From 5033ada17bc4f10fffbfefe980a3ebf9002ebcff Mon Sep 17 00:00:00 2001
From: Ram Sai Nanduri <sai.rama7412@gmail.com>
Date: Tue, 25 Jul 2023 12:04:11 +0200
Subject: [PATCH] Update stubs for samtools idxstats (#3665)

* Update stubs

* Update stubs for samtools idxstats

---------

Co-authored-by: Ram Nanduri <ram@MTLUCMDS1.lund.skane.se>
---
 modules/nf-core/samtools/idxstats/main.nf        | 12 ++++++++++++
 tests/modules/nf-core/samtools/idxstats/main.nf  | 15 ++++++++++++---
 tests/modules/nf-core/samtools/idxstats/test.yml |  9 +++++++++
 3 files changed, 33 insertions(+), 3 deletions(-)

diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf
index a257d7002e4..83c7c34b9d9 100644
--- a/modules/nf-core/samtools/idxstats/main.nf
+++ b/modules/nf-core/samtools/idxstats/main.nf
@@ -33,4 +33,16 @@ process SAMTOOLS_IDXSTATS {
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    touch ${prefix}.idxstats
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
 }
diff --git a/tests/modules/nf-core/samtools/idxstats/main.nf b/tests/modules/nf-core/samtools/idxstats/main.nf
index 4a29252eb3b..9a0f5aec23c 100644
--- a/tests/modules/nf-core/samtools/idxstats/main.nf
+++ b/tests/modules/nf-core/samtools/idxstats/main.nf
@@ -6,9 +6,18 @@ include { SAMTOOLS_IDXSTATS } from '../../../../../modules/nf-core/samtools/idxs
 
 workflow test_samtools_idxstats {
     input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
-            ]
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+    ]
+
+    SAMTOOLS_IDXSTATS ( input )
+}
+
+workflow test_samtools_idxstats_stub {
+    input = [ [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+    ]
 
     SAMTOOLS_IDXSTATS ( input )
 }
diff --git a/tests/modules/nf-core/samtools/idxstats/test.yml b/tests/modules/nf-core/samtools/idxstats/test.yml
index d2c6f94d2ab..f2be79899fc 100644
--- a/tests/modules/nf-core/samtools/idxstats/test.yml
+++ b/tests/modules/nf-core/samtools/idxstats/test.yml
@@ -7,3 +7,12 @@
     - path: output/samtools/test.idxstats
       md5sum: df60a8c8d6621100d05178c93fb053a2
     - path: output/samtools/versions.yml
+
+- name: samtools idxstats test_samtools_idxstats_stub
+  command: nextflow run ./tests/modules/nf-core/samtools/idxstats -entry test_samtools_idxstats_stub -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/idxstats/nextflow.config -stub
+  tags:
+    - samtools/idxstats
+    - samtools
+  files:
+    - path: output/samtools/test.idxstats
+    - path: output/samtools/versions.yml