feat(pints): Add initial caller module (#1983)

* feat(pints): Add initial caller module

* docs(pints): Add initial documentation

* chore: Add TODOs

* test(pypints): Use docker image for singularity

The image doesn't exist yet for some reason

* test(pints): Remove unidirectional peaks hash

* style(pints): Align emits

modules/pints/caller/main.nf

@@ -0,0 +1,43 @@
+process PINTS_CALLER {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda    (params.enable_conda ? "bioconda::pypints=1.1.6" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/pypints:1.1.6--pyh5e36f6f_1' :
+        'quay.io/biocontainers/pypints:1.1.6--pyh5e36f6f_1' }"
+
+    input:
+    tuple val(meta), path(bams)
+
+    output:
+    tuple val(meta), path("*_divergent_peaks.bed")     , emit: divergent_TREs
+    tuple val(meta), path("*_bidirectional_peaks.bed") , emit: bidirectional_TREs
+    tuple val(meta), path("*_unidirectional_peaks.bed"), emit: unidirectional_TREs
+    path  "versions.yml"     , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    // TODO handle bigwigs
+    // def input_type  = ("${input[0]}".endsWith(".bam")) ? "--bam-file $input" :
+    //                    ("$input".contains(".bw")) ? "--bw-pl ${input[0]} --bw-mn ${input[1]}" :
+    //                    error "Please use bam or BigWig files"
+    """
+    pints_caller \\
+        --bam-file $bams \\
+        --save-to . \\
+        --file-prefix $prefix \\
+        --thread $task.cpus \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        python: \$(python --version | sed 's/Python //g')
+        pints: \$(pints_caller --version)
+    END_VERSIONS
+    """
+}

modules/pints/caller/meta.yml

@@ -0,0 +1,59 @@
+name: "pints_caller"
+description: Main caller script for peak calling
+keywords:
+  - peak-calling
+  - 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: "https://doi.org/10.1038/s41587-022-01211-7"
+      licence: "['GPL']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bams:
+      type: file
+      description: BAM/ file
+      pattern: "*.{bam}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - divergent_TREs:
+      type: file
+      description: Divergent TREs
+      pattern: "*_divergent_peaks.bed"
+  - bidirectional_TREs:
+      type: file
+      description: Divergent TREs and convergent TREs
+      pattern: "*_bidirectional_peaks.bed"
+  - unidirectional_TREs:
+      type: file
+      description: Unidirectional TREs, maybe lncRNAs transcribed from enhancers (e-lncRNAs)
+      pattern: "*_unidirectional_peaks.bed"
+
+authors:
+  - "@Emiller88"

tests/config/pytest_modules.yml

@@ -1747,6 +1747,10 @@ picard/sortvcf:
   - modules/picard/sortvcf/**
   - tests/modules/picard/sortvcf/**
 
+pints/caller:
+  - modules/pints/caller/**
+  - tests/modules/pints/caller/**
+
 pirate:
   - modules/pirate/**
   - tests/modules/pirate/**

tests/modules/pints/caller/main.nf

@@ -0,0 +1,21 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PINTS_CALLER } from '../../../../modules/pints/caller/main.nf'
+
+workflow test_pints_caller {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        // FIXME Fails if it doesn't find any signals
+        [file("https://raw.githubusercontent.com/Kraus-Lab/groHMM/master/inst/extdata/S0mR1.bam", checkIfExists: true),
+         file("https://raw.githubusercontent.com/Kraus-Lab/groHMM/master/inst/extdata/S40mR1.bam", checkIfExists: true)]
+    ]
+
+    PINTS_CALLER ( input )
+}
+
+// TODO Test single bam input
+// TODO Test single bigwig input
+// TODO Test multiple bigwig input

tests/modules/pints/caller/nextflow.config

@@ -0,0 +1,9 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: PINTS_CALLER {
+        ext.args = "--exp-type GROseq"
+        ext.singularity_pull_docker_container = true
+    }
+}

tests/modules/pints/caller/test.yml

@@ -0,0 +1,16 @@
+- name: "pints caller"
+  command: nextflow run ./tests/modules/pints/caller -entry test_pints_caller -c ./tests/config/nextflow.config -c ./tests/modules/pints/caller/nextflow.config
+  tags:
+    - "pints"
+    - "pints/caller"
+  files:
+    - path: output/pints/test_1_bidirectional_peaks.bed
+      md5sum: 8c69305ab896bd772e450e938ddf45f0
+    - path: output/pints/test_1_divergent_peaks.bed
+      md5sum: 2078c643951071f5836d365e5dc7ba1c
+    - path: output/pints/test_1_unidirectional_peaks.bed
+    - path: output/pints/test_2_bidirectional_peaks.bed
+      md5sum: c4efa0f297ba4cdb00659c5e6700ebe5
+    - path: output/pints/test_2_divergent_peaks.bed
+      md5sum: 213a2ba5d9930768d76bf2a7d8c3f7fb
+    - path: output/pints/test_2_unidirectional_peaks.bed