From b3e9b88e80880f450ad79a95b2b7aa05e1de5484 Mon Sep 17 00:00:00 2001
From: Praveen Raj S <43108054+praveenraj2018@users.noreply.github.com>
Date: Thu, 28 Apr 2022 14:41:01 +0200
Subject: [PATCH] csi output in TABIX (#1579)

* Added: csi output to TABIX

* Added: tests for csi

* Fix tiddit/sv (#1580)

* Fix fasta ref option for TIDDIT_SV

* Add md5sum's to tiddit/sv tests

Co-authored-by: Daniel Cooke <dcooke@well.ox.ac.uk>

* Fix: prettier issues

Co-authored-by: Daniel Cooke <daniel.cooke@invitae.com>
Co-authored-by: Daniel Cooke <dcooke@well.ox.ac.uk>
---
 modules/tabix/tabix/main.nf               |  3 ++-
 modules/tabix/tabix/meta.yml              |  4 ++++
 tests/modules/tabix/tabix/main.nf         | 19 ++++++++++++++-----
 tests/modules/tabix/tabix/nextflow.config |  6 +++++-
 tests/modules/tabix/tabix/test.yml        | 10 +++++++++-
 5 files changed, 34 insertions(+), 8 deletions(-)

diff --git a/modules/tabix/tabix/main.nf b/modules/tabix/tabix/main.nf
index c9dab068..e155e468 100644
--- a/modules/tabix/tabix/main.nf
+++ b/modules/tabix/tabix/main.nf
@@ -11,7 +11,8 @@ process TABIX_TABIX {
     tuple val(meta), path(tab)
 
     output:
-    tuple val(meta), path("*.tbi"), emit: tbi
+    tuple val(meta), path("*.tbi"), optional:true, emit: tbi
+    tuple val(meta), path("*.csi"), optional:true, emit: csi
     path  "versions.yml"          , emit: versions
 
     when:
diff --git a/modules/tabix/tabix/meta.yml b/modules/tabix/tabix/meta.yml
index 89478abe..fcc6e524 100644
--- a/modules/tabix/tabix/meta.yml
+++ b/modules/tabix/tabix/meta.yml
@@ -31,6 +31,10 @@ output:
       type: file
       description: tabix index file
       pattern: "*.{tbi}"
+  - csi:
+      type: file
+      description: coordinate sorted index file
+      pattern: "*.{csi}"
   - versions:
       type: file
       description: File containing software versions
diff --git a/tests/modules/tabix/tabix/main.nf b/tests/modules/tabix/tabix/main.nf
index 993ee812..da26f4d7 100644
--- a/tests/modules/tabix/tabix/main.nf
+++ b/tests/modules/tabix/tabix/main.nf
@@ -2,9 +2,10 @@
 
 nextflow.enable.dsl = 2
 
-include { TABIX_TABIX as TABIX_BED } from '../../../../modules/tabix/tabix/main.nf'
-include { TABIX_TABIX as TABIX_GFF } from '../../../../modules/tabix/tabix/main.nf'
-include { TABIX_TABIX as TABIX_VCF } from '../../../../modules/tabix/tabix/main.nf'
+include { TABIX_TABIX as TABIX_BED     } from '../../../../modules/tabix/tabix/main.nf'
+include { TABIX_TABIX as TABIX_GFF     } from '../../../../modules/tabix/tabix/main.nf'
+include { TABIX_TABIX as TABIX_VCF_TBI } from '../../../../modules/tabix/tabix/main.nf'
+include { TABIX_TABIX as TABIX_VCF_CSI } from '../../../../modules/tabix/tabix/main.nf'
 
 workflow test_tabix_tabix_bed {
     input = [ [ id:'B.bed' ], // meta map
@@ -22,10 +23,18 @@ workflow test_tabix_tabix_gff {
     TABIX_GFF ( input )
 }
 
-workflow test_tabix_tabix_vcf {
+workflow test_tabix_tabix_vcf_tbi {
     input = [ [ id:'test.vcf' ], // meta map
               [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ] 
             ]
 
-    TABIX_VCF ( input )
+    TABIX_VCF_TBI ( input )
+}
+
+workflow test_tabix_tabix_vcf_csi {
+    input = [ [ id:'test.vcf' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ]
+            ]
+
+    TABIX_VCF_CSI ( input )
 }
diff --git a/tests/modules/tabix/tabix/nextflow.config b/tests/modules/tabix/tabix/nextflow.config
index aa97a873..139e0865 100644
--- a/tests/modules/tabix/tabix/nextflow.config
+++ b/tests/modules/tabix/tabix/nextflow.config
@@ -10,8 +10,12 @@ process {
         ext.args = '-p gff'
     }
 
-    withName: TABIX_VCF {
+    withName: TABIX_VCF_TBI {
         ext.args = '-p vcf'
     }
 
+   withName: TABIX_VCF_CSI {
+        ext.args = '-p vcf --csi'
+    }
+
 }
diff --git a/tests/modules/tabix/tabix/test.yml b/tests/modules/tabix/tabix/test.yml
index 46be28dd..6d168ef5 100644
--- a/tests/modules/tabix/tabix/test.yml
+++ b/tests/modules/tabix/tabix/test.yml
@@ -15,10 +15,18 @@
     - path: ./output/tabix/genome.gff3.gz.tbi
       md5sum: f79a67d95a98076e04fbe0455d825926
 - name: tabix tabix vcf
-  command: nextflow run ./tests/modules/tabix/tabix -entry test_tabix_tabix_vcf -c ./tests/config/nextflow.config -c ./tests/modules/tabix/tabix/nextflow.config
+  command: nextflow run ./tests/modules/tabix/tabix -entry test_tabix_tabix_vcf_tbi -c ./tests/config/nextflow.config -c ./tests/modules/tabix/tabix/nextflow.config
   tags:
     - tabix
     - tabix/tabix
   files:
     - path: output/tabix/test.vcf.gz.tbi
       md5sum: 36e11bf96ed0af4a92caa91a68612d64
+- name: tabix tabix vcf csi
+  command: nextflow run ./tests/modules/tabix/tabix -entry test_tabix_tabix_vcf_csi -c ./tests/config/nextflow.config -c ./tests/modules/tabix/tabix/nextflow.config
+  tags:
+    - tabix
+    - tabix/tabix
+  files:
+    - path: output/tabix/test.vcf.gz.csi
+      md5sum: 5f930522d2b9dcdba2807b7da4dfa3fd