From 8039493ba9c36fe893af938a31cda61e7a3951f9 Mon Sep 17 00:00:00 2001
From: shahirnm <uoi4@cdc.gov>
Date: Mon, 7 Oct 2024 13:48:36 -0400
Subject: [PATCH] adding amplicov modules. Issue nf-test has not been run yet
 for module

---
 modules/ph-core/amplicov/enviromental.yml   |  7 +++
 modules/ph-core/amplicov/main.nf            | 58 +++++++++++++++++++++
 modules/ph-core/amplicov/meta.yml           | 53 +++++++++++++++++++
 modules/ph-core/amplicov/tests/main.nf.test | 34 ++++++++++++
 4 files changed, 152 insertions(+)
 create mode 100644 modules/ph-core/amplicov/enviromental.yml
 create mode 100644 modules/ph-core/amplicov/main.nf
 create mode 100644 modules/ph-core/amplicov/meta.yml
 create mode 100644 modules/ph-core/amplicov/tests/main.nf.test

diff --git a/modules/ph-core/amplicov/enviromental.yml b/modules/ph-core/amplicov/enviromental.yml
new file mode 100644
index 0000000..c3f5be3
--- /dev/null
+++ b/modules/ph-core/amplicov/enviromental.yml
@@ -0,0 +1,7 @@
+name: amplicov
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  -bioconda::amplicon_coverage_plot=0.3.3
\ No newline at end of file
diff --git a/modules/ph-core/amplicov/main.nf b/modules/ph-core/amplicov/main.nf
new file mode 100644
index 0000000..c5d97cc
--- /dev/null
+++ b/modules/ph-core/amplicov/main.nf
@@ -0,0 +1,58 @@
+
+process AMPLICOV {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/amplicon_coverage_plot:0.3.3--pyhdfd78af_0':
+        'biocontainers/amplicon_coverage_plot:0.3.3--pyhdfd78af_0' }"
+
+
+
+    input:
+
+    tuple val(meta), path(bam)
+    tuple val(meta), val(irma_type)
+    path bedpe
+
+    output:
+
+//  output of amplicov is not a sorted bam but just coverage files.
+
+    tuple val(meta), path("*amplicon_coverage.txt"), emit: coverage
+    tuple val(meta), path("*amplicon_coverage.html"), emit: coverage_html
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def refname = irma_type
+
+    """
+    amplicov --bedpe ${bedpe}  --bam ${bam}  --count_primer -o .  -p ${bam.BaseName}  -r ${refname}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        amplicov: \$(amplicov --version |& sed '1!d ; s/amplicov //')
+    END_VERSIONS
+
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    mkdir -p ${meta}/
+    touch ${meta}/stub.amplicon_coverage.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        amplicov: \$(samtools --version |& sed '1!d ; s/samtools //')
+    END_VERSIONS
+    """
+}
diff --git a/modules/ph-core/amplicov/meta.yml b/modules/ph-core/amplicov/meta.yml
new file mode 100644
index 0000000..bb4218a
--- /dev/null
+++ b/modules/ph-core/amplicov/meta.yml
@@ -0,0 +1,53 @@
+name: amplicov
+description: Script to generate amplicon coverage
+keywords:
+  - amplicon
+  - genome
+  - coverage
+tools:
+  - amplicov:
+      description: |
+        Will generate information around amplicon coverage given a bam file and amplicon information provided in a bedpe/bed6 format
+      homepage: https://pypi.org/project/amplicov/0.3.3/
+      documentation: https://github.com/chienchi/amplicon_coverage_plot
+      doi: 10.1093/bioinformatics/btp352 **
+      license: ["MIT"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM/CRAM/SAM file(s)
+      pattern: "*.{bam,cram,sam}"
+  - bedpe:
+      type: file
+      description: |
+        file format that concisely describe disjoint genome features, such as structural variations or paired-end sequence alignments
+      pattern: "*.{bedpe,bed6}"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - coverage:
+      type: file
+      description: amplicon coverage information in tsv format
+      pattern: "*.{txt}"
+  - coverage_html:
+      type: file
+      description: amplicon coverage information in html format
+      pattern: "*.{html}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@chienchi"
+  - "@pvanheus"
+maintainers:
+  - "@chienchi"
+  - "@pvanheus"
diff --git a/modules/ph-core/amplicov/tests/main.nf.test b/modules/ph-core/amplicov/tests/main.nf.test
new file mode 100644
index 0000000..a9972b4
--- /dev/null
+++ b/modules/ph-core/amplicov/tests/main.nf.test
@@ -0,0 +1,34 @@
+nextflow_process {
+
+    name "Test Process AMPLICOV"
+    script "../main.nf"
+    process "AMPLICOV"
+
+    test("Test Process AMPLICOV") {
+        config "./nextflow.config"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/bam/test.paired_end.bam", checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    "SARS-CoV-2"])
+                input[2] = Channel.of([
+                    file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/bed/test.bedpe', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert process.trace.tasks().size() == 1
+
+        }
+
+    }
+
+}
\ No newline at end of file