feat(#115): Add PINTS visualizer module

Author: edmundmiller

conf/test.config

@@ -50,4 +50,8 @@ process {
     withName: PINTS_CALLER {
         ext.args = { "--disable-small" }
     }
+
+    withName: PINTS_VISUALIZER {
+        errorStrategy = 'ignore'
+    }
 }

modules/local/pints/visualizer/environment.yml

@@ -0,0 +1,15 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - pybedtools
+  - bedtools
+  - htslib
+  - python=3.12.6
+  - pip
+  - pybigwig
+  - numpy
+  - pip: # FIXME https://github.com/nf-core/modules/issues/5814
+      # NOTE PINTS isn't adding conda builds and is a few versions behind.
+      # renovate: datasource=pypi depName=pypints
+      - pypints==1.1.15

modules/local/pints/visualizer/main.nf

@@ -0,0 +1,61 @@
+process PINTS_VISUALIZER {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    // NOTE Stopped publishing at 1.1.9 https://quay.io/repository/biocontainers/pypints?tab=tags
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f1/f1a9e30012e1b41baf9acd1ff94e01161138d8aa17f4e97aa32f2dc4effafcd1/data' :
+        'community.wave.seqera.io/library/pybedtools_bedtools_htslib_pip_pypints:39699b96998ec5f6' }"
+
+    input:
+    tuple val(meta), path(bam)
+    val(assay_type)
+    // val(norm_factor)
+    // val(rpm_normalize)
+    // val(reverse_complement)
+
+    output:
+    tuple val(meta), path("*_pl.bw"), emit: plus_bw
+    tuple val(meta), path("*_mn.bw"), emit: minus_bw
+    path "versions.yml", emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    // def chr_arg = chr_name ? "--chrom ${chr_name}" : ''
+    // def norm_arg = norm_factor != null ? "--norm-fact ${norm_factor}" : ''
+    // def rpm_arg = rpm_normalize ? "--rpm" : ''
+    // def rc_arg = reverse_complement ? "--reverse-complement" : ''
+
+    """
+    pints_visualizer \\
+        --bam ${bam} \\
+        --exp-type ${assay_type} \\
+        --output-prefix ${prefix} \\
+        ${args}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        python: \$(python --version | sed 's/Python //g')
+        pints: \$(pints_visualizer --version)
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_${chr_name}_plus.bigwig
+    touch ${prefix}_${chr_name}_minus.bigwig
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        python: \$(python --version | sed 's/Python //g')
+        pints: \$(pints_visualizer --version)
+    END_VERSIONS
+    """
+}
+

modules/local/pints/visualizer/meta.yml

@@ -0,0 +1,66 @@
+name: "pints_visualizer"
+description: Visualization script for creating strand-specific bigWig files from nascent RNA-seq data
+keywords:
+  - bigWig
+  - visualization
+  - CoPRO
+  - GRO-cap
+  - PRO-cap
+  - CAGE
+  - NETCAGE
+  - RAMPAGE
+  - csRNA-seq
+  - STRIPE-seq
+  - PRO-seq
+  - GRO-seq
+tools:
+  - "pints":
+      description: "Peak Identifier for Nascent Transcripts Starts (PINTS)"
+      homepage: "https://pints.yulab.org/"
+      documentation: "https://github.com/hyulab/PINTS/blob/main/README.md"
+      tool_dev_url: "https://github.com/hyulab/PINTS"
+      doi: "10.1038/s41587-022-01211-7"
+      licence: ["GPL v3"]
+      identifier: biotools:pyPINTS
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - bam:
+        type: file
+        description: BAM file to generate bigWig files from
+        pattern: "*.{bam}"
+    - chr_name:
+        type: string
+        description: Optional chromosome name prefix to filter
+  - assay_type:
+      type: string
+      description: Type of experiment (CoPRO/GROcap/GROseq/PROcap/PROseq)
+  - norm_factor:
+      type: float
+      description: Normalization factor for signal
+  - rpm_normalize:
+      type: boolean
+      description: Whether to apply RPM normalization
+  - reverse_complement:
+      type: boolean
+      description: Whether the reads represent the reverse complement of nascent RNAs
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bigwigs:
+      type: file
+      description: Two strand-specific bigWig files (forward and reverse)
+      pattern: "*_{pl,mn}.bw"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@hyulab"
+  - "@edmiller01"

modules/local/pints/visualizer/tests/main.nf.test

@@ -0,0 +1,68 @@
+nextflow_process {
+
+    name "Test Process PINTS_VISUALIZER"
+    script "../main.nf"
+    process "PINTS_VISUALIZER"
+    tag "modules"
+    tag "modules_local"
+    tag "pints"
+    tag "pints/visualizer"
+
+    test("Should run PINTS_VISUALIZER with PROseq data and produce strand-specific bigwigs") {
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test_sample', single_end:false ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    'chr1'
+                ])
+                input[1] = 'PROseq'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.plus_bw.size() == 1 },
+                { assert process.out.minus_bw.size() == 1 },
+                { assert snapshot(
+                    process.out.plus_bw.get(0)[1],
+                    process.out.minus_bw.get(0)[1]
+                    ).match()
+                },
+                { assert snapshot(path(process.out.versions[0]).yaml).match("flipped_versions") }
+            )
+        }
+    }
+
+    test("Should run PINTS_VISUALIZER with GROseq data without reverse complement") {
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test_gro', single_end:false ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    'chr1'
+                ])
+                input[1] = 'GROseq'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.plus_bw.size() == 1 },
+                { assert process.out.minus_bw.size() == 1 },
+                { assert snapshot(
+                    process.out.plus_bw.get(0)[1],
+                    process.out.minus_bw.get(0)[1]
+                    ).match()
+                },
+                { assert snapshot(path(process.out.versions[0]).yaml).match("versions") }
+            )
+        }
+    }
+}

