From b5da92285bf155cb49f4a46b0771f571cceebe9f Mon Sep 17 00:00:00 2001
From: Julia Amorim <apoloniojulia@gmail.com>
Date: Wed, 26 Mar 2025 17:03:24 -0300
Subject: [PATCH 01/20] add gcta/gsmr tool

---
 modules/nf-core/gcta/gsmr/environment.yml     |   7 ++
 modules/nf-core/gcta/gsmr/main.nf             |  63 +++++++++++
 modules/nf-core/gcta/gsmr/meta.yml            |  67 ++++++++++++
 modules/nf-core/gcta/gsmr/nextflow.config     |  12 +++
 modules/nf-core/gcta/gsmr/tests/main.nf.test  | 102 ++++++++++++++++++
 .../nf-core/gcta/gsmr/tests/main.nf.test.snap |  38 +++++++
 6 files changed, 289 insertions(+)
 create mode 100644 modules/nf-core/gcta/gsmr/environment.yml
 create mode 100644 modules/nf-core/gcta/gsmr/main.nf
 create mode 100644 modules/nf-core/gcta/gsmr/meta.yml
 create mode 100644 modules/nf-core/gcta/gsmr/nextflow.config
 create mode 100644 modules/nf-core/gcta/gsmr/tests/main.nf.test
 create mode 100644 modules/nf-core/gcta/gsmr/tests/main.nf.test.snap

diff --git a/modules/nf-core/gcta/gsmr/environment.yml b/modules/nf-core/gcta/gsmr/environment.yml
new file mode 100644
index 000000000000..543862387283
--- /dev/null
+++ b/modules/nf-core/gcta/gsmr/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::gcta=1.94.1"
diff --git a/modules/nf-core/gcta/gsmr/main.nf b/modules/nf-core/gcta/gsmr/main.nf
new file mode 100644
index 000000000000..6d3849c36680
--- /dev/null
+++ b/modules/nf-core/gcta/gsmr/main.nf
@@ -0,0 +1,63 @@
+process GCTA_GSMR {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gcta:1.94.1--h9ee0642_0':
+        'quay.io/biocontainers/gcta:1.94.1--h9ee0642_0' }"
+
+    input:
+
+    tuple val(meta), path(exposure)
+    tuple val(meta2), path(outcome)
+    path(reference)
+
+    output:
+    path "${meta.id}_${meta2.id}.log", emit: log
+    path "${meta.id}_${meta2.id}.gsmr", emit: gsmr
+    path "${meta.id}_${meta2.id}.eff_plot.gz", emit: eff_plot, optional: true
+    path "${meta.id}_${meta2.id}.mono.badsnps", emit: mono_badsnps, optional: true
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    echo "${meta.id} ${exposure}" > ${meta.id}.input.txt
+    echo "${meta2.id} ${outcome}" > outcome.txt
+    file=\$(ls $reference | sed 's/\\.[^.]*\$//')
+    echo "${reference}/\$file" | head -n1 > reference.txt
+
+    gcta  \
+    --mbfile reference.txt  \
+    --gsmr-file ${meta.id}.input.txt outcome.txt \
+    --out "${meta.id}_${meta2.id}"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+            gcta: \$(gcta 2>&1 | awk '/no analysis has been launched/ {exit 0} {print}' | sed -n 's/.*version \\(v[0-9.]*\\).*/\\1/p')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    touch ${meta.id}_${meta2.id}.log
+    touch ${meta.id}_${meta2.id}.gsmr
+    touch ${meta.id}_${meta2.id}.mono.badsnps
+    echo "" | gzip > ${meta.id}_${meta2.id}.eff_plot.gz
+
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+            gcta: \$(gcta 2>&1 | awk '/no analysis has been launched/ {exit 0} {print}' | sed -n 's/.*version \\(v[0-9.]*\\).*/\\1/p')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/gcta/gsmr/meta.yml b/modules/nf-core/gcta/gsmr/meta.yml
new file mode 100644
index 000000000000..1ec6f6af4027
--- /dev/null
+++ b/modules/nf-core/gcta/gsmr/meta.yml
@@ -0,0 +1,67 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "gcta_gsmr"
+description: Module that performs a Mendelian Randomization analysis with summary data and plink bfile
+keywords:
+  - Mendelian Randomization
+  - GWAS
+  - gsmr
+tools:
+  - "gcta":
+      description: "GCTA (Genome-wide Complex Trait Analysis) estimates the proportion of phenotypic variance explained by all genome-wide SNPs for complex traits."
+      homepage: "https://yanglab.westlake.edu.cn/software/gcta"
+      documentation: "https://yanglab.westlake.edu.cn/software/gcta/"
+      tool_dev_url: "https://github.com/jianyangqt/gcta"
+      doi: "10.1038/s41467-017-02317-2"
+      licence: ['GPL v3']
+      identifier: biotools:gcta
+
+input:
+  - meta:
+      type: map
+      description: Groovy Map containing sample information e.g. `[ id:'sample1' ]`
+  - exposure:
+      type: file
+      description: Exposure data file for GSMR analysis
+      pattern: "*.txt"
+  - meta2:
+      type: map
+      description: Groovy Map containing sample information for outcome e.g. `[ id:'sample2' ]`
+  - outcome:
+      type: file
+      description: Outcome data file for GSMR analysis
+      pattern: "*.txt"
+  - reference:
+      type: directory
+      description: Directory containing reference files (BED, BIM, FAM) for GCTA analysis
+      pattern: "*"
+
+output:
+  - gsmr_log:
+      type: file
+      description: Log file from GSMR analysis
+      pattern: "*.log"
+  - gsmr_res:
+      type: file
+      description: Results file from GSMR analysis
+      pattern: "*.gsmr"
+  - gsmr_effplot:
+      type: file
+      description: Effect plot from GSMR analysis (optional)
+      pattern: "*.eff_plot.gz"
+  - mono_badsnps:
+      type: file
+      description: File containing bad SNPs identified in GSMR analysis (optional)
+      pattern: "*.mono.badsnps"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@juliaapolonio"
+maintainers:
+  - "@juliaapolonio"
+
+thread_id:
+  - 1d3cb393-7630-45b3-b965-4cf5d1fc7272
diff --git a/modules/nf-core/gcta/gsmr/nextflow.config b/modules/nf-core/gcta/gsmr/nextflow.config
new file mode 100644
index 000000000000..09b1312c3a38
--- /dev/null
+++ b/modules/nf-core/gcta/gsmr/nextflow.config
@@ -0,0 +1,12 @@
+process {
+    publishDir = [
+        path: { "${params.outdir}/${task.process.tokenize(':')[-1].toLowerCase()}" },
+        mode: 'copy',
+        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+    ]
+}
+
+docker.enabled = true
+
+// Uncomment and modify the following line if you want to use a specific container
+// process.container = 'biocontainers/gcta:1.94.1--h9ee0642_0'
diff --git a/modules/nf-core/gcta/gsmr/tests/main.nf.test b/modules/nf-core/gcta/gsmr/tests/main.nf.test
new file mode 100644
index 000000000000..29ed85d7f66a
--- /dev/null
+++ b/modules/nf-core/gcta/gsmr/tests/main.nf.test
@@ -0,0 +1,102 @@
+// nf-core modules test gcta/gsmr
+nextflow_process {
+
+    name "Test Process GCTA_GSMR"
+    script "../main.nf"
+    process "GCTA_GSMR"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gcta"
+    tag "gcta/gsmr"
+
+    test("homo_sapiens - gsmr") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_exposure' ],
+                    file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/gsmr/sumstats.tsv")
+                ]
+                input[1] = [
+                    [ id:'test_outcome' ],
+                    file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/gsmr/sumstats_copy.tsv")
+                ]
+
+                // Stage individual files
+                def bedFile = file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/gsmr/bfile/bfile.bed")
+                def bimFile = file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/gsmr/bfile/bfile.bim")
+                def famFile = file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/gsmr/bfile/bfile.fam")
+
+                // Create a folder and move files into it
+                def referenceDir = file("reference")
+                referenceDir.mkdirs()
+                bedFile.copyTo(referenceDir.resolve("reference.bed"))
+                bimFile.copyTo(referenceDir.resolve("reference.bim"))
+                famFile.copyTo(referenceDir.resolve("reference.fam"))
+
+                // Pass the folder as input
+                input[2] = referenceDir                 """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(
+                process.out.gsmr,
+                process.out.eff_plot,
+                process.out.mono_badsnps
+            ).match()
+            assert path(process.out.versions.get(0)).text.contains("GSMR")
+        }
+
+    }
+
+    test("homo_sapiens - gsmr - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_exposure' ],
+                    file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/gsmr/sumstats.tsv")
+                ]
+                input[1] = [
+                    [ id:'test_outcome' ],
+                    file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/gsmr/sumstats_copy.tsv")
+                ]
+
+                // Stage individual files
+                def bedFile = file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/gsmr/bfile/bfile.bed")
+                def bimFile = file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/gsmr/bfile/bfile.bim")
+                def famFile = file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/gsmr/bfile/bfile.fam")
+
+                // Create a folder and move files into it
+                def referenceDir = file("reference")
+                referenceDir.mkdirs()
+                bedFile.copyTo(referenceDir.resolve("reference.bed"))
+                bimFile.copyTo(referenceDir.resolve("reference.bim"))
+                famFile.copyTo(referenceDir.resolve("reference.fam"))
+
+                // Pass the folder as input
+                input[2] = referenceDir                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(
+                process.out.gsmr,
+                process.out.eff_plot,
+                process.out.mono_badsnps
+            ).match()
+
+            assert path(process.out.versions.get(0)).text.contains("GSMR")
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/gcta/gsmr/tests/main.nf.test.snap b/modules/nf-core/gcta/gsmr/tests/main.nf.test.snap
new file mode 100644
index 000000000000..a6b54899deaf
--- /dev/null
+++ b/modules/nf-core/gcta/gsmr/tests/main.nf.test.snap
@@ -0,0 +1,38 @@
+{
+    "homo_sapiens - gsmr": {
+        "content": [
+            [
+                "test_exposure_test_outcome.gsmr:md5,f137c763773522ea37849d919f6de9aa"
+            ],
+            [
+                
+            ],
+            [
+                "test_exposure_test_outcome.mono.badsnps:md5,0fe7dcfd9384c40361e7009ed28098cc"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-03-26T15:38:16.042312787"
+    },
+    "homo_sapiens - gsmr - stub": {
+        "content": [
+            [
+                "test_exposure_test_outcome.gsmr:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "test_exposure_test_outcome.eff_plot.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+            ],
+            [
+                "test_exposure_test_outcome.mono.badsnps:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-03-26T15:38:25.616277161"
+    }
+}
\ No newline at end of file

