Leviosam2 index (nf-core#5316)

* first version

* improvments

* whitespaces

* whitespaces

* whitespaces

* prettier

---------

Co-authored-by: zxBIB Grochowalski,Lukasz (GCBDS) EXTERNAL <[email protected]>

modules/nf-core/leviosam2/index/environment.yml

@@ -0,0 +1,8 @@
+---
+name: "leviosam2_index"
+channels:
+ - conda-forge
+ - bioconda
+ - defaults
+dependencies:
+ - "bioconda::leviosam2=0.4.2"

modules/nf-core/leviosam2/index/main.nf

@@ -0,0 +1,49 @@
+process LEVIOSAM2_INDEX {
+ tag "$meta.id"
+ label 'process_low'
+
+ conda "${moduleDir}/environment.yml"
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/leviosam2:0.4.2--h4ac6f70_0':
+ 'biocontainers/leviosam2:0.4.2--h4ac6f70_0' }"
+
+ input:
+ tuple val(meta), path(fai)
+ path(chain)
+
+ output:
+ tuple val(meta), path("*.clft"), emit: clft
+ path "versions.yml" , emit: versions
+
+ when:
+ task.ext.when == null || task.ext.when
+
+ script:
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.prefix ?: "${meta.id}"
+
+ """
+ leviosam2 \\
+ index \\
+ -c ${chain} \\
+ -p ${prefix} \\
+ -F ${fai}
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ leviosam2: \$(leviosam2 --version)
+ END_VERSIONS
+ """
+
+ stub:
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.prefix ?: "${meta.id}"
+ """
+ touch ${prefix}.clft
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ leviosam2: \$(leviosam2 --version)
+ END_VERSIONS
+ """
+}

modules/nf-core/leviosam2/index/meta.yml

@@ -0,0 +1,45 @@
+---
+name: "leviosam2_index"
+description: Index chain files for lift over
+keywords:
+ - leviosam2
+ - index
+ - lift
+tools:
+ - "leviosam2":
+ description: "Fast and accurate coordinate conversion between assemblies"
+ homepage: "https://github.com/milkschen/leviosam2/blob/main/workflow/README.md"
+ documentation: "https://github.com/milkschen/leviosam2/blob/main/workflow/README.md"
+ licence: ["MIT"]
+input:
+ - meta:
+ type: map
+ description: |
+ Groovy Map containing sample information
+ e.g. `[ id:'reference' ]`
+ - fai:
+ type: file
+ description: FAI (FASTA index) file of the target reference
+ pattern: "*.{fai}"
+ - chain:
+ type: file
+ description: Chain file to index.
+ pattern: "*.{chain}"
+output:
+ - meta:
+ type: map
+ description: |
+ Groovy Map containing sample information
+ e.g. `[ id:'reference' ]`
+ - clft:
+ type: file
+ description: Clft file of indexed chain
+ pattern: "*.{clft}"
+ - versions:
+ type: file
+ description: File containing software versions
+ pattern: "versions.yml"
+authors:
+ - "@lgrochowalski"
+maintainers:
+ - "@lgrochowalski"

modules/nf-core/leviosam2/index/tests/main.nf.test

@@ -0,0 +1,75 @@
+nextflow_process {
+
+ name "Test Process LEVIOSAM2_INDEX"
+ script "../main.nf"
+ process "LEVIOSAM2_INDEX"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "leviosam2"
+ tag "leviosam2/index"
+ tag "gunzip"
+
+ test("index") {
+ setup {
+ run("GUNZIP") {
+ script "../../../gunzip/main.nf"
+ process {
+ """
+ input[0] = [
+ [ id:'test' ],
+ file(params.test_data['homo_sapiens']['genome']['genome_chain_gz'], checkIfExists: true)
+ ]
+ """
+ }
+
+ }
+ }
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test' ], 
+ file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+ ]
+ input[1] = GUNZIP.out.gunzip.map{ meta, gunzip -> gunzip }
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+
+ }
+
+ test("index - stub") {
+
+ options "-stub"
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test' ], // meta map
+ file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+ ]
+ input[1] = file(params.test_data['homo_sapiens']['genome']['genome_chain_gz'], checkIfExists: true)
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+
+ }
+
+}

modules/nf-core/leviosam2/index/tests/tags.yml

@@ -0,0 +1,3 @@
+leviosam2/index:
+ - "modules/nf-core/leviosam2/index/**"
+ - "modules/nf-core/gunzip/**"