Update outputs and test data set

modules/genomescope2/main.nf

@@ -11,13 +11,13 @@ process GENOMESCOPE2 {
     tuple val(meta), path(histogram)
 
     output:
-    tuple val(meta), path("$prefix-linear_plot.png")            , emit: linear_plot_png
+    tuple val(meta), path("*_linear_plot.png")            , emit: linear_plot_png
-    tuple val(meta), path("$prefix-transformed_linear_plot.png"), emit: transformed_linear_plot_png
+    tuple val(meta), path("*_transformed_linear_plot.png"), emit: transformed_linear_plot_png
-    tuple val(meta), path("$prefix-log_plot.png")               , emit: log_plot_png
+    tuple val(meta), path("*_log_plot.png")               , emit: log_plot_png
-    tuple val(meta), path("$prefix-transformed_log_plot.png")   , emit: transformed_log_plot_png
+    tuple val(meta), path("*_transformed_log_plot.png")   , emit: transformed_log_plot_png
-    tuple val(meta), path("$prefix-model.txt")                  , emit: model
+    tuple val(meta), path("*_model.txt")                  , emit: model
-    tuple val(meta), path("$prefix-summary.txt")                , emit: summary
+    tuple val(meta), path("*_summary.txt")                , emit: summary
-    path "versions.yml"                                         , emit: versions
+    path "versions.yml"                                   , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -32,8 +32,6 @@ process GENOMESCOPE2 {
         --output . \\
         --name_prefix $prefix
 
-    ls -l
-
     cat <<-END_VERSIONS > versions.yml
     '${task.process}':
         genomescope2: \$( genomescope2 -v | sed 's/GenomeScope //' )

modules/genomescope2/meta.yml

@@ -37,7 +37,31 @@ output:
   - linear_plot_png:
       type: file
       description: A genomescope2 linear plot in PNG format
-      pattern: "*.png"
+      pattern: "*_linear_plot.png"
+  - linear_plot_png:
+      type: file
+      description: A genomescope2 linear plot in PNG format
+      pattern: "*_linear_plot.png"
+  - transformed_linear_plot_png:
+      type: file
+      description: A genomescope2 transformed linear plot in PNG format
+      pattern: "*_transformed_linear_plot.png"
+  - log_plot_png:
+      type: file
+      description: A genomescope2 log plot in PNG format
+      pattern: "*_log_plot.png"
+  - transformed_log_plot_png:
+      type: file
+      description: A genomescope2 transformed log plot in PNG format
+      pattern: "*_transformed_log_plot.png"
+  - model:
+      type: file
+      description: Genomescope2 model fit summary
+      pattern: "*_model.txt"
+  - summary:
+      type: file
+      description: Genomescope2 histogram summary
+      pattern: "*_summary.txt"
 
 authors:
   - "@mahesh-panchal"

tests/modules/genomescope2/main.nf

@@ -10,7 +10,7 @@ workflow test_genomescope2 {
 
     input = [
         [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+        file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true)
     ]
 
     MERYL_COUNT ( input )

tests/modules/genomescope2/test.yml

@@ -1,12 +1,23 @@
-## TODO nf-core: Please run the following command to build this file:
+- name: genomescope2 test_genomescope2
-#                nf-core modules create-test-yml genomescope2
+  command: nextflow run tests/modules/genomescope2 -entry test_genomescope2 -c tests/config/nextflow.config
-- name: "genomescope2"
-  command: nextflow run ./tests/modules/genomescope2 -entry test_genomescope2 -c ./tests/config/nextflow.config -c ./tests/modules/genomescope2/nextflow.config
   tags:
-    - "genomescope2"
+    - genomescope2
-    #
   files:
-    - path: "output/genomescope2/test.bam"
+    - path: output/genomescope2/test_linear_plot.png
-      md5sum: e667c7caad0bc4b7ac383fd023c654fc
+      md5sum: 94c165c5028156299a1d4d05766cac51
+    - path: output/genomescope2/test_log_plot.png
+      md5sum: 9d25ca463d92a0c73a893da7fd3979ba
+    - path: output/genomescope2/test_model.txt
+      md5sum: 3caf62f715f64a2f2b8fdff5d079cb84
+    - path: output/genomescope2/test_summary.txt
+      md5sum: 7452860e2cea99b85f3ff60daeac77f5
+    - path: output/genomescope2/test_transformed_linear_plot.png
+      md5sum: 99a64c1c18d8670f64cb863d4334abbb
+    - path: output/genomescope2/test_transformed_log_plot.png
+      md5sum: b4e029c9fb9987ca33b17392a691c1b4
     - path: output/genomescope2/versions.yml
-      md5sum: a01fe51bc4c6a3a6226fbf77b2c7cf3b
+      md5sum: 18afeb26f62a47f680b2bb3e27da9cbc
+    - path: output/meryl/test.hist
+      md5sum: f75362ab9cd70d96621b3690e952085f
+    - path: output/meryl/versions.yml
+      md5sum: 944b7ea81a82bd20174c5042857003fc