From 179a1b30ac41497b58f97fc69aeb078c287f127c Mon Sep 17 00:00:00 2001
From: Julia Amorim <apoloniojulia@gmail.com>
Date: Thu, 27 Mar 2025 08:05:16 -0300
Subject: [PATCH 02/20] solve part of linting issues

---
 modules/nf-core/gcta/gsmr/main.nf                |  2 +-
 modules/nf-core/gcta/gsmr/meta.yml               | 16 ++++++++--------
 modules/nf-core/gcta/gsmr/tests/main.nf.test     |  6 ++++--
 .../nf-core/gcta/gsmr/tests/main.nf.test.snap    | 10 ++++++++--
 4 files changed, 21 insertions(+), 13 deletions(-)

diff --git a/modules/nf-core/gcta/gsmr/main.nf b/modules/nf-core/gcta/gsmr/main.nf
index 6d3849c36680..418b0b2f21b9 100644
--- a/modules/nf-core/gcta/gsmr/main.nf
+++ b/modules/nf-core/gcta/gsmr/main.nf
@@ -5,7 +5,7 @@ process GCTA_GSMR {
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/gcta:1.94.1--h9ee0642_0':
-        'quay.io/biocontainers/gcta:1.94.1--h9ee0642_0' }"
+        'biocontainers/gcta:1.94.1--h9ee0642_0' }"
 
     input:
 
diff --git a/modules/nf-core/gcta/gsmr/meta.yml b/modules/nf-core/gcta/gsmr/meta.yml
index 1ec6f6af4027..16da6c5d050a 100644
--- a/modules/nf-core/gcta/gsmr/meta.yml
+++ b/modules/nf-core/gcta/gsmr/meta.yml
@@ -32,20 +32,21 @@ input:
       description: Outcome data file for GSMR analysis
       pattern: "*.txt"
   - reference:
-      type: directory
-      description: Directory containing reference files (BED, BIM, FAM) for GCTA analysis
-      pattern: "*"
+      type: file
+      description: Reference files (BED, BIM, FAM) for GCTA analysis
+      pattern: "*.{bed,bim,fam}"
+      multiple: true
 
 output:
-  - gsmr_log:
+  - gsmr:
       type: file
       description: Log file from GSMR analysis
       pattern: "*.log"
-  - gsmr_res:
+  - gsmr:
       type: file
       description: Results file from GSMR analysis
       pattern: "*.gsmr"
-  - gsmr_effplot:
+  - eff_plot:
       type: file
       description: Effect plot from GSMR analysis (optional)
       pattern: "*.eff_plot.gz"
@@ -63,5 +64,4 @@ authors:
 maintainers:
   - "@juliaapolonio"
 
-thread_id:
-  - 1d3cb393-7630-45b3-b965-4cf5d1fc7272
+
diff --git a/modules/nf-core/gcta/gsmr/tests/main.nf.test b/modules/nf-core/gcta/gsmr/tests/main.nf.test
index 29ed85d7f66a..5f273d0fbe0b 100644
--- a/modules/nf-core/gcta/gsmr/tests/main.nf.test
+++ b/modules/nf-core/gcta/gsmr/tests/main.nf.test
@@ -46,7 +46,8 @@ nextflow_process {
             assert snapshot(
                 process.out.gsmr,
                 process.out.eff_plot,
-                process.out.mono_badsnps
+                process.out.mono_badsnps,
+                process.out.versions
             ).match()
             assert path(process.out.versions.get(0)).text.contains("GSMR")
         }
@@ -91,7 +92,8 @@ nextflow_process {
             assert snapshot(
                 process.out.gsmr,
                 process.out.eff_plot,
-                process.out.mono_badsnps
+                process.out.mono_badsnps,
+                process.out.versions
             ).match()
 
             assert path(process.out.versions.get(0)).text.contains("GSMR")
diff --git a/modules/nf-core/gcta/gsmr/tests/main.nf.test.snap b/modules/nf-core/gcta/gsmr/tests/main.nf.test.snap
index a6b54899deaf..05b8bc648eed 100644
--- a/modules/nf-core/gcta/gsmr/tests/main.nf.test.snap
+++ b/modules/nf-core/gcta/gsmr/tests/main.nf.test.snap
@@ -9,13 +9,16 @@
             ],
             [
                 "test_exposure_test_outcome.mono.badsnps:md5,0fe7dcfd9384c40361e7009ed28098cc"
+            ],
+            [
+                "versions.yml:md5,9d63b9cb692159dbd3c08b55eca5212b"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.5"
         },
-        "timestamp": "2025-03-26T15:38:16.042312787"
+        "timestamp": "2025-03-26T16:57:12.009292265"
     },
     "homo_sapiens - gsmr - stub": {
         "content": [
@@ -27,12 +30,15 @@
             ],
             [
                 "test_exposure_test_outcome.mono.badsnps:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "versions.yml:md5,9d63b9cb692159dbd3c08b55eca5212b"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.5"
         },
-        "timestamp": "2025-03-26T15:38:25.616277161"
+        "timestamp": "2025-03-26T16:57:20.670192583"
     }
 }
\ No newline at end of file

From acab75fcc3d161c4f50b558ec6bf17435ce84f2f Mon Sep 17 00:00:00 2001
From: Julia Amorim <apoloniojulia@gmail.com>
Date: Thu, 27 Mar 2025 08:23:27 -0300
Subject: [PATCH 03/20] fix identation of meta.yml

---
 modules/nf-core/gcta/gsmr/meta.yml | 91 +++++++++++++++---------------
 1 file changed, 45 insertions(+), 46 deletions(-)

diff --git a/modules/nf-core/gcta/gsmr/meta.yml b/modules/nf-core/gcta/gsmr/meta.yml
index 16da6c5d050a..9a314b26657f 100644
--- a/modules/nf-core/gcta/gsmr/meta.yml
+++ b/modules/nf-core/gcta/gsmr/meta.yml
@@ -1,67 +1,66 @@
----
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "gcta_gsmr"
-description: Module that performs a Mendelian Randomization analysis with summary data and plink bfile
+description: "Module that performs a Mendelian Randomization analysis with summary
+  data and plink bfile."
 keywords:
   - Mendelian Randomization
   - GWAS
-  - gsmr
+  - GSMR
 tools:
-  - "gcta":
-      description: "GCTA (Genome-wide Complex Trait Analysis) estimates the proportion of phenotypic variance explained by all genome-wide SNPs for complex traits."
+  - gcta:
+      description: "GCTA (Genome-wide Complex Trait Analysis) estimates the proportion
+        of phenotypic variance explained by all genome-wide SNPs for complex traits."
       homepage: "https://yanglab.westlake.edu.cn/software/gcta"
       documentation: "https://yanglab.westlake.edu.cn/software/gcta/"
       tool_dev_url: "https://github.com/jianyangqt/gcta"
       doi: "10.1038/s41467-017-02317-2"
-      licence: ['GPL v3']
-      identifier: biotools:gcta
+      licence:
+        - "GPL v3"
+      identifier: "biotools:gcta"
 
 input:
-  - meta:
-      type: map
-      description: Groovy Map containing sample information e.g. `[ id:'sample1' ]`
-  - exposure:
-      type: file
-      description: Exposure data file for GSMR analysis
-      pattern: "*.txt"
-  - meta2:
-      type: map
-      description: Groovy Map containing sample information for outcome e.g. `[ id:'sample2' ]`
-  - outcome:
-      type: file
-      description: Outcome data file for GSMR analysis
-      pattern: "*.txt"
-  - reference:
-      type: file
-      description: Reference files (BED, BIM, FAM) for GCTA analysis
-      pattern: "*.{bed,bim,fam}"
-      multiple: true
-
+  - - meta:
+        type: "map"
+        description: "Groovy Map containing sample information e.g. `[ id:'sample1'
+          ]`"
+    - exposure:
+        type: "file"
+        description: "Exposure data file for GSMR analysis."
+        pattern: "*.txt"
+  - - meta2:
+        type: "map"
+        description: "Groovy Map containing sample information for outcome e.g. `[ id:'sample2'
+          ]`"
+    - outcome:
+        type: "file"
+        description: "Outcome data file for GSMR analysis."
+        pattern: "*.txt"
+  - - reference:
+        type: "file"
+        description: "Reference files (BED, BIM, FAM) for GCTA analysis."
+        pattern: "*.{bed,bim,fam}"
+        multiple: true
 output:
+  - log:
+      - ${meta.id}_${meta2.id}.log: {}
   - gsmr:
-      type: file
-      description: Log file from GSMR analysis
-      pattern: "*.log"
-  - gsmr:
-      type: file
-      description: Results file from GSMR analysis
-      pattern: "*.gsmr"
+      - ${meta.id}_${meta2.id}.gsmr: {}
   - eff_plot:
-      type: file
-      description: Effect plot from GSMR analysis (optional)
-      pattern: "*.eff_plot.gz"
+      - ${meta.id}_${meta2.id}.eff_plot.gz:
+          type: "file"
+          description: "Effect plot from GSMR analysis (optional)."
+          pattern: "*.eff_plot.gz"
   - mono_badsnps:
-      type: file
-      description: File containing bad SNPs identified in GSMR analysis (optional)
-      pattern: "*.mono.badsnps"
+      - ${meta.id}_${meta2.id}.mono.badsnps:
+          type: "file"
+          description: "File containing bad SNPs identified in GSMR analysis (optional)."
+          pattern: "*.mono.badsnps"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-
+      - versions.yml:
+          type: "file"
+          description: "File containing software versions."
+          pattern: "versions.yml"
 authors:
   - "@juliaapolonio"
 maintainers:
   - "@juliaapolonio"
-
-

