Adding module for miniprot_index. Closes #1. (#29)

* Adding module for miniprot_index. Closes #1. * Adding module for miniprot_index. Closes #1. * Adding module for miniprot_index. Closes #1. * Adding module for miniprot_index. Closes #1. * Adding module for miniprot_index. Closes #1. * Adding module for miniprot_index. Closes #1. * update the wrong file name * put back the test data path * change index file name Co-authored-by: Guoying Qi <[email protected]>
nf-core · Nov 4, 2022 · 5f56c87 · 5f56c87
1 parent b7c199a
commit 5f56c87
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diff --git a/modules/miniprot/index/main.nf b/modules/miniprot/index/main.nf
@@ -0,0 +1,35 @@
+process MINIPROT_INDEX {
+    tag "$meta.id"
+    label 'process_medium'
+    def version = '0.5-c2'
+    if (params.enable_conda) {
+        exit 1, "Conda environments cannot be used when using the miniprot process. Please use docker or singularity containers."
+    }
+    container "quay.io/sanger-tol/miniprot:${version}"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("*.mpi"), emit: index
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+
+    """
+    miniprot \\
+        -t $task.cpus \\
+        -d ${fasta.baseName}.mpi \\
+        $args \\
+        $fasta
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        miniprot: $version
+    END_VERSIONS
+    """
+}
diff --git a/modules/miniprot/index/meta.yml b/modules/miniprot/index/meta.yml
@@ -0,0 +1,39 @@
+name: miniprot_index
+description: Provides fasta index required by miniprot alignment.
+keywords:
+  - index
+  - fasta
+  - reference
+tools:
+  - miniprot:
+      description: |
+        A versatile pairwise aligner for genomic and protein sequences.
+      homepage: https://github.com/lh3/miniprot
+      documentation: https://github.com/lh3/miniprot
+      licence: ["MIT"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fasta:
+      type: file
+      description: |
+        Reference database in FASTA format.
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - index:
+      type: file
+      description: miniprot fasta index.
+      pattern: "*.mpi"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@yumisims"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -1682,6 +1682,10 @@ minimap2/index:
   - modules/minimap2/index/**
   - tests/modules/minimap2/index/**
 
+miniprot/index:
+  - modules/miniprot/index/**
+  - tests/modules/miniprot/index/**
+
 mlst:
   - modules/mlst/**
   - tests/modules/mlst/**

diff --git a/tests/config/test_data.config b/tests/config/test_data.config
@@ -554,6 +554,9 @@ params {
                 }
             }
             'Oscheius_sp' {
+                'assembly'{
+                    assembly_fasta                                 ="${tol_test_data_dir}/Oscheius_sp/assembly//nxOscSpef2.fasta"                        
+                }
                 'genomic_data' {
                     'nxOscSpen2' {
                         'selfcomp' {

diff --git a/tests/modules/miniprot/index/main.nf b/tests/modules/miniprot/index/main.nf
@@ -0,0 +1,10 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MINIPROT_INDEX } from '../../../../modules/miniprot/index/main.nf'
+
+workflow test_miniprot_index {
+    fasta =file(params.tol_test_data['small_genome']['Oscheius_sp']['assembly']['assembly_fasta'],checkIfExists: true)
+    MINIPROT_INDEX ( [ [id:'test'], fasta ] )
+}
diff --git a/tests/modules/miniprot/index/nextflow.config b/tests/modules/miniprot/index/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/miniprot/index/test.yml b/tests/modules/miniprot/index/test.yml
@@ -0,0 +1,10 @@
+- name: miniprot index
+  command: nextflow run ./tests/modules/miniprot/index -entry test_miniprot_index -c ./tests/config/nextflow.config -c ./tests/modules/miniprot/index/nextflow.config
+  tags:
+    - miniprot
+    - miniprot/index
+  files:
+    - path: output/miniprot/nxOscSpef2.mpi
+      md5sum: ec3d98dc989e73873afe5b529c84c022
+    - path: output/miniprot/versions.yml
+      md5sum: b191a09118135126e3da7080ad64983d