Now using a minimal bioconda recipe for ltr_finder_parallel (nf-core#…

…4931) * Now using a minimal bioconda recipe for ltr_finder_parallel * Added missing tag
asp8200 · Feb 16, 2024 · 85b12bc · 85b12bc
1 parent 9ac53f7
commit 85b12bc
Show file tree

Hide file tree

Showing 5 changed files with 77 additions and 39 deletions.
diff --git a/modules/nf-core/ltrfinder/environment.yml b/modules/nf-core/ltrfinder/environment.yml
@@ -6,4 +6,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - "bioconda::edta=2.2.0"
+  - "bioconda::ltr_finder_parallel=1.1"
diff --git a/modules/nf-core/ltrfinder/main.nf b/modules/nf-core/ltrfinder/main.nf
@@ -4,8 +4,8 @@ process LTRFINDER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/edta:2.2.0--hdfd78af_1':
-        'biocontainers/edta:2.2.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/ltr_finder_parallel:1.1--hdfd78af_0':
+        'biocontainers/ltr_finder_parallel:1.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(fasta)

diff --git a/modules/nf-core/ltrfinder/tests/main.nf.test b/modules/nf-core/ltrfinder/tests/main.nf.test
@@ -7,16 +7,29 @@ nextflow_process {
     tag "modules"
     tag "modules_nfcore"
     tag "ltrfinder"
+    tag "gunzip/main"
 
-    test("homo_sapiens-genome_fasta-success") {
+    test("actinidia_chinensis-genome_21_fasta_gz-success") {
+
+        setup {
+            run('GUNZIP') {
+                script "../../gunzip/main"
+
+                process {
+                    """
+                    input[0] = [
+                        [ id:'test' ], // meta map
+                        file(params.test_data['actinidia_chinensis']['genome']['genome_21_fasta_gz'], checkIfExists: true)
+                    ]
+                    """
+                }
+            }
+        }
 
         when {
             process {
                 """
-                input[0] = [
-                    [ id:'test' ], // meta map
-                    file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-                ]
+                input[0] = GUNZIP.out.gunzip
                 """
             }
         }
@@ -25,7 +38,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(process.out).match() },
-                { assert snapshot(process.out.versions).match("versions") }
+                { assert snapshot(path(process.out.versions[0]).text).match("versions") }
             )
         }
 
@@ -40,7 +53,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+                    file(params.test_data['actinidia_chinensis']['genome']['genome_21_fasta_gz'], checkIfExists: true)
                 ]
                 """
             }
@@ -50,7 +63,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(process.out).match() },
-                { assert snapshot(process.out.versions).match("versions") }
+                { assert snapshot(path(process.out.versions[0]).text).match("stub_versions") }
             )
         }
 

diff --git a/modules/nf-core/ltrfinder/tests/main.nf.test.snap b/modules/nf-core/ltrfinder/tests/main.nf.test.snap
diff --git a/tests/config/test_data.config b/tests/config/test_data.config
@@ -626,10 +626,15 @@ params {
         }
         'saccharomyces_cerevisiae' {
             'genome' {
-                samplesheet                                    = "${params.test_data_base}/data/genomics/eukaryotes/saccharomyces_cerevisiae/samplesheet.csv"
-                genome_gfp_gtf                                 = "${params.test_data_base}/data/genomics/eukaryotes/saccharomyces_cerevisiae/genome_gfp.gtf"
-		kallisto_results                               = "${params.test_data_base}/data/genomics/eukaryotes/saccharomyces_cerevisiae/kallisto_results.tar.gz"
-                salmon_results                                 = "${params.test_data_base}/data/genomics/eukaryotes/saccharomyces_cerevisiae/salmon_results.tar.gz"
+                samplesheet                     = "${params.test_data_base}/data/genomics/eukaryotes/saccharomyces_cerevisiae/samplesheet.csv"
+                genome_gfp_gtf                  = "${params.test_data_base}/data/genomics/eukaryotes/saccharomyces_cerevisiae/genome_gfp.gtf"
+		        kallisto_results                = "${params.test_data_base}/data/genomics/eukaryotes/saccharomyces_cerevisiae/kallisto_results.tar.gz"
+                salmon_results                  = "${params.test_data_base}/data/genomics/eukaryotes/saccharomyces_cerevisiae/salmon_results.tar.gz"
+            }
+        }
+        'actinidia_chinensis' {
+            'genome' {
+                genome_21_fasta_gz              = "${params.test_data_base}/data/genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.fasta.gz"
             }
         }
         'generic' {