From ed697657e767a1841d8d70f68b2406ee6bfd2c25 Mon Sep 17 00:00:00 2001
From: Julia Amorim <apoloniojulia@gmail.com>
Date: Thu, 27 Mar 2025 08:38:42 -0300
Subject: [PATCH 04/20] fix all linting issues

---
 modules/nf-core/gcta/gsmr/meta.yml | 84 +++++++++++++++++-------------
 1 file changed, 49 insertions(+), 35 deletions(-)

diff --git a/modules/nf-core/gcta/gsmr/meta.yml b/modules/nf-core/gcta/gsmr/meta.yml
index 9a314b26657f..90345ef8406f 100644
--- a/modules/nf-core/gcta/gsmr/meta.yml
+++ b/modules/nf-core/gcta/gsmr/meta.yml
@@ -1,65 +1,79 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
-name: "gcta_gsmr"
-description: "Module that performs a Mendelian Randomization analysis with summary
-  data and plink bfile."
+name: gcta_gsmr
+description: Module that performs a Mendelian Randomization analysis with summary
+  data and plink bfile.
 keywords:
   - Mendelian Randomization
   - GWAS
-  - GSMR
+  - gsmr
 tools:
   - gcta:
-      description: "GCTA (Genome-wide Complex Trait Analysis) estimates the proportion
-        of phenotypic variance explained by all genome-wide SNPs for complex traits."
-      homepage: "https://yanglab.westlake.edu.cn/software/gcta"
-      documentation: "https://yanglab.westlake.edu.cn/software/gcta/"
-      tool_dev_url: "https://github.com/jianyangqt/gcta"
-      doi: "10.1038/s41467-017-02317-2"
-      licence:
-        - "GPL v3"
-      identifier: "biotools:gcta"
-
+      description: |
+        GCTA (Genome-wide Complex Trait Analysis) estimates the proportion of phenotypic variance explained
+        by all genome-wide SNPs for complex traits.
+      homepage: https://yanglab.westlake.edu.cn/software/gcta
+      documentation: https://yanglab.westlake.edu.cn/software/gcta/
+      tool_dev_url: https://github.com/jianyangqt/gcta
+      doi: 10.1038/s41467-017-02317-2
+      licence: ["GPL v3"]
+      identifier: biotools:gcta
 input:
   - - meta:
-        type: "map"
-        description: "Groovy Map containing sample information e.g. `[ id:'sample1'
-          ]`"
+        type: map
+        description: |
+          Groovy Map containing sample information for exposure
+          e.g. [ id:'sample1' ]
     - exposure:
-        type: "file"
-        description: "Exposure data file for GSMR analysis."
+        type: file
+        description: Exposure data file for GSMR analysis
         pattern: "*.txt"
+        ontologies: []
   - - meta2:
-        type: "map"
-        description: "Groovy Map containing sample information for outcome e.g. `[ id:'sample2'
-          ]`"
+        type: map
+        description: |
+          Groovy Map containing sample information for outcome
+          e.g. [ id:'sample2' ]
     - outcome:
-        type: "file"
-        description: "Outcome data file for GSMR analysis."
+        type: file
+        description: Outcome data file for GSMR analysis
         pattern: "*.txt"
+        ontologies: []
   - - reference:
-        type: "file"
-        description: "Reference files (BED, BIM, FAM) for GCTA analysis."
+        type: file
+        description: Reference files (BED, BIM, FAM) for GCTA analysis
         pattern: "*.{bed,bim,fam}"
         multiple: true
+        ontologies: []
 output:
   - log:
-      - ${meta.id}_${meta2.id}.log: {}
+      - ${meta.id}_${meta2.id}.log:
+          type: file
+          description: Log file from GSMR analysis
+          pattern: "*.log"
+          ontologies: []
   - gsmr:
-      - ${meta.id}_${meta2.id}.gsmr: {}
+      - ${meta.id}_${meta2.id}.gsmr:
+          type: file
+          description: Results file from GSMR analysis
+          pattern: "*.gsmr"
+          ontologies: []
   - eff_plot:
       - ${meta.id}_${meta2.id}.eff_plot.gz:
-          type: "file"
-          description: "Effect plot from GSMR analysis (optional)."
+          type: file
+          description: Effect plot from GSMR analysis (optional)
           pattern: "*.eff_plot.gz"
+          ontologies: []
   - mono_badsnps:
       - ${meta.id}_${meta2.id}.mono.badsnps:
-          type: "file"
-          description: "File containing bad SNPs identified in GSMR analysis (optional)."
+          type: file
+          description: File containing bad SNPs identified in GSMR analysis (optional)
           pattern: "*.mono.badsnps"
+          ontologies: []
   - versions:
       - versions.yml:
-          type: "file"
-          description: "File containing software versions."
+          type: file
+          description: File containing software versions
           pattern: "versions.yml"
+          ontologies: []
 authors:
   - "@juliaapolonio"
 maintainers:

From 6b09431a84c10eef58c50f3ad87a4f860c265c63 Mon Sep 17 00:00:00 2001
From: Julia Amorim <apoloniojulia@gmail.com>
Date: Thu, 27 Mar 2025 09:14:33 -0300
Subject: [PATCH 05/20] remove unecessary file

---
 modules/nf-core/gcta/gsmr/nextflow.config | 12 ------------
 1 file changed, 12 deletions(-)
 delete mode 100644 modules/nf-core/gcta/gsmr/nextflow.config

diff --git a/modules/nf-core/gcta/gsmr/nextflow.config b/modules/nf-core/gcta/gsmr/nextflow.config
deleted file mode 100644
index 09b1312c3a38..000000000000
--- a/modules/nf-core/gcta/gsmr/nextflow.config
+++ /dev/null
@@ -1,12 +0,0 @@
-process {
-    publishDir = [
-        path: { "${params.outdir}/${task.process.tokenize(':')[-1].toLowerCase()}" },
-        mode: 'copy',
-        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-    ]
-}
-
-docker.enabled = true
-
-// Uncomment and modify the following line if you want to use a specific container
-// process.container = 'biocontainers/gcta:1.94.1--h9ee0642_0'

From 662c58271b62f6823806a79bee2d2a0a13c05d05 Mon Sep 17 00:00:00 2001
From: Julia Amorim <apoloniojulia@gmail.com>
Date: Thu, 27 Mar 2025 09:15:34 -0300
Subject: [PATCH 06/20] fix prefix definition

---
 modules/nf-core/gcta/gsmr/main.nf | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/modules/nf-core/gcta/gsmr/main.nf b/modules/nf-core/gcta/gsmr/main.nf
index 418b0b2f21b9..3d9c5887ddb1 100644
--- a/modules/nf-core/gcta/gsmr/main.nf
+++ b/modules/nf-core/gcta/gsmr/main.nf
@@ -9,14 +9,14 @@ process GCTA_GSMR {
 
     input:
 
-    tuple val(meta), path(exposure)
+    tuple val(meta),  path(exposure)
     tuple val(meta2), path(outcome)
     path(reference)
 
     output:
-    path "${meta.id}_${meta2.id}.log", emit: log
-    path "${meta.id}_${meta2.id}.gsmr", emit: gsmr
-    path "${meta.id}_${meta2.id}.eff_plot.gz", emit: eff_plot, optional: true
+    path "${meta.id}_${meta2.id}.log"         , emit: log
+    path "${meta.id}_${meta2.id}.gsmr"        , emit: gsmr
+    path "${meta.id}_${meta2.id}.eff_plot.gz" , emit: eff_plot, optional: true
     path "${meta.id}_${meta2.id}.mono.badsnps", emit: mono_badsnps, optional: true
     path "versions.yml"           , emit: versions
 
@@ -24,8 +24,8 @@ process GCTA_GSMR {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def args   = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}_${meta2.id}"
 
     """
     echo "${meta.id} ${exposure}" > ${meta.id}.input.txt
@@ -36,7 +36,7 @@ process GCTA_GSMR {
     gcta  \
     --mbfile reference.txt  \
     --gsmr-file ${meta.id}.input.txt outcome.txt \
-    --out "${meta.id}_${meta2.id}"
+    --out "${prefix}"
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -45,14 +45,14 @@ process GCTA_GSMR {
     """
 
     stub:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def args   = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}_${meta2.id}"
 
     """
-    touch ${meta.id}_${meta2.id}.log
-    touch ${meta.id}_${meta2.id}.gsmr
-    touch ${meta.id}_${meta2.id}.mono.badsnps
-    echo "" | gzip > ${meta.id}_${meta2.id}.eff_plot.gz
+    touch ${prefix}.log
+    touch ${prefix}.gsmr
+    touch ${prefix}.mono.badsnps
+    echo "" | gzip > ${prefix}.eff_plot.gz
 
 
     cat <<-END_VERSIONS > versions.yml

From 5f3af7c7c8ebd485fb933bdee85027009ab4b490 Mon Sep 17 00:00:00 2001
From: Julia Amorim <apoloniojulia@gmail.com>
Date: Thu, 27 Mar 2025 09:21:19 -0300
Subject: [PATCH 07/20] fix harshil alignment

---
 modules/nf-core/gcta/gsmr/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/gcta/gsmr/main.nf b/modules/nf-core/gcta/gsmr/main.nf
index 3d9c5887ddb1..2dd5dcd452fa 100644
--- a/modules/nf-core/gcta/gsmr/main.nf
+++ b/modules/nf-core/gcta/gsmr/main.nf
@@ -9,7 +9,7 @@ process GCTA_GSMR {
 
     input:
 
-    tuple val(meta),  path(exposure)
+    tuple val(meta) , path(exposure)
     tuple val(meta2), path(outcome)
     path(reference)
 
