Check for multiple sample before splitting

nf-core · Nov 11, 2024 · 01e0927 · 01e0927
1 parent b5e7d91
commit 01e0927
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Showing 12 changed files with 449 additions and 8 deletions.
diff --git a/modules.json b/modules.json
@@ -50,6 +50,11 @@
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/bcftools/pluginsplit/bcftools-pluginsplit.diff"
                     },
+                    "bcftools/query": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
                     "bcftools/stats": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",

diff --git a/modules/nf-core/bcftools/query/environment.yml b/modules/nf-core/bcftools/query/environment.yml
diff --git a/modules/nf-core/bcftools/query/main.nf b/modules/nf-core/bcftools/query/main.nf
diff --git a/modules/nf-core/bcftools/query/meta.yml b/modules/nf-core/bcftools/query/meta.yml
diff --git a/modules/nf-core/bcftools/query/tests/main.nf.test b/modules/nf-core/bcftools/query/tests/main.nf.test
diff --git a/modules/nf-core/bcftools/query/tests/main.nf.test.snap b/modules/nf-core/bcftools/query/tests/main.nf.test.snap
diff --git a/modules/nf-core/bcftools/query/tests/nextflow.config b/modules/nf-core/bcftools/query/tests/nextflow.config
diff --git a/modules/nf-core/bcftools/query/tests/tags.yml b/modules/nf-core/bcftools/query/tests/tags.yml
diff --git a/subworkflows/local/vcf_split_bcftools/main.nf b/subworkflows/local/vcf_split_bcftools/main.nf
@@ -1,4 +1,5 @@
 include { BCFTOOLS_PLUGINSPLIT  } from '../../../modules/nf-core/bcftools/pluginsplit'
+include { BCFTOOLS_QUERY        } from '../../../modules/nf-core/bcftools/query/main'
 
 workflow VCF_SPLIT_BCFTOOLS {
     take:
@@ -8,7 +9,25 @@ workflow VCF_SPLIT_BCFTOOLS {
 
     ch_versions = Channel.empty()
 
-    BCFTOOLS_PLUGINSPLIT(ch_vcf, [], [], [], [])
+    BCFTOOLS_QUERY(ch_vcf, [], [], []) // List samples
+
+    BCFTOOLS_QUERY.out.output.splitText().groupTuple().view()
+
+    ch_samples = ch_vcf
+        .join(BCFTOOLS_QUERY.out.output.splitText().groupTuple())
+        .branch {
+            one : it[3].size() == 1
+            multiple : it[3].size() > 1
+            other : true
+        }
+
+    ch_samples.other.map {
+        def file = it[1]
+        def id = it[0].id
+        error "File ${file} with id : ${id} does not have any samples information"
+    }
+
+    BCFTOOLS_PLUGINSPLIT(ch_samples.multiple.map{it[0..2]}, [], [], [], [])
     ch_versions = ch_versions.mix(BCFTOOLS_PLUGINSPLIT.out.versions.first())
 
     ch_vcf_samples = BCFTOOLS_PLUGINSPLIT.out.vcf
@@ -19,8 +38,11 @@ workflow VCF_SPLIT_BCFTOOLS {
         .transpose()
         .map{metaITC, tbi -> [metaITC + [id: tbi.getBaseName().tokenize(".")[0]], tbi]}
 
-    ch_vcf_tbi_samples = ch_vcf_samples
-        .join(ch_tbi_samples)
+    ch_vcf_tbi_samples = ch_samples.one
+        .map{ it[0..2] }
+        .mix(ch_vcf_samples
+            .join(ch_tbi_samples)
+        )
 
     emit:
     vcf_tbi        = ch_vcf_tbi_samples   // channel: [ [id, chr, tools], vcf, index ]