added impute info

modules/local/bcftools_impute_info/main.nf

@@ -0,0 +1,17 @@
+process BCFTOOLS_IMPUTE_INFO {
+
+    label 'process_medium'
+
+    input:
+    tuple val(meta), path(vcf), path(csi)
+
+    output:
+    tuple val(meta), path('glimpse_vcf_annotated.vcf.gz'), path('glimpse_vcf_annotated.vcf.gz.csi'), emit: annotated_variants
+
+    script:
+    """
+    bcftools +impute-info -Oz -o glimpse_vcf_annotated.vcf.gz ${vcf}
+    bcftools index glimpse_vcf_annotated.vcf.gz
+    """
+
+}

modules/local/bcftools_impute_info/meta.yml

@@ -0,0 +1,18 @@
+name: bcftools_impute_info
+description: Run bcftools impute info plugin
+keywords:
+  - bcftools
+  - impute info
+input:
+  - meta:
+      type: map
+      description: sample information
+  - vcf:
+      type: file
+      description: Input VCF file
+output:
+  - out:
+      type: path
+      description: Output VCF file
+authors:
+  - "@Ruth Eberhardt"

modules/local/split_samples/meta.yml

@@ -1,7 +1,7 @@
 name: split_samples
 description: Split samples in a VCF into batches
 keywords:
-  - cutadapt
+  - batch samples
 input:
   - batch_size:
       type: var

workflows/run_glimpse.nf

@@ -6,6 +6,7 @@ include { BCFTOOLS_INDEX as INDEX_PHASE  } from '../modules/nf-core/bcftools/ind
 include { BCFTOOLS_INDEX as INDEX_LIGATE } from '../modules/nf-core/bcftools/index/main.nf'
 include { BCFTOOLS_MERGE } from '../modules/nf-core/bcftools/merge/main.nf'
 include { BCFTOOLS_INDEX as INDEX_MERGE } from '../modules/nf-core/bcftools/index/main.nf'
+include { BCFTOOLS_IMPUTE_INFO } from '../modules/local/bcftools_impute_info/main'
 
 workflow RUN_GLIMPSE {
 
@@ -58,7 +59,8 @@ workflow RUN_GLIMPSE {
     BCFTOOLS_MERGE ( merge_ch, merge_input_2, merge_input_3, params.ref_bed )
 
     INDEX_MERGE ( BCFTOOLS_MERGE.out.merged_variants )
-
-
+
+    impute_info_ch = BCFTOOLS_MERGE.out.merged_variants.join(INDEX_MERGE.out.csi)
+    BCFTOOLS_IMPUTE_INFO ( impute_info_ch )
 
 }