.caller
             ]
-            [ groupKey(new_meta, meta.family_count.toInteger()), gvcf, tbi ]
+            [ groupKey(new_meta, meta.family_count.toInteger()), gvcf, tbi, meta.sample ]
         }
         .groupTuple()
+        .map { meta, gvcf, tbi, samples ->
+            def new_meta = meta + [samples: "${samples.sort(false).join(',')}"] // Having a comma-separated string ensures that joins don't fail
+            [ new_meta, gvcf, tbi ]
+        }
         .combine(GAWK.out.output.map { it[1] })
         .map { meta, gvcfs, tbis, bed ->
             [ meta, gvcfs, tbis, bed, [], [] ]
@@ -89,9 +93,13 @@ workflow GVCF_JOINT_GENOTYPE_GATK4 {
                     family_count:   meta.family_count,
                     caller:         meta.caller
                 ]
-                [ groupKey(new_meta, meta.family_count.toInteger()), bed ]
+                [ groupKey(new_meta, meta.family_count.toInteger()), bed, meta.sample ]
             }
             .groupTuple()
+            .map { meta, bed, samples ->
+                def new_meta = meta + [samples: "${samples.sort(false).join(',')}"] // Having a comma-separated string ensures that joins don't fail
+                [ new_meta, bed ]
+            }
             .dump(tag:'merge_beds_input', pretty: true)
             .set { ch_merge_beds_input }
 

diff --git a/tests/subworkflows/local/cram_call_genotype_gatk4/main.nf.test.snap b/tests/subworkflows/local/cram_call_genotype_gatk4/main.nf.test.snap
@@ -24,7 +24,8 @@
                         "family": "Ashkenazim",
                         "id": "Ashkenazim",
                         "family_count": 3,
-                        "caller": "haplotypecaller"
+                        "caller": "haplotypecaller",
+                        "samples": "NA24143,NA24149,NA24835"
                     },
                     "Ashkenazim.haplotypecaller.vcf.gz",
                     "Ashkenazim.haplotypecaller.vcf.gz.tbi"
@@ -37,10 +38,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.02.0"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-03-27T10:07:15.389498873"
+        "timestamp": "2024-08-06T13:01:36.711373912"
     },
     "filter - family": {
         "content": [
@@ -50,7 +51,8 @@
                         "family": "Ashkenazim",
                         "id": "Ashkenazim",
                         "family_count": 3,
-                        "caller": "haplotypecaller"
+                        "caller": "haplotypecaller",
+                        "samples": "NA24143,NA24149,NA24835"
                     },
                     "Ashkenazim.haplotypecaller.vcf.gz",
                     "Ashkenazim.haplotypecaller.vcf.gz.tbi"
@@ -63,10 +65,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.02.0"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-03-27T10:11:00.537979751"
+        "timestamp": "2024-08-06T13:02:26.651064532"
     },
     "default - gvcfs": {
         "content": [
@@ -76,7 +78,8 @@
                         "family": "Ashkenazim",
                         "id": "Ashkenazim",
                         "family_count": 1,
-                        "caller": "haplotypecaller"
+                        "caller": "haplotypecaller",
+                        "samples": "NA24143"
                     },
                     "Ashkenazim.haplotypecaller.vcf.gz",
                     "Ashkenazim.haplotypecaller.vcf.gz.tbi"
@@ -87,10 +90,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.02.0"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-03-27T10:09:15.858225835"
+        "timestamp": "2024-08-06T12:56:23.435795439"
     },
     "default - crams": {
         "content": [
@@ -100,7 +103,8 @@
                         "family": "Ashkenazim",
                         "id": "Ashkenazim",
                         "family_count": 1,
-                        "caller": "haplotypecaller"
+                        "caller": "haplotypecaller",
+                        "samples": "NA24143"
                     },
                     "Ashkenazim.haplotypecaller.vcf.gz",
                     "Ashkenazim.haplotypecaller.vcf.gz.tbi"
@@ -113,10 +117,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.02.0"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-03-27T10:06:11.00007181"
+        "timestamp": "2024-08-06T12:55:51.608812907"
     },
     "only_call - family": {
         "content": [
@@ -143,7 +147,8 @@
                         "family": "Ashkenazim",
                         "id": "Ashkenazim",
                         "family_count": 2,
-                        "caller": "haplotypecaller"
+                        "caller": "haplotypecaller",
+                        "samples": "NA24143,NA24835"
                     },
                     "Ashkenazim.haplotypecaller.vcf.gz",
                     "Ashkenazim.haplotypecaller.vcf.gz.tbi"
@@ -156,9 +161,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.02.0"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-03-27T10:22:47.471505664"
+        "timestamp": "2024-08-06T13:04:20.473178165"
     }
 }
