Merge pull request #380 from nf-core/update_local_modules

Update local modules

CHANGELOG.md

@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#345](https://github.com/nf-core/differentialabundance/pull/345)] - Plot differentially expressed genes by gene biotype ([@atrigila](https://github.com/atrigila), review by [@grst](https://github.com/grst))
 - [[#343](https://github.com/nf-core/differentialabundance/pull/343)] - Add pipeline-level nf-tests ([@atrigila](https://github.com/atrigila), review by [@pinin4fjords](https://github.com/pinin4fjords) and [@nschcolnicov](https://github.com/nschcolnicov))
 - [[#286](https://github.com/nf-core/differentialabundance/pull/286)] - Integration of limma voom for rnaseq data ([@KamilMaliszArdigen](https://github.com/KamilMaliszArdigen), review by [@pinin4fjords](https://github.com/pinin4fjords))
+- [[#380](https://github.com/nf-core/differentialabundance/pull/380)] - Replace local filter_diff_table module with nf-core one, and create nf-tests for tabular_to_gsea_chip. ([@nschcolnicov](https://github.com/nschcolnicov), review by [@pinin4fjords](https://github.com/pinin4fjords))
 
 ### Fixed
 

conf/modules.config

@@ -281,8 +281,8 @@ process {
         ].join(' ').trim() }
     }
 
-    withName: FILTER_DIFFTABLE {
-        ext.prefix = { "${meta.id}" }
+    withName: CUSTOM_FILTERDIFFERENTIALTABLE {
+        ext.prefix = { "${input_file.toString().split("\\.").init().join(".")}" }
         publishDir = [
             [
                 path: { "${params.outdir}/tables/differential" },

modules.json

@@ -15,6 +15,11 @@
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
+                    "custom/filterdifferentialtable": {
+                        "branch": "master",
+                        "git_sha": "833a65446ea117d092d4940f098236b6766e7aac",
+                        "installed_by": ["modules"]
+                    },
                     "custom/matrixfilter": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",

modules/local/tabulartogseachip/environment.yml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+
+dependencies:
+  - conda-forge::gawk=5.1.0

modules/local/tabular_to_gsea_chip.nf → modules/local/tabulartogseachip/main.nf

@@ -1,11 +1,10 @@
 process TABULAR_TO_GSEA_CHIP {
 
+    tag "$id"
     label 'process_single'
 
-    conda "conda-forge::gawk=5.1.0"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gawk:5.1.0' :
-        'biocontainers/gawk:5.1.0' }"
+    conda "${moduleDir}/environment.yml"
+    container "community.wave.seqera.io/library/gawk:5.1.0--fa97c4ccf4cfbc4b"
 
     input:
     path tsv
@@ -41,4 +40,15 @@ process TABULAR_TO_GSEA_CHIP {
         bash: \$(echo \$(bash --version | grep -Eo 'version [[:alnum:].]+' | sed 's/version //'))
     END_VERSIONS
     """
+
+    stub:
+    """
+    touch stub.chip
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bash: \$(echo \$(bash --version | grep -Eo 'version [[:alnum:].]+' | sed 's/version //'))
+    END_VERSIONS
+    """
+
 }

modules/local/tabulartogseachip/meta.yml

@@ -0,0 +1,41 @@
+name: tabular_to_gsea_chip
+description: Convert tabular data into GSEA-compatible CHIP files.
+keywords:
+  - GSEA
+  - CHIP
+  - Bioinformatics
+tools:
+  - gawk:
+      description: |
+        GNU Awk (gawk) is a powerful programming language designed for text processing and typically used as a data extraction and reporting tool.
+        It is used here to manipulate tabular data and create the CHIP file format.
+      homepage: https://www.gnu.org/software/gawk/
+      documentation: https://www.gnu.org/software/gawk/manual/
+      licence: ["GPL-3.0-or-later"]
+input:
+  - tsv:
+      type: file
+      description: |
+        Tab-separated values (TSV) file containing data to be converted into a CHIP file.
+  - - id:
+        type: string
+        description: |
+          Feature ID attribute in the abundance table as well as in the GTF file (e.g. the gene_id field).
+    - symbol:
+        type: string
+        description: |
+          Feature name attribute in the abundance table as well as in the GTF file (e.g. the gene symbol field).
+output:
+  - chip:
+      type: file
+      description: Generated GSEA-compatible CHIP file.
+      pattern: "*.chip"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@pinin4fjords" # Replace with actual author handles
+maintainers:
+  - "@nschcolnicov"

modules/local/tabulartogseachip/tests/main.nf.test

@@ -0,0 +1,49 @@
+nextflow_process {
+
+    name "Test Process TABULAR_TO_GSEA_CHIP"
+    script "../main.nf"
+    process "TABULAR_TO_GSEA_CHIP"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "tabular_to_gsea_chip"
+
+    test("test_tabular_to_gsea_chip") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.fromPath("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/differentialabundance/modules_testdata/Mus_musculus.anno.feature_metadata.tsv")
+                input[1] = ["gene_id", "gene_name"]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+            )
+        }
+    }
+
+    test("test_tabular_to_gsea_chip - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.fromPath("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/differentialabundance/modules_testdata/Mus_musculus.anno.feature_metadata.tsv")
+                input[1] = ["gene_id", "gene_name"]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+            )
+        }
+    }
+}

modules/local/tabulartogseachip/tests/main.nf.test.snap

@@ -0,0 +1,48 @@
+{
+    "test_tabular_to_gsea_chip - stub": {
+        "content": [
+            {
+                "0": [
+                    "stub.chip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "1": [
+                    "versions.yml:md5,a422b1a01e86be433a25d1776d497f5a"
+                ],
+                "chip": [
+                    "stub.chip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "versions": [
+                    "versions.yml:md5,a422b1a01e86be433a25d1776d497f5a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-06T21:03:06.781994447"
+    },
+    "test_tabular_to_gsea_chip": {
+        "content": [
+            {
+                "0": [
+                    "Mus_musculus.anno.feature_metadata.chip:md5,5abf60bb982bb2ff5b8b3e37f14a21e4"
+                ],
+                "1": [
+                    "versions.yml:md5,a422b1a01e86be433a25d1776d497f5a"
+                ],
+                "chip": [
+                    "Mus_musculus.anno.feature_metadata.chip:md5,5abf60bb982bb2ff5b8b3e37f14a21e4"
+                ],
+                "versions": [
+                    "versions.yml:md5,a422b1a01e86be433a25d1776d497f5a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-06T21:02:58.608468636"
+    }
+}