From b8dda67338cfe2deac074c3ce7c085ccde825f37 Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Thu, 23 Jan 2020 11:35:49 +0100
Subject: [PATCH] add htslib tabix to index bgzipped vcf files

---
 tools/htslib/tabix/main.nf              | 16 +++++++++++++++
 tools/htslib/tabix/meta.yml             | 26 +++++++++++++++++++++++++
 tools/htslib/tabix/test/main.nf         | 13 +++++++++++++
 tools/htslib/tabix/test/nextflow.config |  2 ++
 4 files changed, 57 insertions(+)
 create mode 100644 tools/htslib/tabix/main.nf
 create mode 100644 tools/htslib/tabix/meta.yml
 create mode 100644 tools/htslib/tabix/test/main.nf
 create mode 100644 tools/htslib/tabix/test/nextflow.config

diff --git a/tools/htslib/tabix/main.nf b/tools/htslib/tabix/main.nf
new file mode 100644
index 00000000..e228bb02
--- /dev/null
+++ b/tools/htslib/tabix/main.nf
@@ -0,0 +1,16 @@
+process htslib_tabix {
+    tag {vcf}
+
+    container 'quay.io/biocontainers/tabix:0.2.6--ha92aebf_0'
+
+    input:
+        path(vcf)
+
+    output:
+        path("${vcf}.tbi")
+
+    script:
+    """
+    tabix -p vcf ${vcf}
+    """
+}
diff --git a/tools/htslib/tabix/meta.yml b/tools/htslib/tabix/meta.yml
new file mode 100644
index 00000000..027780c3
--- /dev/null
+++ b/tools/htslib/tabix/meta.yml
@@ -0,0 +1,26 @@
+name: htslib tabix
+description: create tabix index from a bgzip vcf file
+keywords:
+    - index
+    - tabix
+tools:
+    - bwa:
+        description: |
+            Generic indexer for TAB-delimited genome position files.
+        homepage: https://www.htslib.org/
+        documentation: https://www.htslib.org/doc/tabix.1.html
+        doi: 10.1093/bioinformatics/btq671
+input:
+    -
+        - input:
+            type: file
+            description: Input vcf.gz file
+            pattern: *.{vcf.gz}
+output:
+    -
+        - index:
+            type: file
+            description: tabix index file
+            pattern: *.{vcf.gz.tbi}
+authors:
+    - @maxulysse
\ No newline at end of file
diff --git a/tools/htslib/tabix/test/main.nf b/tools/htslib/tabix/test/main.nf
new file mode 100644
index 00000000..6fd80089
--- /dev/null
+++ b/tools/htslib/tabix/test/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+nextflow.preview.dsl = 2
+include '../../../nf-core/module_testing/check_process_outputs.nf' params(params)
+include '../main.nf' params(params)
+
+// Define input channels
+input = '../../../test-datasets/tools/file.vcf.gz'
+
+// Run the workflow
+workflow {
+    tabix_index(ch_read_files)
+    // .check_output()
+}
diff --git a/tools/htslib/tabix/test/nextflow.config b/tools/htslib/tabix/test/nextflow.config
new file mode 100644
index 00000000..c137a138
--- /dev/null
+++ b/tools/htslib/tabix/test/nextflow.config
@@ -0,0 +1,2 @@
+docker.enabled = true
+params.outdir = './results'