@@ -18,7 +18,7 @@ process GCTA_GSMR {
     path "${meta.id}_${meta2.id}.gsmr"        , emit: gsmr
     path "${meta.id}_${meta2.id}.eff_plot.gz" , emit: eff_plot, optional: true
     path "${meta.id}_${meta2.id}.mono.badsnps", emit: mono_badsnps, optional: true
-    path "versions.yml"           , emit: versions
+    path "versions.yml"                       , emit: versions
 
     when:
     task.ext.when == null || task.ext.when

From 5d734e06be0fb1d3a54c628f58319e81e60d24a1 Mon Sep 17 00:00:00 2001
From: Julia Amorim <apoloniojulia@gmail.com>
Date: Thu, 3 Apr 2025 09:18:11 -0300
Subject: [PATCH 08/20] address daniel suggestions

---
 modules/nf-core/gcta/gsmr/main.nf | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/modules/nf-core/gcta/gsmr/main.nf b/modules/nf-core/gcta/gsmr/main.nf
index 2dd5dcd452fa..8ce26b67f7f1 100644
--- a/modules/nf-core/gcta/gsmr/main.nf
+++ b/modules/nf-core/gcta/gsmr/main.nf
@@ -8,7 +8,6 @@ process GCTA_GSMR {
         'biocontainers/gcta:1.94.1--h9ee0642_0' }"
 
     input:
-
     tuple val(meta) , path(exposure)
     tuple val(meta2), path(outcome)
     path(reference)
@@ -33,10 +32,11 @@ process GCTA_GSMR {
     file=\$(ls $reference | sed 's/\\.[^.]*\$//')
     echo "${reference}/\$file" | head -n1 > reference.txt
 
-    gcta  \
-    --mbfile reference.txt  \
-    --gsmr-file ${meta.id}.input.txt outcome.txt \
-    --out "${prefix}"
+    gcta  \\
+        $args \\
+        --mbfile reference.txt  \\
+        --gsmr-file ${meta.id}.input.txt outcome.txt \\
+        --out "${prefix}"
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

From fff21d87d45ed95447b0a0bdf9945fc9bf623d40 Mon Sep 17 00:00:00 2001
From: Julia Apolonio <apoloniojulia@gmail.com>
Date: Thu, 3 Apr 2025 09:22:14 -0300
Subject: [PATCH 09/20] Apply suggestions from code review
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>
---
 modules/nf-core/gcta/gsmr/main.nf            | 11 ++++-------
 modules/nf-core/gcta/gsmr/tests/main.nf.test |  7 ++++---
 2 files changed, 8 insertions(+), 10 deletions(-)

diff --git a/modules/nf-core/gcta/gsmr/main.nf b/modules/nf-core/gcta/gsmr/main.nf
index 8ce26b67f7f1..40e6df91b4c0 100644
--- a/modules/nf-core/gcta/gsmr/main.nf
+++ b/modules/nf-core/gcta/gsmr/main.nf
@@ -13,10 +13,10 @@ process GCTA_GSMR {
     path(reference)
 
     output:
-    path "${meta.id}_${meta2.id}.log"         , emit: log
-    path "${meta.id}_${meta2.id}.gsmr"        , emit: gsmr
-    path "${meta.id}_${meta2.id}.eff_plot.gz" , emit: eff_plot, optional: true
-    path "${meta.id}_${meta2.id}.mono.badsnps", emit: mono_badsnps, optional: true
+    path "*.log"         , emit: log
+    path "*.gsmr"        , emit: gsmr
+    path "*.eff_plot.gz" , emit: eff_plot, optional: true
+    path "*.mono.badsnps", emit: mono_badsnps, optional: true
     path "versions.yml"                       , emit: versions
 
     when:
@@ -25,7 +25,6 @@ process GCTA_GSMR {
     script:
     def args   = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}_${meta2.id}"
-
     """
     echo "${meta.id} ${exposure}" > ${meta.id}.input.txt
     echo "${meta2.id} ${outcome}" > outcome.txt
@@ -47,14 +46,12 @@ process GCTA_GSMR {
     stub:
     def args   = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}_${meta2.id}"
-
     """
     touch ${prefix}.log
     touch ${prefix}.gsmr
     touch ${prefix}.mono.badsnps
     echo "" | gzip > ${prefix}.eff_plot.gz
 
-
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
             gcta: \$(gcta 2>&1 | awk '/no analysis has been launched/ {exit 0} {print}' | sed -n 's/.*version \\(v[0-9.]*\\).*/\\1/p')
diff --git a/modules/nf-core/gcta/gsmr/tests/main.nf.test b/modules/nf-core/gcta/gsmr/tests/main.nf.test
index 5f273d0fbe0b..3edfeec456c0 100644
--- a/modules/nf-core/gcta/gsmr/tests/main.nf.test
+++ b/modules/nf-core/gcta/gsmr/tests/main.nf.test
@@ -1,4 +1,3 @@
-// nf-core modules test gcta/gsmr
 nextflow_process {
 
     name "Test Process GCTA_GSMR"
@@ -37,7 +36,8 @@ nextflow_process {
                 famFile.copyTo(referenceDir.resolve("reference.fam"))
 
                 // Pass the folder as input
-                input[2] = referenceDir                 """
+                input[2] = referenceDir                 
+                """
             }
         }
 
@@ -83,7 +83,8 @@ nextflow_process {
                 famFile.copyTo(referenceDir.resolve("reference.fam"))
 
                 // Pass the folder as input
-                input[2] = referenceDir                """
+                input[2] = referenceDir               
+                """
             }
         }
 

From dacd85209b4e33c1f34673fe3fd6f069102c1342 Mon Sep 17 00:00:00 2001
From: Julia Amorim <apoloniojulia@gmail.com>
Date: Thu, 3 Apr 2025 09:39:17 -0300
Subject: [PATCH 10/20] fix linting

---
 modules/nf-core/gcta/gsmr/package-lock.json |  6 +++++
 modules/nf-core/gcta/gsmr/run_gcta_gsmr.nf  | 28 +++++++++++++++++++++
 2 files changed, 34 insertions(+)
 create mode 100644 modules/nf-core/gcta/gsmr/package-lock.json
 create mode 100644 modules/nf-core/gcta/gsmr/run_gcta_gsmr.nf

diff --git a/modules/nf-core/gcta/gsmr/package-lock.json b/modules/nf-core/gcta/gsmr/package-lock.json
new file mode 100644
index 000000000000..2efcc1c4a954
--- /dev/null
+++ b/modules/nf-core/gcta/gsmr/package-lock.json
@@ -0,0 +1,6 @@
+{
+  "name": "gsmr",
+  "lockfileVersion": 3,
+  "requires": true,
+  "packages": {}
+}
diff --git a/modules/nf-core/gcta/gsmr/run_gcta_gsmr.nf b/modules/nf-core/gcta/gsmr/run_gcta_gsmr.nf
new file mode 100644
index 000000000000..5683b66d76b2
--- /dev/null
+++ b/modules/nf-core/gcta/gsmr/run_gcta_gsmr.nf
@@ -0,0 +1,28 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+// Import the GCTA_GSMR module
+include { GCTA_GSMR } from './'
+
+// Define the workflow
+workflow {
+    // Create input channels
+    exposure_ch = Channel.of([[id: "exposure"], [file(params.exposure)]])
+    outcome_ch = Channel.of([[id: "outcome"], [file(params.outcome)]])
+
+
+    // Run GCTA_GSMR
+
+    GCTA_GSMR (
+        exposure_ch,
+        outcome_ch,
+        params.reference
+    )
+
+    // Publish results
+    GCTA_GSMR.out.gsmr_log.collectFile(name: 'gsmr_logs.txt', storeDir: params.outdir)
+    GCTA_GSMR.out.gsmr_res.collectFile(name: 'gsmr_results.txt', storeDir: params.outdir)
+    GCTA_GSMR.out.gsmr_effplot.collectFile(name: 'gsmr_effplots.txt', storeDir: params.outdir)
+    GCTA_GSMR.out.versions.collectFile(name: 'software_versions.yml', storeDir: params.outdir)
+}

From a8d926fc7224a0214cc7990f7f630aade26f8d8f Mon Sep 17 00:00:00 2001
From: Julia Amorim <apoloniojulia@gmail.com>
Date: Thu, 3 Apr 2025 09:51:22 -0300
Subject: [PATCH 11/20] delete unnecessary files

---
 modules/nf-core/gcta/gsmr/package-lock.json |  6 -----
 modules/nf-core/gcta/gsmr/run_gcta_gsmr.nf  | 28 ---------------------
 2 files changed, 34 deletions(-)
 delete mode 100644 modules/nf-core/gcta/gsmr/package-lock.json
 delete mode 100644 modules/nf-core/gcta/gsmr/run_gcta_gsmr.nf

diff --git a/modules/nf-core/gcta/gsmr/package-lock.json b/modules/nf-core/gcta/gsmr/package-lock.json
deleted file mode 100644
index 2efcc1c4a954..000000000000
--- a/modules/nf-core/gcta/gsmr/package-lock.json
+++ /dev/null
@@ -1,6 +0,0 @@
-{
-  "name": "gsmr",
-  "lockfileVersion": 3,
-  "requires": true,
-  "packages": {}
-}
diff --git a/modules/nf-core/gcta/gsmr/run_gcta_gsmr.nf b/modules/nf-core/gcta/gsmr/run_gcta_gsmr.nf
deleted file mode 100644
index 5683b66d76b2..000000000000
--- a/modules/nf-core/gcta/gsmr/run_gcta_gsmr.nf
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-// Import the GCTA_GSMR module
-include { GCTA_GSMR } from './'
-
-// Define the workflow
-workflow {
-    // Create input channels
-    exposure_ch = Channel.of([[id: "exposure"], [file(params.exposure)]])
-    outcome_ch = Channel.of([[id: "outcome"], [file(params.outcome)]])
-
-
-    // Run GCTA_GSMR
-
-    GCTA_GSMR (
-        exposure_ch,
-        outcome_ch,
-        params.reference
-    )
-
-    // Publish results
-    GCTA_GSMR.out.gsmr_log.collectFile(name: 'gsmr_logs.txt', storeDir: params.outdir)
-    GCTA_GSMR.out.gsmr_res.collectFile(name: 'gsmr_results.txt', storeDir: params.outdir)
-    GCTA_GSMR.out.gsmr_effplot.collectFile(name: 'gsmr_effplots.txt', storeDir: params.outdir)
-    GCTA_GSMR.out.versions.collectFile(name: 'software_versions.yml', storeDir: params.outdir)
-}