diff --git a/tests/subworkflows/local/cram_call_vardictjava/main.nf.test.snap b/tests/subworkflows/local/cram_call_vardictjava/main.nf.test.snap
@@ -8,18 +8,19 @@
                         "sample": "NA24143",
                         "family": "Ashkenazim",
                         "family_count": 1,
-                        "caller": "vardict"
+                        "caller": "vardict",
+                        "samples": "NA24143"
                     },
                     "NA24143.vardict.vcf.gz",
                     "NA24143.vardict.vcf.gz.tbi"
                 ]
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.02.0"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-03-27T10:30:53.553985963"
+        "timestamp": "2024-08-06T13:05:31.562298546"
     },
     "default": {
         "content": [
@@ -30,18 +31,19 @@
                         "sample": "NA24143",
                         "family": "Ashkenazim",
                         "family_count": 1,
-                        "caller": "vardict"
+                        "caller": "vardict",
+                        "samples": "NA24143"
                     },
                     "NA24143.vardict.vcf.gz",
                     "NA24143.vardict.vcf.gz.tbi"
                 ]
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.02.0"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-03-27T10:31:27.5084132"
+        "timestamp": "2024-08-06T13:05:04.322416692"
     },
     "family": {
         "content": [
@@ -52,7 +54,8 @@
                         "sample": "NA24143",
                         "family": "Ashkenazim",
                         "family_count": 2,
-                        "caller": "vardict"
+                        "caller": "vardict",
+                        "samples": "NA24143"
                     },
                     "NA24143.vardict.vcf.gz",
                     "NA24143.vardict.vcf.gz.tbi"
@@ -63,17 +66,18 @@
                         "sample": "NA24149",
                         "family": "Ashkenazim",
                         "family_count": 2,
-                        "caller": "vardict"
+                        "caller": "vardict",
+                        "samples": "NA24149"
                     },
                     "NA24149.vardict.vcf.gz",
                     "NA24149.vardict.vcf.gz.tbi"
                 ]
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.02.0"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-03-27T10:33:57.915748864"
+        "timestamp": "2024-08-06T13:06:05.012625054"
     }
 }
diff --git a/tests/subworkflows/local/vcf_roh_automap/main.nf.test b/tests/subworkflows/local/vcf_roh_automap/main.nf.test
@@ -18,7 +18,7 @@ nextflow_workflow {
             workflow {
                 """
                 input[0] = Channel.of([
-                    [id:"Ashkenazim", family:"Ashkenazim", family_count:3, caller:"haplotypecaller"],
+                    [id:"Ashkenazim", family:"Ashkenazim", family_count:3, caller:"haplotypecaller", samples: "NA24143,NA24835,NA24149"],
                     file(params.famvcf, checkIfExists:true),
                     file(params.famtbi, checkIfExists:true)
                 ])
@@ -58,7 +58,7 @@ nextflow_workflow {
             workflow {
                 """
                 input[0] = Channel.of([
-                    [id:"NA24143", family:"NA24143", family_count:1, caller:"haplotypecaller"],
+                    [id:"NA24143", family:"NA24143", family_count:1, caller:"haplotypecaller", samples: "NA24143,NA24835,NA24149"],
                     file(params.vcf1, checkIfExists:true),
                     file(params.tbi1, checkIfExists:true)
                 ])

diff --git a/tests/subworkflows/local/vcf_roh_automap/main.nf.test.snap b/tests/subworkflows/local/vcf_roh_automap/main.nf.test.snap
@@ -7,7 +7,8 @@
                         "id": "Ashkenazim",
                         "family": "Ashkenazim",
                         "family_count": 3,
-                        "caller": "haplotypecaller"
+                        "caller": "haplotypecaller",
+                        "samples": "NA24143,NA24835,NA24149"
                     },
                     [
                         [
@@ -24,10 +25,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.02.0"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-04-04T16:13:43.925198036"
+        "timestamp": "2024-08-06T13:06:37.322068108"
     },
     "default - sample": {
         "content": [
@@ -37,7 +38,8 @@
                         "id": "NA24143",
                         "family": "NA24143",
                         "family_count": 1,
-                        "caller": "haplotypecaller"
+                        "caller": "haplotypecaller",
+                        "samples": "NA24143,NA24835,NA24149"
                     },
                     [
                         "NA24143.HomRegions.cmgg_bio.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -49,9 +51,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.02.0"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-04-04T16:03:23.276826691"
+        "timestamp": "2024-08-06T13:06:47.205904762"
     }
 }