Update Modkit pileup

modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test

@@ -9,6 +9,7 @@ nextflow_process {
     tag "modkit"
     tag "modkit/bedmethyltobigwig"
     tag "modkit/pileup"
+    tag "tabix/bgzip"
 
     setup {
         run("MODKIT_PILEUP"){
@@ -25,14 +26,23 @@ nextflow_process {
                 """
             }
         }
+
+        run("TABIX_BGZIP"){
+            script "../../../tabix/bgzip/main.nf"
+            process {
+                """
+                input[0] = MODKIT_PILEUP.out.bedgz
+                """
+            }
+        }
     }
 
     test("homo sapiens - bedmethyl, fai, list") {
 
         when {
             process {
                 """
-                input[0] = MODKIT_PILEUP.out.bed
+                input[0] = TABIX_BGZIP.out.output
                 input[1] = [
                     [ id : 'hg38' ],
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
@@ -55,7 +65,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = MODKIT_PILEUP.out.bed
+                input[0] = TABIX_BGZIP.out.output
                 input[1] = [
                     [ id : 'hg38' ],
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
@@ -78,7 +88,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = MODKIT_PILEUP.out.bed
+                input[0] = TABIX_BGZIP.out.output
                 input[1] = [
                     [ id : 'hg38' ],
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)

modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test.snap

@@ -30,7 +30,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-11T09:38:52.912687858"
+        "timestamp": "2025-12-11T14:18:11.382889943"
     },
     "homo sapiens - bedmethyl, fai, list": {
         "content": [
@@ -63,7 +63,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-11T09:38:35.894897541"
+        "timestamp": "2025-12-11T14:17:52.811754475"
     },
     "homo sapiens - bedmethyl, fai, string": {
         "content": [
@@ -96,6 +96,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-11T09:38:44.647742811"
+        "timestamp": "2025-12-11T14:18:02.079953932"
     }
 }

modules/nf-core/modkit/pileup/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - ont-modkit=0.5.0
+  - ont-modkit=0.6.0

modules/nf-core/modkit/pileup/main.nf

@@ -4,17 +4,16 @@ process MODKIT_PILEUP {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ont-modkit:0.5.0--hcdda2d0_2':
-        'biocontainers/ont-modkit:0.5.0--hcdda2d0_2' }"
+        'https://depot.galaxyproject.org/singularity/ont-modkit:0.6.0--hcdda2d0_0':
+        'biocontainers/ont-modkit:0.6.0--hcdda2d0_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai)
     tuple val(meta2), path(fasta), path(fai)
     tuple val(meta3), path(bed)
 
     output:
-    tuple val(meta), path("*.bed")     , emit: bed     , optional: true
-    tuple val(meta), path("*.bedgraph"), emit: bedgraph, optional: true
+    tuple val(meta), path("*.bed.gz")  , emit: bedgz   , optional: true
     tuple val(meta), path("*.log")     , emit: log     , optional: true
     path "versions.yml"                , emit: versions
 
@@ -31,6 +30,8 @@ process MODKIT_PILEUP {
     modkit \\
         pileup \\
         $args \\
+        --bgzf \\
+        --bgzf-threads ${task.cpus} \\
         --threads ${task.cpus} \\
         --prefix ${prefix} \\
         $reference \\
@@ -45,7 +46,7 @@ process MODKIT_PILEUP {
             fi
         done
     else
-        mv ${prefix}.tmp ${prefix}.bed
+        mv ${prefix}.tmp ${prefix}.bed.gz
     fi
 
     cat <<-END_VERSIONS > versions.yml

modules/nf-core/modkit/pileup/meta.yml

@@ -6,8 +6,8 @@ keywords:
   - long-read
 tools:
   - "modkit":
-      description: A bioinformatics tool for working with modified bases in Oxford Nanopore
-        sequencing data
+      description: A bioinformatics tool for working with modified bases in Oxford
+        Nanopore sequencing data
       homepage: https://github.com/nanoporetech/modkit
       documentation: https://github.com/nanoporetech/modkit
       tool_dev_url: https://github.com/nanoporetech/modkit
@@ -36,8 +36,8 @@ input:
           e.g. `[ id:'hg38' ]`
     - fasta:
         type: file
-        description: Reference sequence in FASTA format. Required for motif (e.g. CpG)
-          filtering
+        description: Reference sequence in FASTA format. Required for motif (e.g.
+          CpG) filtering
         pattern: "*.fasta"
         ontologies: []
     - fai:
@@ -52,33 +52,22 @@ input:
           e.g. `[ id:'regions' ]`
     - bed:
         type: file
-        description: BED file that will restrict threshold estimation and pileup results
-          to positions overlapping intervals in the file
+        description: BED file that will restrict threshold estimation and pileup
+          results to positions overlapping intervals in the file
         pattern: "*.bed"
         ontologies: []
 output:
-  bed:
+  bedgz:
     - - meta:
           type: map
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'test', single_end:false ]`
-      - "*.bed":
+      - "*.bed.gz":
           type: file
-          description: bedMethyl output file(s)
+          description: bgzf-compressed bedMethyl output file(s)
           pattern: "*.bed"
           ontologies: []
-  bedgraph:
-    - - meta:
-          type: map
-          description: |
-            Groovy Map containing sample information
-            e.g. `[ id:'test', single_end:false ]`
-      - "*.bedgraph":
-          type: file
-          description: bedgraph output files
-          pattern: "*.bedgraph"
-          ontologies: []
   log:
     - - meta:
           type: map
@@ -102,3 +91,4 @@ authors:
   - "@fellen31"
 maintainers:
   - "@fellen31"
+  - "@jkh00"