From a55519ee954a3f7bd6e228254ecc7204d9eee877 Mon Sep 17 00:00:00 2001
From: DavideBag <96130443+DavideBag@users.noreply.github.com>
Date: Tue, 26 Mar 2024 17:28:17 +0100
Subject: [PATCH] Plink linkage disequilibrium additional output (#5388)

* adding outputs

* output and style correction

* fixing stub

---------

Co-authored-by: Francesco Lescai <53608000+lescai@users.noreply.github.com>
---
 modules/nf-core/plink/ld/main.nf              |  8 +++++--
 modules/nf-core/plink/ld/meta.yml             | 11 +++++++--
 modules/nf-core/plink/ld/tests/main.nf.test   | 18 ++++++++++----
 .../nf-core/plink/ld/tests/main.nf.test.snap  | 24 +++++++++++++++----
 4 files changed, 49 insertions(+), 12 deletions(-)

diff --git a/modules/nf-core/plink/ld/main.nf b/modules/nf-core/plink/ld/main.nf
index 72493681d97..b6315689d79 100644
--- a/modules/nf-core/plink/ld/main.nf
+++ b/modules/nf-core/plink/ld/main.nf
@@ -14,8 +14,10 @@ process PLINK_LD {
     tuple val(meta4), path(snpfile)
 
     output:
-    tuple val(meta), path("*.ld")    , emit: ld
-    path "versions.yml"              , emit: versions
+    tuple val(meta), path("*.ld")   , emit: ld
+    tuple val(meta), path("*.log")  , emit: log
+    tuple val(meta), path("*.nosex"), emit: nosex, optional:true
+    path "versions.yml"             , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -83,6 +85,8 @@ process PLINK_LD {
     }
     """
     touch ${prefix}.ld
+    touch ${prefix}.log
+    touch ${prefix}.nosex
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/plink/ld/meta.yml b/modules/nf-core/plink/ld/meta.yml
index b948141ffd7..3e16ab4b6bc 100644
--- a/modules/nf-core/plink/ld/meta.yml
+++ b/modules/nf-core/plink/ld/meta.yml
@@ -38,7 +38,7 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-        meta is associated to phenotype files input
+        meta is associated to randomly selected snp files input
   - bed:
       type: file
       description: PLINK binary biallelic genotype table file
@@ -76,11 +76,18 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-
   - ld:
       type: file
       description: |
         The output of a linkage disequilibrium analysis in PLINK typically includes a table showing variant pairs and their associated LD values, often expressed as R².
+  - log:
+      type: file
+      description: |
+        Log file of the ld process
+  - nosex:
+      type: file
+      description: |
+        Ambiguous sex ID file
 authors:
   - "@davidebag"
 maintainers:
diff --git a/modules/nf-core/plink/ld/tests/main.nf.test b/modules/nf-core/plink/ld/tests/main.nf.test
index d05fdb676c5..66384aae897 100644
--- a/modules/nf-core/plink/ld/tests/main.nf.test
+++ b/modules/nf-core/plink/ld/tests/main.nf.test
@@ -1,4 +1,3 @@
-
 nextflow_process {
 
     name "Test Process PLINK_LD"
@@ -35,7 +34,11 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(process.out.version).match("version") },
-                { assert snapshot(process.out.ld).match() }
+                { assert snapshot(
+                    process.out.ld,
+                    process.out.nosex
+                    ).match() },
+                { assert process.out.log.get(0).get(1) ==~ ".*/*.log" }
             )
         }
     }
@@ -66,7 +69,10 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.ld).match() }
+                { assert snapshot(
+                    process.out.ld
+                ).match() },
+            { assert process.out.log.get(0).get(1) ==~ ".*/*.log" }
             )
         }
     }
@@ -95,7 +101,11 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.ld).match() }
+                { assert snapshot(
+                    process.out.ld,
+                    process.out.nosex
+                    ).match() },
+                { assert process.out.log.get(0).get(1) ==~ ".*/*.log" }
             )
         }
     }
diff --git a/modules/nf-core/plink/ld/tests/main.nf.test.snap b/modules/nf-core/plink/ld/tests/main.nf.test.snap
index 49a979eb172..fccd93e6b4d 100644
--- a/modules/nf-core/plink/ld/tests/main.nf.test.snap
+++ b/modules/nf-core/plink/ld/tests/main.nf.test.snap
@@ -8,13 +8,21 @@
                     },
                     "test.ld:md5,647636ceb985a3ff66b17c79004d284f"
                 ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.nosex:md5,4f9aa36c44a417ff6d7caa9841e66ad9"
+                ]
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-03-20T10:33:55.438572792"
+        "timestamp": "2024-03-22T13:56:51.1545332"
     },
     "plink - binary": {
         "content": [
@@ -31,7 +39,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-03-20T10:33:36.640948294"
+        "timestamp": "2024-03-22T13:56:40.371392669"
     },
     "plink - VCF": {
         "content": [
@@ -42,13 +50,21 @@
                     },
                     "test.ld:md5,647636ceb985a3ff66b17c79004d284f"
                 ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.nosex:md5,4f9aa36c44a417ff6d7caa9841e66ad9"
+                ]
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-03-20T10:33:15.208380485"
+        "timestamp": "2024-03-22T13:56:29.029809559"
     },
     "version": {
         "content": null,
@@ -56,6 +72,6 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-03-20T10:33:15.199523947"
+        "timestamp": "2024-03-22T13:56:29.02167666"
     }
 }
\ No newline at end of file