From 8ee10830fc5b3cbe8613316ff57bc4296f221e5e Mon Sep 17 00:00:00 2001
From: Julia Amorim <apoloniojulia@gmail.com>
Date: Thu, 3 Apr 2025 09:53:35 -0300
Subject: [PATCH 12/20] fix one linting issue

---
 modules/nf-core/gcta/gsmr/meta.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/gcta/gsmr/meta.yml b/modules/nf-core/gcta/gsmr/meta.yml
index 90345ef8406f..60175f773e6b 100644
--- a/modules/nf-core/gcta/gsmr/meta.yml
+++ b/modules/nf-core/gcta/gsmr/meta.yml
@@ -45,25 +45,25 @@ input:
         ontologies: []
 output:
   - log:
-      - ${meta.id}_${meta2.id}.log:
+      - "*.log":
           type: file
           description: Log file from GSMR analysis
           pattern: "*.log"
           ontologies: []
   - gsmr:
-      - ${meta.id}_${meta2.id}.gsmr:
+      - "*.gsmr":
           type: file
           description: Results file from GSMR analysis
           pattern: "*.gsmr"
           ontologies: []
   - eff_plot:
-      - ${meta.id}_${meta2.id}.eff_plot.gz:
+      - "*.eff_plot.gz":
           type: file
           description: Effect plot from GSMR analysis (optional)
           pattern: "*.eff_plot.gz"
           ontologies: []
   - mono_badsnps:
-      - ${meta.id}_${meta2.id}.mono.badsnps:
+      - "*.mono.badsnps":
           type: file
           description: File containing bad SNPs identified in GSMR analysis (optional)
           pattern: "*.mono.badsnps"

From 0431c2bce1e489f3a355aa276634459ec0d77cc2 Mon Sep 17 00:00:00 2001
From: Julia Amorim <apoloniojulia@gmail.com>
Date: Thu, 3 Apr 2025 10:03:25 -0300
Subject: [PATCH 13/20] change meta.yml according to main

---
 modules/nf-core/gcta/gsmr/main.nf | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/gcta/gsmr/main.nf b/modules/nf-core/gcta/gsmr/main.nf
index 40e6df91b4c0..129faa4369fb 100644
--- a/modules/nf-core/gcta/gsmr/main.nf
+++ b/modules/nf-core/gcta/gsmr/main.nf
@@ -13,10 +13,10 @@ process GCTA_GSMR {
     path(reference)
 
     output:
-    path "*.log"         , emit: log
-    path "*.gsmr"        , emit: gsmr
-    path "*.eff_plot.gz" , emit: eff_plot, optional: true
-    path "*.mono.badsnps", emit: mono_badsnps, optional: true
+    path "${meta.id}_${meta2.id}.log"         , emit: log
+    path "${meta.id}_${meta2.id}.gsmr"        , emit: gsmr
+    path "${meta.id}_${meta2.id}.eff_plot.gz" , emit: eff_plot, optional: true
+    path "${meta.id}_${meta2.id}.mono.badsnps", emit: mono_badsnps, optional: true
     path "versions.yml"                       , emit: versions
 
     when:

From 1086cef1b6f27991d9e2883497d622635c075c96 Mon Sep 17 00:00:00 2001
From: Julia Amorim <apoloniojulia@gmail.com>
Date: Thu, 3 Apr 2025 10:09:40 -0300
Subject: [PATCH 14/20] forgot to add meta.yml

---
 modules/nf-core/gcta/gsmr/meta.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/gcta/gsmr/meta.yml b/modules/nf-core/gcta/gsmr/meta.yml
index 60175f773e6b..90345ef8406f 100644
--- a/modules/nf-core/gcta/gsmr/meta.yml
+++ b/modules/nf-core/gcta/gsmr/meta.yml
@@ -45,25 +45,25 @@ input:
         ontologies: []
 output:
   - log:
-      - "*.log":
+      - ${meta.id}_${meta2.id}.log:
           type: file
           description: Log file from GSMR analysis
           pattern: "*.log"
           ontologies: []
   - gsmr:
-      - "*.gsmr":
+      - ${meta.id}_${meta2.id}.gsmr:
           type: file
           description: Results file from GSMR analysis
           pattern: "*.gsmr"
           ontologies: []
   - eff_plot:
-      - "*.eff_plot.gz":
+      - ${meta.id}_${meta2.id}.eff_plot.gz:
           type: file
           description: Effect plot from GSMR analysis (optional)
           pattern: "*.eff_plot.gz"
           ontologies: []
   - mono_badsnps:
-      - "*.mono.badsnps":
+      - ${meta.id}_${meta2.id}.mono.badsnps:
           type: file
           description: File containing bad SNPs identified in GSMR analysis (optional)
           pattern: "*.mono.badsnps"

From 7755b75131b5f3c3d62915e616fdd788323d5e6a Mon Sep 17 00:00:00 2001
From: Julia Amorim <apoloniojulia@gmail.com>
Date: Thu, 3 Apr 2025 11:54:56 -0300
Subject: [PATCH 15/20] change output format to tuple

---
 modules/nf-core/gcta/gsmr/main.nf            | 10 ++--
 modules/nf-core/gcta/gsmr/meta.yml           | 53 +++++++++++++++-----
 modules/nf-core/gcta/gsmr/tests/main.nf.test |  5 +-
 3 files changed, 48 insertions(+), 20 deletions(-)

diff --git a/modules/nf-core/gcta/gsmr/main.nf b/modules/nf-core/gcta/gsmr/main.nf
index 129faa4369fb..7f415de0a8d5 100644
--- a/modules/nf-core/gcta/gsmr/main.nf
+++ b/modules/nf-core/gcta/gsmr/main.nf
@@ -13,11 +13,11 @@ process GCTA_GSMR {
     path(reference)
 
     output:
-    path "${meta.id}_${meta2.id}.log"         , emit: log
-    path "${meta.id}_${meta2.id}.gsmr"        , emit: gsmr
-    path "${meta.id}_${meta2.id}.eff_plot.gz" , emit: eff_plot, optional: true
-    path "${meta.id}_${meta2.id}.mono.badsnps", emit: mono_badsnps, optional: true
-    path "versions.yml"                       , emit: versions
+    tuple val(meta), val(meta2), path("*.log")          , emit: log
+    tuple val(meta), val(meta2), path("*.gsmr")         , emit: gsmr
+    tuple val(meta), val(meta2), path("*.eff_plot.gz")  , emit: eff_plot, optional: true
+    tuple val(meta), val(meta2), path("*.mono.badsnsps"), emit: mono_badsnps, optional: true
+    path "versions.yml"                                 , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/gcta/gsmr/meta.yml b/modules/nf-core/gcta/gsmr/meta.yml
index 90345ef8406f..b6d76fed1d78 100644
--- a/modules/nf-core/gcta/gsmr/meta.yml
+++ b/modules/nf-core/gcta/gsmr/meta.yml
@@ -45,35 +45,64 @@ input:
         ontologies: []
 output:
   - log:
-      - ${meta.id}_${meta2.id}.log:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information for exposure
+      - meta2:
+          type: map
+          description: |
+            Groovy Map containing sample information for outcome
+      - "*.log":
           type: file
           description: Log file from GSMR analysis
           pattern: "*.log"
-          ontologies: []
   - gsmr:
-      - ${meta.id}_${meta2.id}.gsmr:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information for exposure
+      - meta2:
+          type: map
+          description: |
+            Groovy Map containing sample information for outcome
+      - "*.gsmr":
           type: file
-          description: Results file from GSMR analysis
+          description: Result file from GSMR analysis
           pattern: "*.gsmr"
-          ontologies: []
   - eff_plot:
-      - ${meta.id}_${meta2.id}.eff_plot.gz:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information for exposure
+      - meta2:
+          type: map
+          description: |
+            Groovy Map containing sample information for outcome
+      - "*.eff_plot.gz":
           type: file
-          description: Effect plot from GSMR analysis (optional)
+          description: Effect plot file from GSMR analysis (gzipped)
           pattern: "*.eff_plot.gz"
-          ontologies: []
+          optional: true
   - mono_badsnps:
-      - ${meta.id}_${meta2.id}.mono.badsnps:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information for exposure
+      - meta2:
+          type: map
+          description: |
+            Groovy Map containing sample information for outcome
+      - "*.mono.badsnsps":
           type: file
-          description: File containing bad SNPs identified in GSMR analysis (optional)
+          description: Bad SNPs file from GSMR analysis
           pattern: "*.mono.badsnps"
-          ontologies: []
+          optional: true
   - versions:
       - versions.yml:
           type: file
           description: File containing software versions
           pattern: "versions.yml"
-          ontologies: []
 authors:
   - "@juliaapolonio"
 maintainers:
diff --git a/modules/nf-core/gcta/gsmr/tests/main.nf.test b/modules/nf-core/gcta/gsmr/tests/main.nf.test
index 3edfeec456c0..0a3c1707de9f 100644
--- a/modules/nf-core/gcta/gsmr/tests/main.nf.test
+++ b/modules/nf-core/gcta/gsmr/tests/main.nf.test
@@ -36,7 +36,7 @@ nextflow_process {
                 famFile.copyTo(referenceDir.resolve("reference.fam"))
 
                 // Pass the folder as input
-                input[2] = referenceDir                 
+                input[2] = referenceDir
                 """
             }
         }
@@ -83,7 +83,7 @@ nextflow_process {
                 famFile.copyTo(referenceDir.resolve("reference.fam"))
 
