Simplify number of biobox feature tests run

features/biobox.feature

@@ -14,6 +14,7 @@ Feature: A CLI to run biobox-compatible Docker containers
       | --version |
       | -v        |
 
+
   Scenario Outline: Getting help documentation
     When I run the command:
       """
@@ -31,6 +32,7 @@ Feature: A CLI to run biobox-compatible Docker containers
       | --help |
       | -h     |
 
+
   Scenario: Getting help documentation for a biobox type
     When I run the command:
       """
@@ -44,6 +46,28 @@ Feature: A CLI to run biobox-compatible Docker containers
       """
     And the exit code should be 0
 
+
+  Scenario: Using absolute paths when passing command line arguments
+    Given I copy the example data files:
+      | source                                         | dest        |
+      | short_read_assembler/genome_paired_reads.fq.gz | reads.fq.gz |
+    When I run the command:
+      """
+      biobox \
+        run \
+        short_read_assembler \
+        bioboxes/velvet \
+        --no-rm \
+        --input=$(realpath reads.fq.gz) \
+        --output=$(realpath .)/contigs.fa
+      """
+    Then the stdout should be empty
+    And the stderr should be empty
+    And the exit code should be 0
+    And the file "contigs.fa" should exist
+    And the file "contigs.fa" should not be empty
+
+
   Scenario Outline: Running a biobox short read assembler container
     Given I copy the example data files:
       | source                                         | dest        |
@@ -54,10 +78,10 @@ Feature: A CLI to run biobox-compatible Docker containers
         run \
         short_read_assembler \
         <assembler> \
-        <ressources> \
+        <resources> \
         --no-rm \
-        --input=<input> \
-        --output=<output>
+        --input=reads.fq.gz \
+        --output=contigs.fa
       """
     Then the stdout should be empty
     And the stderr should be empty
@@ -66,12 +90,10 @@ Feature: A CLI to run biobox-compatible Docker containers
     And the file "contigs.fa" should not be empty
 
     Examples:
-      | assembler       | ressources                   | input                   | output                   |
-      | bioboxes/velvet |                              | reads.fq.gz             | contigs.fa               |
-      | bioboxes/velvet |                              | $(realpath reads.fq.gz) | contigs.fa               |
-      | bioboxes/velvet |                              | reads.fq.gz             | $(realpath .)/contigs.fa |
-      | bioboxes/velvet | --memory=1g --cpu-shares=512 | reads.fq.gz             | $(realpath .)/contigs.fa |
-      | bioboxes/velvet | -m 1g -c 512                 | $(realpath reads.fq.gz) | contigs.fa               |
+      | assembler       | resources        |
+      | bioboxes/velvet | --memory=1g      |
+      | bioboxes/velvet | --cpu-shares=512 |
+
 
   Scenario Outline: Running a biobox assembler benchmark container
     Given I create the directory "input"
@@ -87,23 +109,19 @@ Feature: A CLI to run biobox-compatible Docker containers
       biobox \
         run \
         assembler_benchmark \
-        <benchmark> \
-        <ressources> \
+        bioboxes/quast \
+        <resources> \
         --no-rm \
-        --input-fasta=<input-fasta> \
-        <input-ref> \
-        --output=<output>
+        --input-fasta=input/assembly.fasta \
+        --output=output
       """
     Then the stdout should be empty
     And the stderr should be empty
     And the exit code should be 0
-    And the file "output/biobox.yaml" should exist
-    And the file "output/biobox.yaml" should not be empty
+    And the file "output/report.tsv" should exist
+    And the file "output/report.tsv" should not be empty
+
     Examples:
-      | benchmark      | ressources                   | input-fasta                      | input-ref                                | output             |
-      | bioboxes/quast |                              | $(realpath input/assembly.fasta) | --input-ref=$(realpath input/references) | $(realpath output) |
-      | bioboxes/quast |                              | input/assembly.fasta             | --input-ref=input/references             | output             |
-      | bioboxes/quast |                              | input/assembly.fasta             |                                          | output             |
-      | bioboxes/quast | --memory=1g --cpu-shares=512 | $(realpath input/assembly.fasta) | --input-ref=$(realpath input/references) | $(realpath output) |
-      | bioboxes/quast | -m 1g -c 512                 | input/assembly.fasta             | --input-ref=input/references             | output             |
-      | bioboxes/quast | -m 1g -c 512                 | input/assembly.fasta             |                                          | output             |
+      | resources        | input-ref                    |
+      | --cpu-shares=512 |                              |
+      | --memory=1g      | --input-ref=input/references |