Plink linkage disequilibrium additional output (#5388)

* adding outputs * output and style correction * fixing stub --------- Co-authored-by: Francesco Lescai <[email protected]>
nf-core · Mar 26, 2024 · a55519e · a55519e
1 parent 3234616
commit a55519e
Show file tree

Hide file tree

Showing 4 changed files with 49 additions and 12 deletions.
diff --git 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
@@ -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
@@ -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