                 // Pass the folder as input
-                input[2] = referenceDir               
+                input[2] = referenceDir
                 """
             }
         }
@@ -97,7 +97,6 @@ nextflow_process {
                 process.out.versions
             ).match()
 
-            assert path(process.out.versions.get(0)).text.contains("GSMR")
         }
 
     }

From 3448573020df0d0da8b67f1cebed5d5240b5c41a Mon Sep 17 00:00:00 2001
From: juliaapolonio <apoloniojulia@gmail.com>
Date: Fri, 13 Mar 2026 16:20:14 -0300
Subject: [PATCH 16/20] migrate to topics; fix linting and nf-test

---
 modules/nf-core/gcta/gsmr/main.nf             |  20 +--
 modules/nf-core/gcta/gsmr/meta.yml            | 127 +++++++++---------
 modules/nf-core/gcta/gsmr/tests/main.nf.test  |  42 ++----
 .../nf-core/gcta/gsmr/tests/main.nf.test.snap | 120 +++++++++++++----
 4 files changed, 178 insertions(+), 131 deletions(-)

diff --git a/modules/nf-core/gcta/gsmr/main.nf b/modules/nf-core/gcta/gsmr/main.nf
index 7f415de0a8d5..44b33cab2031 100644
--- a/modules/nf-core/gcta/gsmr/main.nf
+++ b/modules/nf-core/gcta/gsmr/main.nf
@@ -13,12 +13,11 @@ process GCTA_GSMR {
     path(reference)
 
     output:
-    tuple val(meta), val(meta2), path("*.log")          , emit: log
-    tuple val(meta), val(meta2), path("*.gsmr")         , emit: gsmr
-    tuple val(meta), val(meta2), path("*.eff_plot.gz")  , emit: eff_plot, optional: true
-    tuple val(meta), val(meta2), path("*.mono.badsnsps"), emit: mono_badsnps, optional: true
-    path "versions.yml"                                 , emit: versions
-
+    tuple val(meta), val(meta2), path("*.log")           , emit: log
+    tuple val(meta), val(meta2), path("*.gsmr")          , emit: gsmr
+    tuple val(meta), val(meta2), path("*.eff_plot.gz")   , emit: eff_plot, optional: true
+    tuple val(meta), val(meta2), path("*.mono.badsnps"), emit: mono_badsnps, optional: true
+    tuple val("${task.process}"), val('gcta'), eval('gcta 2>&1 | grep -oE "v[0-9]+\\.[0-9]+\\.[0-9]+" | sed \'s/v//\''), emit: versions_gcta, topic: versions    
     when:
     task.ext.when == null || task.ext.when
 
@@ -36,11 +35,6 @@ process GCTA_GSMR {
         --mbfile reference.txt  \\
         --gsmr-file ${meta.id}.input.txt outcome.txt \\
         --out "${prefix}"
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-            gcta: \$(gcta 2>&1 | awk '/no analysis has been launched/ {exit 0} {print}' | sed -n 's/.*version \\(v[0-9.]*\\).*/\\1/p')
-    END_VERSIONS
     """
 
     stub:
@@ -52,9 +46,5 @@ process GCTA_GSMR {
     touch ${prefix}.mono.badsnps
     echo "" | gzip > ${prefix}.eff_plot.gz
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-            gcta: \$(gcta 2>&1 | awk '/no analysis has been launched/ {exit 0} {print}' | sed -n 's/.*version \\(v[0-9.]*\\).*/\\1/p')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/gcta/gsmr/meta.yml b/modules/nf-core/gcta/gsmr/meta.yml
index b6d76fed1d78..4808ba933631 100644
--- a/modules/nf-core/gcta/gsmr/meta.yml
+++ b/modules/nf-core/gcta/gsmr/meta.yml
@@ -1,108 +1,115 @@
-name: gcta_gsmr
-description: Module that performs a Mendelian Randomization analysis with summary
-  data and plink bfile.
+name: "gcta_gsmr"
+description: Perform GSMR Mendelian Randomization analysis using GCTA with
+  exposure and outcome summary statistics.
 keywords:
   - Mendelian Randomization
   - GWAS
-  - gsmr
+  - GSMR
+  - causal inference
 tools:
-  - gcta:
-      description: |
-        GCTA (Genome-wide Complex Trait Analysis) estimates the proportion of phenotypic variance explained
-        by all genome-wide SNPs for complex traits.
-      homepage: https://yanglab.westlake.edu.cn/software/gcta
-      documentation: https://yanglab.westlake.edu.cn/software/gcta/
-      tool_dev_url: https://github.com/jianyangqt/gcta
-      doi: 10.1038/s41467-017-02317-2
-      licence: ["GPL v3"]
+  - "gcta":
+      description: "GCTA implements GSMR for Mendelian Randomization using summary statistics."
+      homepage: "https://yanglab.westlake.edu.cn/software/gcta"
+      documentation: "https://yanglab.westlake.edu.cn/software/gcta/"
+      tool_dev_url: "https://github.com/jianyangqt/gcta"
+      doi: "10.1038/s41467-017-02317-2"
+      licence:
+        - "GPL v3"
       identifier: biotools:gcta
 input:
   - - meta:
         type: map
-        description: |
-          Groovy Map containing sample information for exposure
-          e.g. [ id:'sample1' ]
+        description: Groovy Map containing exposure dataset metadata
     - exposure:
         type: file
-        description: Exposure data file for GSMR analysis
+        description: Exposure GWAS summary statistics formatted for GSMR
         pattern: "*.txt"
         ontologies: []
   - - meta2:
         type: map
-        description: |
-          Groovy Map containing sample information for outcome
-          e.g. [ id:'sample2' ]
+        description: Groovy Map containing outcome dataset metadata
     - outcome:
         type: file
-        description: Outcome data file for GSMR analysis
+        description: Outcome GWAS summary statistics formatted for GSMR
         pattern: "*.txt"
         ontologies: []
-  - - reference:
-        type: file
-        description: Reference files (BED, BIM, FAM) for GCTA analysis
-        pattern: "*.{bed,bim,fam}"
-        multiple: true
-        ontologies: []
+  - reference:
+      type: file
+      description: PLINK reference dataset files (BED/BIM/FAM)
+      pattern: "*.{bed,bim,fam}"
+      multiple: true
+      ontologies: []
 output:
-  - log:
-      - meta:
+  log:
+    - - meta:
           type: map
-          description: |
-            Groovy Map containing sample information for exposure
+          description: Groovy Map containing sample information for exposure
       - meta2:
           type: map
-          description: |
-            Groovy Map containing sample information for outcome
+          description: Groovy Map containing sample information for outcome
       - "*.log":
           type: file
           description: Log file from GSMR analysis
           pattern: "*.log"
-  - gsmr:
-      - meta:
+          ontologies: []
+  gsmr:
+    - - meta:
           type: map
-          description: |
-            Groovy Map containing sample information for exposure
+          description: Groovy Map containing sample information for exposure
       - meta2:
           type: map
-          description: |
-            Groovy Map containing sample information for outcome
+          description: Groovy Map containing sample information for outcome
       - "*.gsmr":
           type: file
           description: Result file from GSMR analysis
           pattern: "*.gsmr"
-  - eff_plot:
-      - meta:
+          ontologies: []
+  eff_plot:
+    - - meta:
           type: map
-          description: |
-            Groovy Map containing sample information for exposure
+          description: Groovy Map containing sample information for exposure
       - meta2:
           type: map
-          description: |
-            Groovy Map containing sample information for outcome
+          description: Groovy Map containing sample information for outcome
       - "*.eff_plot.gz":
           type: file
-          description: Effect plot file from GSMR analysis (gzipped)
+          description: Effect plot file from GSMR analysis
           pattern: "*.eff_plot.gz"
-          optional: true
-  - mono_badsnps:
-      - meta:
+          ontologies:
+            - edam: http://edamontology.org/format_3989
+  mono_badsnps:
+    - - meta:
           type: map
-          description: |
-            Groovy Map containing sample information for exposure
+          description: Groovy Map containing sample information for exposure
       - meta2:
           type: map
-          description: |
-            Groovy Map containing sample information for outcome
-      - "*.mono.badsnsps":
+          description: Groovy Map containing sample information for outcome
+      - "*.mono.badsnps":
           type: file
           description: Bad SNPs file from GSMR analysis
           pattern: "*.mono.badsnps"
-          optional: true
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
+          ontologies: []
+  versions_gcta:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - gcta:
+          type: string
+          description: The name of the tool
+      - gcta 2>&1 | grep -oE "v[0-9]+\.[0-9]+\.[0-9]+" | sed 's/v//':
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - gcta:
+          type: string
+          description: The name of the tool
+      - gcta 2>&1 | grep -oE "v[0-9]+\.[0-9]+\.[0-9]+" | sed 's/v//':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@juliaapolonio"
 maintainers:
diff --git a/modules/nf-core/gcta/gsmr/tests/main.nf.test b/modules/nf-core/gcta/gsmr/tests/main.nf.test
index 0a3c1707de9f..9c652b308a1f 100644
--- a/modules/nf-core/gcta/gsmr/tests/main.nf.test
+++ b/modules/nf-core/gcta/gsmr/tests/main.nf.test
@@ -23,35 +23,28 @@ nextflow_process {
                     file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/gsmr/sumstats_copy.tsv")
                 ]
 
-                // Stage individual files
                 def bedFile = file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/gsmr/bfile/bfile.bed")
                 def bimFile = file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/gsmr/bfile/bfile.bim")
                 def famFile = file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/gsmr/bfile/bfile.fam")
 
-                // Create a folder and move files into it
                 def referenceDir = file("reference")
                 referenceDir.mkdirs()
                 bedFile.copyTo(referenceDir.resolve("reference.bed"))
                 bimFile.copyTo(referenceDir.resolve("reference.bim"))
                 famFile.copyTo(referenceDir.resolve("reference.fam"))
 
