Update output.md and remove bcftools query from config

conf/steps/validation.config

@@ -67,13 +67,6 @@ process {
     }
 
     // Split by samples
-    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:SPLIT_TRUTH:BCFTOOLS_QUERY' {
-        tag = { "${meta.id} Batch ${meta.batch} ${meta.tools}" }
-        ext.args = "--list-samples"
-        ext.prefix = { "${meta.id}.batch${meta.batch}" }
-        publishDir = [enabled: false]
-    }
-
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:SPLIT_TRUTH:BCFTOOLS_PLUGINSPLIT' {
         ext.args   = ["--output-type z", "--write-index=tbi"].join(' ')
         ext.prefix = { "${meta.id}" }

docs/output.md

@@ -109,7 +109,7 @@ The results from steps impute will have the following directory structure:
 - `imputation/csv/`
   - `impute.csv`: A single csv containing the path to a vcf and its index, of each imputed sample with their corresponding tool.
 - `imputation/[glimpse1,glimpse2,quilt,stitch]/`
-  - `concat/all.batch*.vcf.gz`: The concatenate vcf of all imputed sample.
+  - `concat/all.batch*.vcf.gz`: The concatenate vcf of all imputed sample by batches.
   - `concat/all.batch*.vcf.gz.tbi`: A tbi for the concatenated samples imputed vcf.
   - `samples/*.vcf.gz`: A vcf of each imputed sample.
   - `samples/*.vcf.gz.tbi`: A tbi for the imputed vcf.