From 1abe23e1592f7cf6a3724589061827df0d8a0252 Mon Sep 17 00:00:00 2001
From: "Maxime U. Garcia" <max.u.garcia@gmail.com>
Date: Wed, 10 Nov 2021 10:30:48 +0100
Subject: [PATCH] Add CRAM to samtools/index (#1049)

* feat: update samtools/index

* feat: add test

* fix: lint

* fix: output file + md5
---
 modules/samtools/index/main.nf        | 11 ++++++-----
 modules/samtools/index/meta.yml       |  5 +++++
 tests/modules/samtools/index/main.nf  | 13 +++++++++++--
 tests/modules/samtools/index/test.yml |  9 +++++++++
 4 files changed, 31 insertions(+), 7 deletions(-)

diff --git a/modules/samtools/index/main.nf b/modules/samtools/index/main.nf
index febbc11c..62254bc8 100644
--- a/modules/samtools/index/main.nf
+++ b/modules/samtools/index/main.nf
@@ -19,16 +19,17 @@ process SAMTOOLS_INDEX {
     }
 
     input:
-    tuple val(meta), path(bam)
+    tuple val(meta), path(input)
 
     output:
-    tuple val(meta), path("*.bai"), optional:true, emit: bai
-    tuple val(meta), path("*.csi"), optional:true, emit: csi
-    path  "versions.yml"          , emit: versions
+    tuple val(meta), path("*.bai") , optional:true, emit: bai
+    tuple val(meta), path("*.crai"), optional:true, emit: crai
+    tuple val(meta), path("*.csi") , optional:true, emit: csi
+    path  "versions.yml"           , emit: versions
 
     script:
     """
-    samtools index $options.args $bam
+    samtools index $options.args $input
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
         ${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
diff --git a/modules/samtools/index/meta.yml b/modules/samtools/index/meta.yml
index 988e8f53..0905b3cd 100644
--- a/modules/samtools/index/meta.yml
+++ b/modules/samtools/index/meta.yml
@@ -35,6 +35,10 @@ output:
         type: file
         description: BAM/CRAM/SAM index file
         pattern: "*.{bai,crai,sai}"
+    - crai:
+        type: file
+        description: BAM/CRAM/SAM index file
+        pattern: "*.{bai,crai,sai}"
     - csi:
         type: file
         description: CSI index file
@@ -46,3 +50,4 @@ output:
 authors:
     - "@drpatelh"
     - "@ewels"
+    - "@maxulysse"
diff --git a/tests/modules/samtools/index/main.nf b/tests/modules/samtools/index/main.nf
index be9014e0..737936fb 100644
--- a/tests/modules/samtools/index/main.nf
+++ b/tests/modules/samtools/index/main.nf
@@ -2,8 +2,9 @@
 
 nextflow.enable.dsl = 2
 
-include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_BAI } from '../../../../modules/samtools/index/main.nf' addParams( options: [:] )
-include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_CSI } from '../../../../modules/samtools/index/main.nf' addParams( options: [args:'-c'] )
+include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_BAI  } from '../../../../modules/samtools/index/main.nf' addParams( options: [:] )
+include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_CRAI } from '../../../../modules/samtools/index/main.nf' addParams( options: [:] )
+include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_CSI  } from '../../../../modules/samtools/index/main.nf' addParams( options: [args:'-c'] )
 
 workflow test_samtools_index_bai {
     input = [ [ id:'test', single_end:false ], // meta map
@@ -13,6 +14,14 @@ workflow test_samtools_index_bai {
     SAMTOOLS_INDEX_BAI ( input )
 }
 
+workflow test_samtools_index_crai {
+    input = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true)
+            ]
+
+    SAMTOOLS_INDEX_CRAI ( input )
+}
+
 workflow test_samtools_index_csi {
     input = [ [ id:'test', single_end:false ], // meta map
                 file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
diff --git a/tests/modules/samtools/index/test.yml b/tests/modules/samtools/index/test.yml
index 31941dd6..66ab8211 100644
--- a/tests/modules/samtools/index/test.yml
+++ b/tests/modules/samtools/index/test.yml
@@ -7,6 +7,15 @@
     - path: output/samtools/test.paired_end.sorted.bam.bai
       md5sum: 704c10dd1326482448ca3073fdebc2f4
 
+- name: samtools index crai
+  command: nextflow run tests/modules/samtools/index -entry test_samtools_index_crai -c tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools/index
+  files:
+    - path: output/samtools/test.paired_end.recalibrated.sorted.cram.crai
+      md5sum: 537e3d8c937bcc4e34e1cf47cd71d484
+
 - name: samtools index csi
   command: nextflow run tests/modules/samtools/index -entry test_samtools_index_csi -c tests/config/nextflow.config
   tags: