From ee5f59705f61a93ed9af59e19da1b1f2240648e8 Mon Sep 17 00:00:00 2001
From: Michael L Heuer <heuermh@acm.org>
Date: Wed, 28 Sep 2022 03:23:18 -0500
Subject: [PATCH] Adding new module gfaffix (#1149)

* Adding new module gfaffix.

* add missing entry to pytest_modules.yml

* update to 0.1.4--hec16e2b_0

* fixup after prettier

* add when section

* update md5sum

* Change to process_single as discussed

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Co-authored-by: Simon Heumos <simon.heumos@qbic.uni-tuebingen.de>
---
 modules/gfaffix/main.nf               | 36 +++++++++++++++++++++
 modules/gfaffix/meta.yml              | 46 +++++++++++++++++++++++++++
 tests/config/pytest_modules.yml       |  4 +++
 tests/modules/gfaffix/main.nf         | 13 ++++++++
 tests/modules/gfaffix/nextflow.config |  5 +++
 tests/modules/gfaffix/test.yml        |  9 ++++++
 6 files changed, 113 insertions(+)
 create mode 100644 modules/gfaffix/main.nf
 create mode 100644 modules/gfaffix/meta.yml
 create mode 100644 tests/modules/gfaffix/main.nf
 create mode 100644 tests/modules/gfaffix/nextflow.config
 create mode 100644 tests/modules/gfaffix/test.yml

diff --git a/modules/gfaffix/main.nf b/modules/gfaffix/main.nf
new file mode 100644
index 00000000..3ae5ad66
--- /dev/null
+++ b/modules/gfaffix/main.nf
@@ -0,0 +1,36 @@
+process GFAFFIX {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda (params.enable_conda ? 'bioconda::gfaffix=0.1.4' : null)
+
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gfaffix:0.1.4--hec16e2b_0' :
+        'quay.io/biocontainers/gfaffix:0.1.4--hec16e2b_0' }"
+
+    input:
+    tuple val(meta), path(gfa)
+
+    output:
+    tuple val(meta), path("*.gfa"), emit: gfa
+    tuple val(meta), path("*.txt"), emit: affixes
+    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}"
+    """
+    gfaffix \\
+        $args \\
+        $gfa \\
+        -o ${prefix}.gfaffix.gfa > ${prefix}.affixes.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gfaffix: \$(gfaffix --version 2>&1 | grep -o 'gfaffix .*' | cut -f2 -d ' ')
+    END_VERSIONS
+    """
+}
diff --git a/modules/gfaffix/meta.yml b/modules/gfaffix/meta.yml
new file mode 100644
index 00000000..0c3924a3
--- /dev/null
+++ b/modules/gfaffix/meta.yml
@@ -0,0 +1,46 @@
+name: gfaffix
+description: Collapse walk-preserving shared affixes in variation graphs in GFA format
+keywords:
+  - gfa
+  - graph
+  - pangenome
+  - variation graph
+tools:
+  - gfaffix:
+      description: |
+        GFAffix identifies walk-preserving shared affixes in variation graphs and
+        collapses them into a non-redundant graph structure.
+      homepage: https://github.com/marschall-lab/GFAffix
+      documentation: https://github.com/marschall-lab/GFAffix
+      licence: ["MIT"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - gfa:
+      type: file
+      description: Variation graph in GFA format
+      pattern: "*.{gfa}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - gfa:
+      type: file
+      description: Non-redundant variation graph in GFA 1.0 format
+      pattern: "*.{gfa}"
+  - affixes:
+      type: file
+      description: Shared affixes in tab-separated values (TSV) text format
+      pattern: "*.{txt}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@heuermh"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 99df6ba1..ec981331 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1087,6 +1087,10 @@ genrich:
   - modules/genrich/**
   - tests/modules/genrich/**
 
+gfaffix:
+  - modules/gfaffix/**
+  - tests/modules/gfaffix/**
+
 gffread:
   - modules/gffread/**
   - tests/modules/gffread/**
diff --git a/tests/modules/gfaffix/main.nf b/tests/modules/gfaffix/main.nf
new file mode 100644
index 00000000..333866c0
--- /dev/null
+++ b/tests/modules/gfaffix/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GFAFFIX } from '../../../modules/gfaffix/main.nf'
+
+workflow test_gfaffix {
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['assembly_gfa'], checkIfExists: true)]
+            ]
+
+    GFAFFIX ( input )
+}
diff --git a/tests/modules/gfaffix/nextflow.config b/tests/modules/gfaffix/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/gfaffix/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/gfaffix/test.yml b/tests/modules/gfaffix/test.yml
new file mode 100644
index 00000000..d88db7c6
--- /dev/null
+++ b/tests/modules/gfaffix/test.yml
@@ -0,0 +1,9 @@
+- name: gfaffix
+  command: nextflow run ./tests/modules/gfaffix -entry test_gfaffix -c ./tests/config/nextflow.config -c ./tests/modules/gfaffix/nextflow.config
+  tags:
+    - gfaffix
+  files:
+    - path: output/gfaffix/test.gfaffix.gfa
+      md5sum: 7b51abeeab7706393957fcb66d31704a
+    - path: output/gfaffix/test.affixes.txt
+      md5sum: c3540baa386462552d7ebe4e4b7eda6a