Merge pull request #425 from genomic-medicine-sweden/addsampletometa

Add a new sample field to meta

CHANGELOG.md

@@ -33,6 +33,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Updated modules from nf-core [#412](https://github.com/nf-core/raredisease/pull/412)
 - If present, remove duplicate entries in probands and upd_children in the meta. [#420](https://github.com/nf-core/raredisease/pull/420)
 - Fixes vep starting as many instances as the square of the number of scatters. [#405](https://github.com/nf-core/raredisease/pull/405)
+- Replaced the logic where we added an arbitrary substring to keep file names unique after alignment which we then removed using a split operator, with a simple copy operation. [#425](https://github.com/nf-core/raredisease/pull/425/files)
 
 ### `Updated`
 

assets/schema_input.json

@@ -10,7 +10,7 @@
             "sample": {
                 "type": "string",
                 "exists": true,
-                "meta": ["id"],
+                "meta": ["id", "sample"],
                 "pattern": "^\\S+$",
                 "errorMessage": "Sample name must be provided and cannot contain spaces"
             },

conf/test.config

@@ -25,6 +25,7 @@ params {
 
     // analysis params
     skip_cnv_calling = true
+    skip_mt_analysis = true
 
     // Input data
     input          = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/samplesheet_trio.csv'

subworkflows/local/alignment/align_bwamem2.nf

@@ -33,7 +33,7 @@ workflow ALIGN_BWAMEM2 {
         // Merge multiple lane samples and index
         BWAMEM2_MEM.out.bam
             .map{ meta, bam ->
-                    new_id   = meta.id.split('_')[0]
+                    new_id   = meta.sample
                     new_meta = meta + [id:new_id, read_group:"\'@RG\\tID:" + new_id + "\\tPL:" + val_platform + "\\tSM:" + new_id + "\'"]
                     [groupKey(new_meta, new_meta.num_lanes), bam]
                 }

subworkflows/local/alignment/align_sentieon.nf

@@ -22,7 +22,7 @@ workflow ALIGN_SENTIEON {
         SENTIEON_BWAMEM.out
             .bam_and_bai
             .map{ meta, bam, bai ->
-                new_id   = meta.id.split('_')[0]
+                new_id   = meta.sample
                 new_meta = meta + [id:new_id, read_group:"\'@RG\\tID:" + new_id + "\\tPL:" + val_platform + "\\tSM:" + new_id + "\'"]
                 [groupKey(new_meta, new_meta.num_lanes), bam, bai]
                 }

workflows/raredisease.nf

@@ -615,9 +615,7 @@ def makePed(samples) {
     outfile.text = ['#family_id', 'sample_id', 'father', 'mother', 'sex', 'phenotype'].join('\t')
     def samples_list = []
     for(int i = 0; i<samples.size(); i++) {
-        sample_tokenized   =  samples[i].id.tokenize("_")
-        sample_tokenized.removeLast()
-        sample_name        =  sample_tokenized.join("_")
+        sample_name        =  samples[i].sample
         if (!samples_list.contains(sample_name)) {
             outfile.append('\n' + [samples[i].case_id, sample_name, samples[i].paternal, samples[i].maternal, samples[i].sex, samples[i].phenotype].join('\t'));
             samples_list.add(sample_name)
@@ -636,10 +634,10 @@ def create_case_channel(List rows) {
 
     for (item in rows) {
         if (item.phenotype == "2") {
-            probands.add(item.id.split("_T")[0])
+            probands.add(item.sample)
         }
         if ( (item.paternal!="0") && (item.paternal!="") && (item.maternal!="0") && (item.maternal!="") ) {
-            upd_children.add(item.id.split("_T")[0])
+            upd_children.add(item.sample)
         }
         if ( (item.paternal!="0") && (item.paternal!="") ) {
             father = item.paternal