modules/local/pints/visualizer/tests/main.nf.test.snap

@@ -0,0 +1,54 @@
+{
+    "versions": {
+        "content": [
+            {
+                "PINTS_VISUALIZER": {
+                    "python": "3.12.6",
+                    "pints": "1.1.13"
+                }
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-05-08T18:07:16.978238"
+    },
+    "flipped_versions": {
+        "content": [
+            {
+                "PINTS_VISUALIZER": {
+                    "python": "3.12.6",
+                    "pints": "1.1.13"
+                }
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-05-08T18:07:07.331434"
+    },
+    "Should run PINTS_VISUALIZER with PROseq data and produce strand-specific bigwigs": {
+        "content": [
+            "test_sample_pl.bw:md5,6fd3346be91cc84750f839b050c6bc5b",
+            "test_sample_mn.bw:md5,9eecf5936bdf1c0c44ec123636a305f5"
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-05-04T18:24:13.206646"
+    },
+    "Should run PINTS_VISUALIZER with GROseq data without reverse complement": {
+        "content": [
+            "test_gro_pl.bw:md5,e399e77f224d993e789bf8f7c4b826e1",
+            "test_gro_mn.bw:md5,21c7ef549d8cb39788e13080dc573848"
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-05-04T18:24:22.747334"
+    }
+}

subworkflows/local/coverage_graphs/main.nf

@@ -5,6 +5,7 @@
 include { DEEPTOOLS_BAMCOVERAGE as DEEPTOOLS_BAMCOVERAGE_PLUS  } from '../../../modules/nf-core/deeptools/bamcoverage/main'
 include { DEEPTOOLS_BAMCOVERAGE as DEEPTOOLS_BAMCOVERAGE_MINUS } from '../../../modules/nf-core/deeptools/bamcoverage/main'
 include { FLIP_STRAND                                          } from '../../../modules/flip_strand'
+include { PINTS_VISUALIZER                                     } from '../../../modules/local/pints/visualizer'
 
 workflow COVERAGE_GRAPHS {
     take:
@@ -33,18 +34,25 @@ workflow COVERAGE_GRAPHS {
     )
     ch_versions = ch_versions.mix(DEEPTOOLS_BAMCOVERAGE_MINUS.out.versions.first())
 
-
-    ch_plus_minus = DEEPTOOLS_BAMCOVERAGE_PLUS.out.bigwig.join(DEEPTOOLS_BAMCOVERAGE_MINUS.out.bigwig)
+    ch_deeptools_plus_minus = DEEPTOOLS_BAMCOVERAGE_PLUS.out.bigwig.join(DEEPTOOLS_BAMCOVERAGE_MINUS.out.bigwig)
 
     if (params.assay_type in ["PROseq", "PROcap", "CoPRO"]) {
         FLIP_STRAND(
-            ch_plus_minus,
+            ch_deeptools_plus_minus
         )
         ch_versions = ch_versions.mix(FLIP_STRAND.out.versions.first())
-        ch_plus_minus = FLIP_STRAND.out.flipped_bigwig
+        ch_deeptools_plus_minus = FLIP_STRAND.out.flipped_bigwig
     }
 
+    PINTS_VISUALIZER(
+        bam_bai,
+        params.assay_type,
+    )
+    ch_versions = ch_versions.mix(PINTS_VISUALIZER.out.versions.first())
+    ch_pints_plus_minus = PINTS_VISUALIZER.out.plus_bw.join(PINTS_VISUALIZER.out.minus_bw)
+
     emit:
-    plus_minus = ch_plus_minus
-    versions   = ch_versions
+    deeptools_plus_minus = ch_deeptools_plus_minus
+    pints_plus_minus     = ch_pints_plus_minus
+    versions             = ch_versions
 }

workflows/tests/aligner/bowtie2.nf.test.snap

@@ -1,7 +1,7 @@
 {
     "Should run with defaults": {
         "content": [
-            68,
+            71,
             {
                 "BBMAP_PILEUP": {
                     "bbmap": 39.01,
@@ -44,6 +44,10 @@
                     "homer": 4.11,
                     "samtools": 1.21
                 },
+                "PINTS_VISUALIZER": {
+                    "python": "3.12.6",
+                    "pints": "1.1.13"
+                },
                 "PRESEQ_CCURVE": {
                     "preseq": "3.1.1"
                 },
@@ -296,8 +300,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nextflow": "25.03.1"
         },
-        "timestamp": "2025-05-11T12:24:05.753243"
+        "timestamp": "2025-05-20T21:52:41.120419"
     }
 }