Merge pull request #1623 from nf-core/correcting_stubs

fix added correct entry workflow in test.yml

tests/modules/gatk4/mergebamalignment/main.nf

@@ -17,11 +17,11 @@ workflow test_gatk4_mergebamalignment {
 
 workflow test_gatk4_mergebamalignment_stubs {
      input    = [ [ id:'test' ], // meta map
-                 "test_foo.bam",
+                 file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
-                 "test_bar.bam"
+                 file(params.test_data['sarscov2']['illumina']['test_unaligned_bam'], checkIfExists: true)
                ]
-    fasta    = "genome.fasta"
+    fasta    = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    dict     = "genome.fasta.dict"
+    dict     = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
 
     GATK4_MERGEBAMALIGNMENT ( input, fasta, dict )
 }

tests/modules/gatk4/mergebamalignment/test.yml

@@ -9,7 +9,7 @@
     - path: output/gatk4/versions.yml
 
 - name: gatk4 mergebamalignment test_gatk4_mergebamalignment_stubs
-  command: nextflow run ./tests/modules/gatk4/mergebamalignment -entry test_gatk4_mergebamalignment -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mergebamalignment/nextflow.config -stub-run
+  command: nextflow run ./tests/modules/gatk4/mergebamalignment -entry test_gatk4_mergebamalignment_stubs -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mergebamalignment/nextflow.config -stub-run
   tags:
     - gatk4
     - gatk4/mergebamalignment

tests/modules/gatk4/mutect2/main.nf

@@ -121,22 +121,22 @@ workflow test_gatk4_mutect2_mitochondria {
 
 workflow test_gatk4_mutect2_tumor_normal_pair_f1r2_stubs {
      input = [ [ id:'test', normal_id:'normal', tumor_id:'tumour' ], // meta map
-              [ "foo_paired.bam",
+              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
-                "foo_paired2.bam"
+                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)
                 ],
-              [ "foo_paired.bam.bai",
+              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
-                "foo_paired2.bam.bai"
+                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)
                 ],
               []
             ]
 
-    fasta = "genome.fasta"
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai = "genome.fasta.fai"
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-    dict = "genome.fasta.dict"
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
-    germline_resource = "genome_gnomAD.r2.1.1.vcf.gz"
+    germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
-    germline_resource_tbi = "genome_gnomAD.r2.1.1.vcf.gz.tbi"
+    germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
-    panel_of_normals = "genome_mills_and_1000G.indels.hg38.vcf.gz"
+    panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true)
-    panel_of_normals_tbi = "genome_mills_and_1000G.indels.hg38.vcf.gz.tbi"
+    panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true)
 
     GATK4_MUTECT2_F1R2 ( input, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
 }

tests/modules/gatk4/mutect2/test.yml

@@ -71,7 +71,7 @@
     - path: output/gatk4/versions.yml
 
 - name: gatk4 mutect2 test_gatk4_mutect2_tumor_normal_pair_f1r2_stubs
-  command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_normal_pair_f1r2 -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/nextflow.config -stub-run
+  command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_normal_pair_f1r2_stubs -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/nextflow.config -stub-run
   tags:
     - gatk4
     - gatk4/mutect2

tests/modules/gatk4/revertsam/main.nf

@@ -14,7 +14,7 @@ workflow test_gatk4_revertsam {
 
 workflow test_gatk4_revertsam_stubs {
     input = [ [ id:'test' ], // meta map
-              "foo_paired_end.bam"
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
             ]
 
     GATK4_REVERTSAM ( input )

tests/modules/gatk4/revertsam/test.yml

@@ -9,7 +9,7 @@
     - path: output/gatk4/versions.yml
 
 - name: gatk4 revertsam test_gatk4_revertsam_stubs
-  command: nextflow run ./tests/modules/gatk4/revertsam -entry test_gatk4_revertsam -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/revertsam/nextflow.config -stub-run
+  command: nextflow run ./tests/modules/gatk4/revertsam -entry test_gatk4_revertsam_stubs -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/revertsam/nextflow.config -stub-run
   tags:
     - gatk4
     - gatk4/revertsam

tests/modules/gatk4/samtofastq/main.nf

@@ -21,8 +21,8 @@ workflow test_gatk4_samtofastq_paired_end {
 }
 
 workflow test_gatk4_samtofastq_paired_end_stubs {
-    input = [ [ id:'test', single_end: false ], // meta map
+    input = [ [ id:'test', single_end: true ], // meta map
-              [ "foo_paired_end.bam" ]
+              [ file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ]
             ]
 
     GATK4_SAMTOFASTQ ( input )

tests/modules/gatk4/samtofastq/test.yml

@@ -21,7 +21,7 @@
     - path: output/gatk4/versions.yml
 
 - name: gatk4 samtofastq test_gatk4_samtofastq_paired_end_stubs
-  command: nextflow run ./tests/modules/gatk4/samtofastq -entry test_gatk4_samtofastq_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/samtofastq/nextflow.config -stub-run
+  command: nextflow run ./tests/modules/gatk4/samtofastq -entry test_gatk4_samtofastq_paired_end_stubs -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/samtofastq/nextflow.config -stub-run
   tags:
     - gatk4
     - gatk4/samtofastq

tests/modules/samtools/view/main.nf

@@ -25,7 +25,7 @@ workflow test_samtools_view_cram {
 
 workflow test_samtools_view_stubs {
     input = [ [ id:'test', single_end:false ], // meta map
-                "foo_paired_end.bam",
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
                 []
             ]
 

tests/modules/samtools/view/test.yml

@@ -16,7 +16,7 @@
     - path: output/samtools/test.cram
 
 - name: samtools view test_samtools_view_stubs
-  command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view -c ./tests/config/nextflow.config -c ./tests/modules/samtools/view/nextflow.config -stub-run
+  command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view_stubs -c ./tests/config/nextflow.config -c ./tests/modules/samtools/view/nextflow.config -stub-run
   tags:
     - samtools/view
     - samtools