From 3ef618fed25c5929a065fe775cef3de1f5dc2b60 Mon Sep 17 00:00:00 2001
From: "Robert A. Petit III" <robbie.petit@gmail.com>
Date: Wed, 7 Sep 2022 09:29:28 -0600
Subject: [PATCH] add module for pasty (#2003)

* add module for pasty

* run prettier

* line up those commas

* Update main.nf
---
 modules/pasty/main.nf               | 36 ++++++++++++++++++++
 modules/pasty/meta.yml              | 52 +++++++++++++++++++++++++++++
 tests/config/pytest_modules.yml     |  4 +++
 tests/modules/pasty/main.nf         | 13 ++++++++
 tests/modules/pasty/nextflow.config |  5 +++
 tests/modules/pasty/test.yml        | 11 ++++++
 6 files changed, 121 insertions(+)
 create mode 100644 modules/pasty/main.nf
 create mode 100644 modules/pasty/meta.yml
 create mode 100644 tests/modules/pasty/main.nf
 create mode 100644 tests/modules/pasty/nextflow.config
 create mode 100644 tests/modules/pasty/test.yml

diff --git a/modules/pasty/main.nf b/modules/pasty/main.nf
new file mode 100644
index 00000000..35aec314
--- /dev/null
+++ b/modules/pasty/main.nf
@@ -0,0 +1,36 @@
+process PASTY {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda (params.enable_conda ? "bioconda::pasty=1.0.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/pasty:1.0.0--hdfd78af_0':
+        'quay.io/biocontainers/pasty:1.0.0--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("${prefix}.tsv")        , emit: tsv
+    tuple val(meta), path("${prefix}.blastn.tsv") , emit: blast
+    tuple val(meta), path("${prefix}.details.tsv"), emit: details
+    path "versions.yml"                           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    pasty \\
+        $args \\
+        --prefix $prefix \\
+        --assembly $fasta
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pasty: \$(echo \$(pasty --version 2>&1) | sed 's/^.*pasty, version //;' )
+    END_VERSIONS
+    """
+}
diff --git a/modules/pasty/meta.yml b/modules/pasty/meta.yml
new file mode 100644
index 00000000..718abf81
--- /dev/null
+++ b/modules/pasty/meta.yml
@@ -0,0 +1,52 @@
+name: "pasty"
+description: Serogroup Pseudomonas aeruginosa assemblies
+keywords:
+  - bacteria
+  - serogroup
+  - fasta
+  - assembly
+tools:
+  - "pasty":
+      description: "A tool for in silico serogrouping of Pseudomonas aeruginosa isolates"
+      homepage: "https://github.com/rpetit3/pasty"
+      documentation: "https://github.com/rpetit3/pasty"
+      tool_dev_url: "https://github.com/rpetit3/pasty"
+      doi: ""
+      licence: "['Apache-2.0']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fasta:
+      type: file
+      description: An assembly in FASTA format
+      pattern: "*.{fasta,fasta.gz,fna,fna.gz,fa,fa.gz}"
+
+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"
+  - tsv:
+      type: file
+      description: A tab-delimited file with the predicted serogroup
+      pattern: "*.tsv"
+  - blast:
+      type: file
+      description: A tab-delimited file of all blast hits
+      pattern: "*.blastn.tsv"
+  - details:
+      type: file
+      description: A tab-delimited file with details for each serogroup
+      pattern: "*.details.tsv"
+
+authors:
+  - "@rpetit3"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 62343b70..0b06af4e 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1707,6 +1707,10 @@ paraclu:
   - modules/paraclu/**
   - tests/modules/paraclu/**
 
+pasty:
+  - modules/pasty/**
+  - tests/modules/pasty/**
+
 pbbam/pbmerge:
   - modules/pbbam/pbmerge/**
   - tests/modules/pbbam/pbmerge/**
diff --git a/tests/modules/pasty/main.nf b/tests/modules/pasty/main.nf
new file mode 100644
index 00000000..2dc5ea98
--- /dev/null
+++ b/tests/modules/pasty/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PASTY } from '../../../modules/pasty/main.nf'
+
+workflow test_pasty {
+    
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    PASTY ( input )
+}
diff --git a/tests/modules/pasty/nextflow.config b/tests/modules/pasty/nextflow.config
new file mode 100644
index 00000000..50f50a7a
--- /dev/null
+++ b/tests/modules/pasty/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}
\ No newline at end of file
diff --git a/tests/modules/pasty/test.yml b/tests/modules/pasty/test.yml
new file mode 100644
index 00000000..3a4e9b12
--- /dev/null
+++ b/tests/modules/pasty/test.yml
@@ -0,0 +1,11 @@
+- name: pasty test_pasty
+  command: nextflow run ./tests/modules/pasty -entry test_pasty -c ./tests/config/nextflow.config  -c ./tests/modules/pasty/nextflow.config
+  tags:
+    - pasty
+  files:
+    - path: output/pasty/test.blastn.tsv
+      md5sum: 45de2825f0bb3cc8fe9f2b7c419f66f2
+    - path: output/pasty/test.details.tsv
+      md5sum: d6822beea048a27af839087dfc14a536
+    - path: output/pasty/test.tsv
+      md5sum: edbae35d3edc17283ea73f7f3eb22087