-                // Pass the folder as input
                 input[2] = referenceDir
                 """
             }
         }
 
         then {
-            assert process.success
-            assert snapshot(
-                process.out.gsmr,
-                process.out.eff_plot,
-                process.out.mono_badsnps,
-                process.out.versions
-            ).match()
-            assert path(process.out.versions.get(0)).text.contains("GSMR")
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.gsmr).match("gsmr")},
+                { assert snapshot(process.out.versions_gcta).match("versions_gcta")}
+            )
         }
-
     }
 
     test("homo_sapiens - gsmr - stub") {
@@ -70,35 +63,22 @@ nextflow_process {
                     file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/gsmr/sumstats_copy.tsv")
                 ]
 
-                // Stage individual files
-                def bedFile = file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/gsmr/bfile/bfile.bed")
-                def bimFile = file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/gsmr/bfile/bfile.bim")
-                def famFile = file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/gsmr/bfile/bfile.fam")
-
-                // Create a folder and move files into it
                 def referenceDir = file("reference")
                 referenceDir.mkdirs()
-                bedFile.copyTo(referenceDir.resolve("reference.bed"))
-                bimFile.copyTo(referenceDir.resolve("reference.bim"))
-                famFile.copyTo(referenceDir.resolve("reference.fam"))
-
-                // Pass the folder as input
                 input[2] = referenceDir
                 """
             }
         }
 
         then {
-            assert process.success
-            assert snapshot(
-                process.out.gsmr,
-                process.out.eff_plot,
-                process.out.mono_badsnps,
-                process.out.versions
-            ).match()
-
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.gsmr).match("gsmr_stub")},
+                { assert snapshot(process.out.versions_gcta).match("versions_gcta_stub")}
+            )
         }
 
     }
 
 }
+
diff --git a/modules/nf-core/gcta/gsmr/tests/main.nf.test.snap b/modules/nf-core/gcta/gsmr/tests/main.nf.test.snap
index 05b8bc648eed..6ff3d0d34976 100644
--- a/modules/nf-core/gcta/gsmr/tests/main.nf.test.snap
+++ b/modules/nf-core/gcta/gsmr/tests/main.nf.test.snap
@@ -1,44 +1,114 @@
 {
-    "homo_sapiens - gsmr": {
+    "gsmr": {
         "content": [
             [
-                "test_exposure_test_outcome.gsmr:md5,f137c763773522ea37849d919f6de9aa"
-            ],
-            [
-                
-            ],
-            [
-                "test_exposure_test_outcome.mono.badsnps:md5,0fe7dcfd9384c40361e7009ed28098cc"
-            ],
+                [
+                    {
+                        "id": "test_exposure"
+                    },
+                    {
+                        "id": "test_outcome"
+                    },
+                    "test_exposure_test_outcome.gsmr:md5,f137c763773522ea37849d919f6de9aa"
+                ]
+            ]
+        ],
+        "timestamp": "2026-03-13T16:02:41.214728046",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    },
+    "homo_sapiens - gsmr": {
+        "content": [
             [
-                "versions.yml:md5,9d63b9cb692159dbd3c08b55eca5212b"
+                [
+                    {
+                        "id": "test_exposure"
+                    },
+                    {
+                        "id": "test_outcome"
+                    },
+                    "test_exposure_test_outcome.gsmr:md5,f137c763773522ea37849d919f6de9aa"
+                ]
             ]
         ],
+        "timestamp": "2026-03-13T15:06:14.608903963",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
-        },
-        "timestamp": "2025-03-26T16:57:12.009292265"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
     "homo_sapiens - gsmr - stub": {
         "content": [
             [
-                "test_exposure_test_outcome.gsmr:md5,d41d8cd98f00b204e9800998ecf8427e"
-            ],
+                [
+                    {
+                        "id": "test_exposure"
+                    },
+                    {
+                        "id": "test_outcome"
+                    },
+                    "test_exposure_test_outcome.gsmr:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "timestamp": "2026-03-13T15:06:21.555456661",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    },
+    "versions_gcta": {
+        "content": [
             [
-                "test_exposure_test_outcome.eff_plot.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
-            ],
+                [
+                    "GCTA_GSMR",
+                    "gcta",
+                    "1.94.1"
+                ]
+            ]
+        ],
+        "timestamp": "2026-03-13T16:16:22.216759135",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    },
+    "versions_gcta_stub": {
+        "content": [
             [
-                "test_exposure_test_outcome.mono.badsnps:md5,d41d8cd98f00b204e9800998ecf8427e"
-            ],
+                [
+                    "GCTA_GSMR",
+                    "gcta",
+                    "1.94.1"
+                ]
+            ]
+        ],
+        "timestamp": "2026-03-13T16:16:27.849357278",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    },
+    "gsmr_stub": {
+        "content": [
             [
-                "versions.yml:md5,9d63b9cb692159dbd3c08b55eca5212b"
+                [
+                    {
+                        "id": "test_exposure"
+                    },
+                    {
+                        "id": "test_outcome"
+                    },
+                    "test_exposure_test_outcome.gsmr:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
             ]
         ],
+        "timestamp": "2026-03-13T16:04:41.062546751",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
-        },
-        "timestamp": "2025-03-26T16:57:20.670192583"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     }
 }
\ No newline at end of file

From d274b217a82eed4626ec39b864ad8d88678f9412 Mon Sep 17 00:00:00 2001
From: juliaapolonio <apoloniojulia@gmail.com>
Date: Fri, 13 Mar 2026 17:01:40 -0300
Subject: [PATCH 17/20] make module pass pre-commit

---
 modules/nf-core/gcta/gsmr/environment.yml |  2 +-
 modules/nf-core/gcta/gsmr/main.nf         |  3 +-
 modules/nf-core/gcta/gsmr/meta.yml        | 60 +++++++----------------
 3 files changed, 20 insertions(+), 45 deletions(-)

diff --git a/modules/nf-core/gcta/gsmr/environment.yml b/modules/nf-core/gcta/gsmr/environment.yml
index 543862387283..3e22ea7b9f20 100644
--- a/modules/nf-core/gcta/gsmr/environment.yml
+++ b/modules/nf-core/gcta/gsmr/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::gcta=1.94.1"
+  - bioconda::gcta=1.94.1
diff --git a/modules/nf-core/gcta/gsmr/main.nf b/modules/nf-core/gcta/gsmr/main.nf
index 44b33cab2031..8901d3c88bd8 100644
--- a/modules/nf-core/gcta/gsmr/main.nf
+++ b/modules/nf-core/gcta/gsmr/main.nf
@@ -17,7 +17,8 @@ process GCTA_GSMR {
     tuple val(meta), val(meta2), path("*.gsmr")          , emit: gsmr
     tuple val(meta), val(meta2), path("*.eff_plot.gz")   , emit: eff_plot, optional: true
     tuple val(meta), val(meta2), path("*.mono.badsnps"), emit: mono_badsnps, optional: true
-    tuple val("${task.process}"), val('gcta'), eval('gcta 2>&1 | grep -oE "v[0-9]+\\.[0-9]+\\.[0-9]+" | sed \'s/v//\''), emit: versions_gcta, topic: versions    
+    tuple val("${task.process}"), val('gcta'), eval('gcta 2>&1 | grep -oE "v[0-9]+\\.[0-9]+\\.[0-9]+" | sed \'s/v//\''), emit: versions_gcta, topic: versions
+
     when:
     task.ext.when == null || task.ext.when
 
diff --git a/modules/nf-core/gcta/gsmr/meta.yml b/modules/nf-core/gcta/gsmr/meta.yml
index 4808ba933631..20762e7bfe5c 100644
--- a/modules/nf-core/gcta/gsmr/meta.yml
+++ b/modules/nf-core/gcta/gsmr/meta.yml
@@ -33,15 +33,15 @@ input:
         description: Outcome GWAS summary statistics formatted for GSMR
         pattern: "*.txt"
         ontologies: []
-  - reference:
-      type: file
-      description: PLINK reference dataset files (BED/BIM/FAM)
-      pattern: "*.{bed,bim,fam}"
-      multiple: true
-      ontologies: []
+      reference:
+        type: file
+        description: PLINK reference dataset files (BED/BIM/FAM)
+        pattern: "*.{bed,bim,fam}"
+        multiple: true
+        ontologies: []
 output:
-  log:
-    - - meta:
+  - log:
+      - meta:
           type: map
           description: Groovy Map containing sample information for exposure
       - meta2:
@@ -51,9 +51,8 @@ output:
           type: file
           description: Log file from GSMR analysis
           pattern: "*.log"
-          ontologies: []
-  gsmr:
-    - - meta:
+  - gsmr:
+      - meta:
           type: map
           description: Groovy Map containing sample information for exposure
       - meta2:
@@ -63,42 +62,17 @@ output:
           type: file
           description: Result file from GSMR analysis
           pattern: "*.gsmr"
-          ontologies: []
-  eff_plot:
-    - - meta:
-          type: map
-          description: Groovy Map containing sample information for exposure
-      - meta2:
-          type: map
-          description: Groovy Map containing sample information for outcome
-      - "*.eff_plot.gz":
-          type: file
-          description: Effect plot file from GSMR analysis
-          pattern: "*.eff_plot.gz"
-          ontologies:
-            - edam: http://edamontology.org/format_3989
-  mono_badsnps:
-    - - meta:
-          type: map
-          description: Groovy Map containing sample information for exposure
-      - meta2:
-          type: map
-          description: Groovy Map containing sample information for outcome
-      - "*.mono.badsnps":
-          type: file
-          description: Bad SNPs file from GSMR analysis
-          pattern: "*.mono.badsnps"
-          ontologies: []
-  versions_gcta:
-    - - ${task.process}:
+  - versions_gcta:
+      - "${task.process}":
           type: string
           description: The name of the process
       - gcta:
           type: string
           description: The name of the tool
-      - gcta 2>&1 | grep -oE "v[0-9]+\.[0-9]+\.[0-9]+" | sed 's/v//':
-          type: eval
+      - gcta 2>&1 | grep -oE 'v[0-9]+\.[0-9]+\.[0-9]+' | sed 's/v//':
+          type: string
           description: The expression to obtain the version of the tool
+
 topics:
   versions:
     - - ${task.process}:
@@ -107,8 +81,8 @@ topics:
       - gcta:
           type: string
           description: The name of the tool
-      - gcta 2>&1 | grep -oE "v[0-9]+\.[0-9]+\.[0-9]+" | sed 's/v//':
-          type: eval
+      - gcta 2>&1 | grep -oE 'v[0-9]+\.[0-9]+\.[0-9]+' | sed 's/v//':
+          type: string
           description: The expression to obtain the version of the tool
 authors:
   - "@juliaapolonio"

