Ucsc/bedgraphtobigwig nftest (nf-core#4136)

* add nf-test and snapshot for umitools/extract

* remove pytest tag and add nf-test tag

* add nftest and snapshot for ucsc/bedgraphtobigwig

* Update modules/nf-core/ucsc/bedgraphtobigwig/tests/tags.yml

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

* Update modules/nf-core/umitools/extract/tests/main.nf.test

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

* [automated] Fix linting with Prettier

* Feat/fastp nf-test (nf-core#4028)

* init nf-test fastp

* add initial test fastp

* init html test fastp

* all tests fastp

* unequal files reads.fastq.gz

* finishing tests (finally)

* removing fastp from pytest

* fixing tag fastp

* adding the s

* adding relative path

---------

Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>

* Rasusa nf test (nf-core#4081)

* Initial main.nf.test

* Full nf-test suite for module rasusa

* add "modules" tag to nf-test

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* Remove tags from tests/config/pytest_modules.yml

---------

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* Glimpse ligate nftest (nf-core#4048)

* Restart as new

* Delete pytest from config

* Update main.nf.test

* Glimpse chunk nftest (nf-core#4034)

* Add nf-test for glimpse_chunk

* Delete pytest for glimpse 1 not glimpse 2

* Update main.nf.test

* Added fq nf-tests (nf-core#4084)

* Added fq nf-tests

* Removed from pytest suite

* Test fix

---------

Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>

* Feat/gunzip nf tests (nf-core#4103)

* add nf-test and snapshot for gunzip

* add modules/nf-core/gunzip/tests/tags.yml

* remove gunzip from tests/config/pytest_modules.yml for switch to nf-test

---------

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* added nf-test files for art/illumina (nf-core#4038)

* added nf-test files

- two tests (single- and paired-end)
- including two nextflow.configs for `ext.args`

* change tests topass on conda/mamba and singularity/docker

- due to gzip the fastq files will have different md5sums with different engines

* added art/illumina

- should trigger the nf-test CI

* extended tag to art/illumina

* fixed typos -.-

* fixed typo again

- missing quote

* renamed test.yml to tags.yml

* removed art/illumina

* added <tool> tag

* added nf-tests for -stub-run

---------

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* nf-test for module sourmash/sketch (nf-core#4104)

* nf-test for module sourmash/sketch

* add "sourmash" and "sourmash/sketch" tags

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

---------

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* Renovate migrate (nf-core#4114)

* chore: Migrate renovate config

https://github.com/renovatebot/renovate/blob/main/docs/usage/config-validation.md
renovate-config-validator

* style: Add renovate to prettier ignore list

* Feat/picard_markduplicates nf-test  (nf-core#4096)

* picard nf-test init

* created first (failing)test

* tests succeeding

---------

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* Rename test.yml in getchromsizes (nf-core#4118)

* Rename test.yml and trigger pytest

* Update main.nf

* Feat/trimgalore nf-test (nf-core#4110)

* trimgalore nf-test init

* relative paths

* Update modules/nf-core/trimgalore/tests/main.nf.test

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

---------

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* nf-test migration (nf-core#4113)

* nf-test for module fastqscan (nf-core#4097)

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* Mlst nf test and version bump to 2.23 (nf-core#4061)

* add nf-test to module mlst

* fix ownership for nf-test

* add "modules" tag to nf-test

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

* Add module keywords to meta.yml

* Lint meta.yml

* Update to mlst version 2.23

* Update snap with new versions.yml after bump to v2.23

* Remove mlst from pytest_modules

---------

Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>

* remove umitools/extract files

* Apply suggestions from code review

* remove umitools tests

* Apply suggestions from code review

* Update tests/config/pytest_modules.yml

---------

Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Co-authored-by: nf-core-bot <core@nf-co.re>
Co-authored-by: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com>
Co-authored-by: Koen Bossers <61537771+koenbossers@users.noreply.github.com>
Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Louis LE NEZET <58640615+LouisLeNezet@users.noreply.github.com>
Co-authored-by: KamilMaliszArdigen <32459801+KamilMaliszArdigen@users.noreply.github.com>
Co-authored-by: Kevin Ryan <65914327+kevinpryan@users.noreply.github.com>
Co-authored-by: MarieLataretu <52002068+MarieLataretu@users.noreply.github.com>
Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>

modules/nf-core/ucsc/bedgraphtobigwig/tests/main.nf.test

@@ -0,0 +1,36 @@
+nextflow_process {
+
+    name "Test Process UCSC_BEDGRAPHTOBIGWIG"
+    script "../main.nf"
+    process "UCSC_BEDGRAPHTOBIGWIG"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "ucsc"
+    tag "ucsc/bedgraphtobigwig"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = [ [ id:'test' ], // meta map
+                    [ file(params.test_data['sarscov2']['illumina']['test_bedgraph'], checkIfExists: true) ]
+                    ]
+                input[1] = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll (
+            { assert process.success },
+            { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/ucsc/bedgraphtobigwig/tests/tags.yml

@@ -0,0 +1,2 @@
+ucsc/bedgraphtobigwig:
+  - modules/nf-core/ucsc/bedgraphtobigwig/**

tests/config/pytest_modules.yml

@@ -3935,10 +3935,6 @@ ucsc/bedclip:
   - modules/nf-core/ucsc/bedclip/**
   - tests/modules/nf-core/ucsc/bedclip/**
 
-ucsc/bedgraphtobigwig:
-  - modules/nf-core/ucsc/bedgraphtobigwig/**
-  - tests/modules/nf-core/ucsc/bedgraphtobigwig/**
-
 ucsc/bedtobigbed:
   - modules/nf-core/ucsc/bedtobigbed/**
   - tests/modules/nf-core/ucsc/bedtobigbed/**
@@ -3981,7 +3977,6 @@ umicollapse:
 
 umitools/dedup:
   - modules/nf-core/umitools/dedup/**
-  - modules/nf-core/umitools/extract/**
   - tests/modules/nf-core/umitools/dedup/**
 
 umitools/extract: