Convert ngscheckmate/vafncm to nf-test (nf-core#5696)

* Add tests for vafncm

* Fix linting

modules/nf-core/ngscheckmate/vafncm/main.nf

@@ -43,6 +43,7 @@ process NGSCHECKMATE_VAFNCM {
 
  stub:
  def args = task.ext.args ?: ''
+ def prefix = task.ext.prefix ?: "${meta.id}"
 
  """
  touch ${prefix}_corr_matrix.txt

modules/nf-core/ngscheckmate/vafncm/tests/main.nf.test

@@ -0,0 +1,155 @@
+nextflow_process {
+
+ name "Test Process NGSCHECKMATE_VAFNCM"
+ script "../main.nf"
+ config "./nextflow.config"
+ process "NGSCHECKMATE_VAFNCM"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "ngscheckmate"
+ tag "ngscheckmate/vafncm"
+ tag "gawk"
+ tag "bedtools/makewindows"
+ tag "bowtie/build"
+ tag "ngscheckmate/patterngenerator"
+ tag "ngscheckmate/fastq"
+
+ setup {
+
+ run("GAWK" , alias: "GAWK_FAI") {
+ script "../../../gawk/main.nf"
+ process {
+ """
+ input[0] = [
+ [ id: 'sarscov2' ],
+ file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+ ]
+ input[1] = []
+ """
+ }
+ }
+
+ run("BEDTOOLS_MAKEWINDOWS") {
+ script "../../../bedtools/makewindows/main.nf"
+ process {
+ """
+ input[0] = GAWK_FAI.out.output
+ """
+ }
+ }
+
+ run("GAWK" , alias: "GAWK_BED") {
+ script "../../../gawk/main.nf"
+ process {
+ """
+ input[0] = BEDTOOLS_MAKEWINDOWS.out.bed
+ input[1] = []
+ """
+ }
+ }
+
+ run("BOWTIE_BUILD") {
+ script "../../../bowtie/build/main.nf"
+ process {
+ """
+ input[0] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+ """
+ }
+ }
+
+ run("NGSCHECKMATE_PATTERNGENERATOR") {
+ script "../../patterngenerator/main.nf"
+ process {
+ """
+ input[0] = GAWK_BED.out.output
+ input[1] = [
+ [ id: 'sarscov2' ],
+ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+ ]
+ input[2] = BOWTIE_BUILD.out.index
+ """
+ }
+ }
+
+ run("NGSCHECKMATE_FASTQ") {
+ script "../../fastq/main.nf"
+ process {
+ """
+ input[0] = channel.fromList(
+ [
+ [
+ [ id:'test1', single_end:false ], // meta map
+ [
+ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+ file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+ ]
+ ],
+ [
+ [ id:'test2', single_end:false ], // meta map
+ [
+ file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true),
+ file(params.test_data['sarscov2']['illumina']['test2_2_fastq_gz'], checkIfExists: true)
+ ]
+ ],
+ [
+ [ id:'test3', single_end:false ], // meta map
+ [
+ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true),
+ file(params.test_data['sarscov2']['illumina']['test_methylated_2_fastq_gz'], checkIfExists: true)
+ ]
+ ],
+ ]
+ )
+ input[1] = NGSCHECKMATE_PATTERNGENERATOR.out.pt
+ """
+ }
+ }
+
+ }
+
+ test("sarscov2 - fastq") {
+
+ when {
+ process {
+ """
+ input[0] = NGSCHECKMATE_FASTQ.out.vaf.map{it[1]}.collect().map{files -> [[id:"combined"], files]}
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ process.out.corr_matrix,
+ process.out.matched,
+ process.out.all,
+ process.out.versions).match() }
+ )
+ }
+
+ }
+
+ test("sarscov2 - fastq - stub") {
+
+ options "-stub"
+
+ when {
+ process {
+ """
+ input[0] = NGSCHECKMATE_FASTQ.out.vaf.map{it[1]}.collect().map{files -> [[id:"combined"], files]}
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+
+ }
+
+}

modules/nf-core/ngscheckmate/vafncm/tests/main.nf.test.snap

@@ -0,0 +1,119 @@
+{
+ "sarscov2 - fastq - stub": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "combined"
+ },
+ "combined.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "1": [
+ [
+ {
+ "id": "combined"
+ },
+ "combined_corr_matrix.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "2": [
+ [
+ {
+ "id": "combined"
+ },
+ "combined_all.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "3": [
+ [
+ {
+ "id": "combined"
+ },
+ "combined_matched.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "4": [
+ "versions.yml:md5,e8fcb7ac4528e05b40b58825c13220f0"
+ ],
+ "all": [
+ [
+ {
+ "id": "combined"
+ },
+ "combined_all.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "corr_matrix": [
+ [
+ {
+ "id": "combined"
+ },
+ "combined_corr_matrix.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "matched": [
+ [
+ {
+ "id": "combined"
+ },
+ "combined_matched.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "pdf": [
+ [
+ {
+ "id": "combined"
+ },
+ "combined.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,e8fcb7ac4528e05b40b58825c13220f0"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.1"
+ },
+ "timestamp": "2024-05-26T08:37:18.164420662"
+ },
+ "sarscov2 - fastq": {
+ "content": [
+ [
+ [
+ {
+ "id": "combined"
+ },
+ "output_corr_matrix.txt:md5,fe8139cc3dffb7df41d17aa24c599dba"
+ ]
+ ],
+ [
+ [
+ {
+ "id": "combined"
+ },
+ "combined_matched.txt:md5,60d6159595026c2365acce3dbaa9677e"
+ ]
+ ],
+ [
+ [
+ {
+ "id": "combined"
+ },
+ "combined_all.txt:md5,6e7c7446bb308af84ee9b1689e1e60ee"
+ ]
+ ],
+ [
+ "versions.yml:md5,e8fcb7ac4528e05b40b58825c13220f0"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.1"
+ },
+ "timestamp": "2024-05-26T08:42:46.60890226"
+ }
+}

tests/modules/nf-core/ngscheckmate/vafncm/nextflow.config → modules/nf-core/ngscheckmate/vafncm/tests/nextflow.config

@@ -1,22 +1,16 @@
 process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
  withName: BEDTOOLS_MAKEWINDOWS {
  ext.args = '-w 1'
  ext.prefix = 'test_split'
  }
-
  withName: GAWK_BED {
  ext.args2 = '\'NR > 20 && NR < 20000 && FS = OFS = "\t" { print $0 FS "rs1" FS "G" FS "C" }\''
  ext.prefix = 'snp'
  ext.suffix = "bed"
  }
-
  withName: GAWK_FAI {
  ext.args2 = '\'BEGIN { FS = OFS = "\t" } { print \$1 FS "0" FS \$2 }\''
  ext.prefix = 'fasta'
  ext.suffix = "bed"
  }
-
 }

modules/nf-core/ngscheckmate/vafncm/tests/tags.yml

@@ -0,0 +1,2 @@
+ngscheckmate/vafncm:
+ - "modules/nf-core/ngscheckmate/vafncm/**"

tests/config/pytest_modules.yml

@@ -1205,9 +1205,6 @@ ngscheckmate/fastq:
 ngscheckmate/patterngenerator:
  - modules/nf-core/ngscheckmate/patterngenerator/**
  - tests/modules/nf-core/ngscheckmate/patterngenerator/**
-ngscheckmate/vafncm:
- - modules/nf-core/ngscheckmate/vafncm/**
- - tests/modules/nf-core/ngscheckmate/vafncm/**
 nucmer:
  - modules/nf-core/nucmer/**
  - tests/modules/nf-core/nucmer/**