From 6fd2487367d5a246d120b31a96daa126c791b568 Mon Sep 17 00:00:00 2001
From: jvfe <jvfecav@gmail.com>
Date: Sat, 14 Mar 2026 10:05:04 -0300
Subject: [PATCH 18/20] fix: Linting & obsolete snap

---
 modules/nf-core/gcta/gsmr/meta.yml            | 60 +++++++++++++------
 .../nf-core/gcta/gsmr/tests/main.nf.test.snap | 40 -------------
 2 files changed, 43 insertions(+), 57 deletions(-)

diff --git a/modules/nf-core/gcta/gsmr/meta.yml b/modules/nf-core/gcta/gsmr/meta.yml
index 20762e7bfe5c..ab6535848ca0 100644
--- a/modules/nf-core/gcta/gsmr/meta.yml
+++ b/modules/nf-core/gcta/gsmr/meta.yml
@@ -33,15 +33,15 @@ input:
         description: Outcome GWAS summary statistics formatted for GSMR
         pattern: "*.txt"
         ontologies: []
-      reference:
-        type: file
-        description: PLINK reference dataset files (BED/BIM/FAM)
-        pattern: "*.{bed,bim,fam}"
-        multiple: true
-        ontologies: []
+  - reference:
+      type: file
+      description: PLINK reference dataset files (BED/BIM/FAM)
+      pattern: "*.{bed,bim,fam}"
+      multiple: true
+      ontologies: []
 output:
-  - log:
-      - meta:
+  log:
+    - - meta:
           type: map
           description: Groovy Map containing sample information for exposure
       - meta2:
@@ -51,8 +51,9 @@ output:
           type: file
           description: Log file from GSMR analysis
           pattern: "*.log"
-  - gsmr:
-      - meta:
+          ontologies: []
+  gsmr:
+    - - meta:
           type: map
           description: Groovy Map containing sample information for exposure
       - meta2:
@@ -62,17 +63,42 @@ output:
           type: file
           description: Result file from GSMR analysis
           pattern: "*.gsmr"
-  - versions_gcta:
-      - "${task.process}":
+          ontologies: []
+  versions_gcta:
+    - - ${task.process}:
           type: string
           description: The name of the process
       - gcta:
           type: string
           description: The name of the tool
-      - gcta 2>&1 | grep -oE 'v[0-9]+\.[0-9]+\.[0-9]+' | sed 's/v//':
-          type: string
+      - gcta 2>&1 | grep -oE "v[0-9]+\.[0-9]+\.[0-9]+" | sed 's/v//':
+          type: eval
           description: The expression to obtain the version of the tool
-
+  eff_plot:
+    - - meta:
+          type: map
+          description: Groovy Map containing sample information for exposure
+      - meta2:
+          type: map
+          description: Groovy Map containing sample information for outcome
+      - "*.eff_plot.gz":
+          type: file
+          description: Result effect plot from GSMR analysis
+          pattern: "*.eff_plot.gz"
+          ontologies:
+            - edam: http://edamontology.org/format_3989
+  mono_badsnps:
+    - - meta:
+          type: map
+          description: Groovy Map containing sample information for exposure
+      - meta2:
+          type: map
+          description: Groovy Map containing sample information for outcome
+      - "*.mono.badsnps":
+          type: file
+          description: Result badsnps file from GSMR analysis
+          pattern: "*.mono.badsnps"
+          ontologies: []
 topics:
   versions:
     - - ${task.process}:
@@ -81,8 +107,8 @@ topics:
       - gcta:
           type: string
           description: The name of the tool
-      - gcta 2>&1 | grep -oE 'v[0-9]+\.[0-9]+\.[0-9]+' | sed 's/v//':
-          type: string
+      - gcta 2>&1 | grep -oE "v[0-9]+\.[0-9]+\.[0-9]+" | sed 's/v//':
+          type: eval
           description: The expression to obtain the version of the tool
 authors:
   - "@juliaapolonio"
diff --git a/modules/nf-core/gcta/gsmr/tests/main.nf.test.snap b/modules/nf-core/gcta/gsmr/tests/main.nf.test.snap
index 6ff3d0d34976..7f3b48236ccf 100644
--- a/modules/nf-core/gcta/gsmr/tests/main.nf.test.snap
+++ b/modules/nf-core/gcta/gsmr/tests/main.nf.test.snap
@@ -19,46 +19,6 @@
             "nextflow": "25.10.4"
         }
     },
-    "homo_sapiens - gsmr": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test_exposure"
-                    },
-                    {
-                        "id": "test_outcome"
-                    },
-                    "test_exposure_test_outcome.gsmr:md5,f137c763773522ea37849d919f6de9aa"
-                ]
-            ]
-        ],
-        "timestamp": "2026-03-13T15:06:14.608903963",
-        "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
-        }
-    },
-    "homo_sapiens - gsmr - stub": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test_exposure"
-                    },
-                    {
-                        "id": "test_outcome"
-                    },
-                    "test_exposure_test_outcome.gsmr:md5,d41d8cd98f00b204e9800998ecf8427e"
-                ]
-            ]
-        ],
-        "timestamp": "2026-03-13T15:06:21.555456661",
-        "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
-        }
-    },
     "versions_gcta": {
         "content": [
             [

From 943d57ee86156309cf82cb8893ef076989f6c105 Mon Sep 17 00:00:00 2001
From: jvfe <jvfecav@gmail.com>
Date: Sat, 14 Mar 2026 10:12:30 -0300
Subject: [PATCH 19/20] fix: Remove linebreak

---
 modules/nf-core/gcta/gsmr/tests/main.nf.test | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/nf-core/gcta/gsmr/tests/main.nf.test b/modules/nf-core/gcta/gsmr/tests/main.nf.test
index 9c652b308a1f..cd9c77a5414e 100644
--- a/modules/nf-core/gcta/gsmr/tests/main.nf.test
+++ b/modules/nf-core/gcta/gsmr/tests/main.nf.test
@@ -81,4 +81,3 @@ nextflow_process {
     }
 
 }
-

From 97e85f95e5b40c2e8d5b2fcab720563ccb96b612 Mon Sep 17 00:00:00 2001
From: Julia Apolonio <apoloniojulia@gmail.com>
Date: Wed, 20 May 2026 12:23:53 -0300
Subject: [PATCH 20/20] Apply suggestions from code review
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>
---
 modules/nf-core/gcta/gsmr/main.nf            | 13 ++++++-------
 modules/nf-core/gcta/gsmr/tests/main.nf.test |  5 ++++-
 2 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/modules/nf-core/gcta/gsmr/main.nf b/modules/nf-core/gcta/gsmr/main.nf
index 8901d3c88bd8..b2e28f3d4d06 100644
--- a/modules/nf-core/gcta/gsmr/main.nf
+++ b/modules/nf-core/gcta/gsmr/main.nf
@@ -13,9 +13,9 @@ process GCTA_GSMR {
     path(reference)
 
     output:
-    tuple val(meta), val(meta2), path("*.log")           , emit: log
-    tuple val(meta), val(meta2), path("*.gsmr")          , emit: gsmr
-    tuple val(meta), val(meta2), path("*.eff_plot.gz")   , emit: eff_plot, optional: true
+    tuple val(meta), val(meta2), path("*.log")          , emit: log
+    tuple val(meta), val(meta2), path("*.gsmr")         , emit: gsmr
+    tuple val(meta), val(meta2), path("*.eff_plot.gz")  , emit: eff_plot, optional: true
     tuple val(meta), val(meta2), path("*.mono.badsnps"), emit: mono_badsnps, optional: true
     tuple val("${task.process}"), val('gcta'), eval('gcta 2>&1 | grep -oE "v[0-9]+\\.[0-9]+\\.[0-9]+" | sed \'s/v//\''), emit: versions_gcta, topic: versions
 
@@ -27,14 +27,14 @@ process GCTA_GSMR {
     def prefix = task.ext.prefix ?: "${meta.id}_${meta2.id}"
     """
     echo "${meta.id} ${exposure}" > ${meta.id}.input.txt
-    echo "${meta2.id} ${outcome}" > outcome.txt
+    echo "${meta2.id} ${outcome}" > ${meta2.id} .outcome.txt
     file=\$(ls $reference | sed 's/\\.[^.]*\$//')
     echo "${reference}/\$file" | head -n1 > reference.txt
 
     gcta  \\
         $args \\
         --mbfile reference.txt  \\
-        --gsmr-file ${meta.id}.input.txt outcome.txt \\
+        --gsmr-file ${meta.id}.input.txt ${meta2.id}.outcome.txt \\
         --out "${prefix}"
     """
 
@@ -45,7 +45,6 @@ process GCTA_GSMR {
     touch ${prefix}.log
     touch ${prefix}.gsmr
     touch ${prefix}.mono.badsnps
-    echo "" | gzip > ${prefix}.eff_plot.gz
-
+    echo | gzip > ${prefix}.eff_plot.gz
     """
 }
diff --git a/modules/nf-core/gcta/gsmr/tests/main.nf.test b/modules/nf-core/gcta/gsmr/tests/main.nf.test
index cd9c77a5414e..9e154501de43 100644
--- a/modules/nf-core/gcta/gsmr/tests/main.nf.test
+++ b/modules/nf-core/gcta/gsmr/tests/main.nf.test
@@ -43,7 +43,10 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(process.out.gsmr).match("gsmr")},
                 { assert snapshot(process.out.versions_gcta).match("versions_gcta")}
-            )
+                { assert snapshot(
+                    process.out.gsmr,
+                    process.out.versions_gcta
+                    ).match("versions_gcta")}
         }
     }