Updated test data paths batch 20 (#6106)

* Updated test data paths batch 20 * Fixed samtools/sort inputs * Updated tuple
nf-core · Aug 3, 2024 · 4ba1155 · 4ba1155
1 parent a941aa2
commit 4ba1155
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Showing 10 changed files with 35 additions and 26 deletions.
diff --git a/modules/nf-core/bamstats/generalstats/tests/main.nf.test b/modules/nf-core/bamstats/generalstats/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true)
                 ]
                 """
             }
@@ -41,7 +41,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true)
                 ]
                 """
             }

diff --git a/modules/nf-core/circularmapper/circulargenerator/tests/main.nf.test b/modules/nf-core/circularmapper/circulargenerator/tests/main.nf.test
@@ -15,7 +15,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                     ]
                 input[1] = [ [ id:'test' ], 500 ]
                 input[2] = [ [ id:'test' ],  "MT192765.1" ]
@@ -41,7 +41,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                     ]
                 input[1] = [ [ id:'test' ], 500 ]
                 input[2] = [ [ id:'test' ],  "MT192765.1" ]

diff --git a/modules/nf-core/circularmapper/realignsamfile/tests/main.nf.test b/modules/nf-core/circularmapper/realignsamfile/tests/main.nf.test
@@ -23,7 +23,7 @@ nextflow_process {
                     """
                     input[0] = [
                         [ id:'test' ], // meta map
-                        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                         ]
                 input[1] = [ [ id:'test' ], 500 ]
                 input[2] = [ [ id:'test' ],  "MT192765.1" ]
@@ -46,7 +46,7 @@ nextflow_process {
                     """
                     input[0] = [
                         [ id:'test', single_end:true ], // meta map
-                        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
                     ]
                     input [1] = BWA_INDEX.out.index
                     """
@@ -59,7 +59,7 @@ nextflow_process {
                     """
                     fastq = Channel.of([
                         [ id:'test', single_end:true ], // meta map
-                        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
                     ])
 
                     input[0] = fastq.join(BWA_ALN.out.sai)
@@ -75,7 +75,7 @@ nextflow_process {
                 input[0] = BWA_SAMSE.out.bam
                 input[1] = [
                         [ id:'test' ], // meta map
-                        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                     ]
                 input[2] = [ [ id:'test' ], 500 ]
                 """
@@ -100,11 +100,11 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id: "test" ], //meta map
-                    file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true)
                 ]
                 input[1] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ]
                 input[2] = [ [ id:'test' ], 500 ]
                 """

diff --git a/modules/nf-core/ganon/report/tests/main.nf.test b/modules/nf-core/ganon/report/tests/main.nf.test
@@ -19,7 +19,7 @@ nextflow_process {
                     """
                     input[0] = [
                                 [ id:'test' ], // meta map
-                                file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
                             ]
                     input[1] = []
                     input[2] = []
@@ -33,7 +33,7 @@ nextflow_process {
                     input[0] = [
                         [ id:'test', single_end:true ], // meta map
                         [
-                            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
                         ]
                     ]
                     input[1] = GANON_BUILDCUSTOM.out.db.map{it[1]}

diff --git a/modules/nf-core/ganon/table/tests/main.nf.test b/modules/nf-core/ganon/table/tests/main.nf.test
@@ -20,7 +20,7 @@ nextflow_process {
                     """
                     input[0] = [
                                 [ id:'test' ], // meta map
-                                file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
                             ]
                     input[1] = []
                     input[2] = []
@@ -34,7 +34,7 @@ nextflow_process {
                 input[0] = [
                     [ id:'test', single_end:true ], // meta map
                     [
-                        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
                     ]
                 ]
                 input[1] = GANON_BUILDCUSTOM.out.db.map{it[1]}

diff --git a/modules/nf-core/mudskipper/bulk/meta.yml b/modules/nf-core/mudskipper/bulk/meta.yml
@@ -34,6 +34,9 @@ input:
   - index:
       type: directory
       description: Annotation index created by mudskipper/index
+  - rad:
+      type: string
+      description: File type
 
 output:
   - meta:

diff --git a/modules/nf-core/mudskipper/bulk/tests/main.nf.test b/modules/nf-core/mudskipper/bulk/tests/main.nf.test
@@ -9,6 +9,8 @@ nextflow_process {
     tag "modules_nfcore"
     tag "mudskipper"
     tag "mudskipper/bulk"
+    tag "samtools/sort"
+    tag "mudskipper/index"
 
     test("homo_sapiens - gtf - bam") {
 
@@ -19,8 +21,9 @@ nextflow_process {
                     """
                     input[0] = [
                         [id:'test', single_end:false ], // meta map
-                         file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam", checkIfExists: true)
+                        file(params.modules_testdata_base_path +  'genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam', checkIfExists: true)
                     ]
+                    input[1] = [ [], [] ]
                     """
                 }
             }
@@ -31,7 +34,7 @@ nextflow_process {
                 """
                 input[0] = SAMTOOLS_SORT.out.bam
                 input[1] = []
-                input[2] = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)
                 input[3] = false
                 """
             }
@@ -55,8 +58,9 @@ nextflow_process {
                     """
                     input[0] = [
                         [id:'test', single_end:false ], // meta map
-                         file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam", checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam', checkIfExists: true)
                     ]
+                    input[1] = [ [], [] ]
                     """
                 }
             }
@@ -65,7 +69,7 @@ nextflow_process {
                 script "../../index/main.nf"
                 process {
                     """
-                    input[0] = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+                    input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)
                     """
                 }
             }

diff --git a/modules/nf-core/vsearch/cluster/environment.yml b/modules/nf-core/vsearch/cluster/environment.yml
@@ -1,8 +1,10 @@
 name: vsearch_cluster
+
 channels:
   - conda-forge
   - bioconda
   - defaults
+
 dependencies:
-  - bioconda::vsearch=2.21.1
   - bioconda::samtools=1.16.1
+  - bioconda::vsearch=2.21.1
diff --git a/modules/nf-core/vsearch/cluster/tests/main.nf.test b/modules/nf-core/vsearch/cluster/tests/main.nf.test
@@ -18,7 +18,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
                 ]
                 """
             }
@@ -42,7 +42,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
                 ]
                 """
             }
@@ -66,7 +66,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
                 ]
                 """
             }
@@ -90,7 +90,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
                 ]
                 """
             }
@@ -114,7 +114,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
                 ]
                 """
             }

diff --git a/modules/nf-core/vsearch/sort/tests/main.nf.test b/modules/nf-core/vsearch/sort/tests/main.nf.test
@@ -18,7 +18,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
                 ]
                 input[1] = "--sortbysize"
                 """
@@ -41,7 +41,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
                 ]
                 input[1] = "--sortbylength"
                 """