ci: drop pytest in favor of Sprocket test

.github/workflows/build-and-test.yaml

@@ -7,6 +7,3 @@ jobs:
     call-build:
         uses: ./.github/workflows/docker-build.yaml
         secrets: inherit
-    call-test:
-        uses: ./.github/workflows/pytest.yaml
-        needs: call-build

.gitignore

@@ -1,3 +1,4 @@
+pytest/
 # Ignore common bioinformatics formats used in these workflows.
 # But only if they are in the root of this repo
 /*.fastq.gz

data_structures/read_group.wdl

@@ -156,15 +156,13 @@ task validate_read_group {
 
     input {
         ReadGroup read_group
-        Array[String] required_fields = []
+        Array[String] required_fields = ["SM"]
         Boolean restrictive = true
     }
 
     # The SAM spec allows any printable ASCII character in header fields.
     String sam_spec_pattern = "[\\ -~]+"
     # We have the opinion that is too permissive for ID and SM.
-    String id_pattern = "id"
-    String sample_pattern = "sample.?"
     String restrictive_pattern = "\\ "  # Disallow spaces
     Array[String] platforms = [
         "CAPILLARY", "DNBSEQ", "ELEMENT", "HELICOS", "ILLUMINA", "IONTORRENT", "LS454",
@@ -174,11 +172,9 @@ task validate_read_group {
     command <<<
         exit_code=0
         if ~{restrictive}; then
-            if [[ ~{read_group.ID} =~ ^~{id_pattern}$ ]] \
-                || [[ ~{read_group.ID} =~ ~{restrictive_pattern} ]]
+            if [[ "~{read_group.ID}" =~ ~{restrictive_pattern} ]]
             then
-                >&2 echo "ID (~{read_group.ID}) must not match patterns:"
-                >&2 echo "'~{id_pattern}' or '~{restrictive_pattern}'"
+                >&2 echo "ID must not contain spaces"
                 exit_code=1
             fi
         fi
@@ -194,11 +190,9 @@ task validate_read_group {
         fi
         if ~{defined(read_group.SM)}; then
             if ~{restrictive}; then
-                if [[ "~{read_group.SM}" =~ ^~{sample_pattern}$ ]] \
-                    || [[ "~{read_group.SM}" =~ ~{restrictive_pattern} ]]
+                if [[ "~{read_group.SM}" =~ ~{restrictive_pattern} ]]
                 then
-                    >&2 echo "SM must not match patterns:"
-                    >&2 echo "'~{sample_pattern}' or '~{restrictive_pattern}'"
+                    >&2 echo "SM must not contain spaces"
                     exit_code=1
                 fi
             fi

data_structures/test/flag_filter.yaml

@@ -0,0 +1,50 @@
+validate_string_is_12bit_int:
+  - name: valid_numbers
+    inputs:
+      number:
+        - "5"
+        - "0x900"
+        - "01"
+        - "4095"
+    assertions:
+      stderr:
+        - Input number \(.*\) is valid
+  - name: invalid_numbers
+    inputs:
+      number:
+        - "0x1000"
+        - ""
+        - "string"
+        - this is not a number
+        - "000000000011"
+        - "-1"
+    assertions:
+      exit_code: 42
+      stderr:
+        - Input number \(.*\) is invalid
+  - name: too_big_decimal_fails
+    inputs:
+      number:
+        - "4096"
+    assertions:
+      exit_code: 42
+      stderr:
+        - Input number \(.*\) interpreted as decimal
+        - But number must be less than 4096!
+validate_flag_filter:
+  - name: valid_FlagFilter_passes
+    inputs:
+      flags:
+        - include_if_all: "3"
+          exclude_if_any: "0xF04"
+          include_if_any: "03"
+          exclude_if_all: "4095"
+  - name: invalid_FlagFilter_fails
+    inputs:
+      flags:
+        - include_if_all: "3"
+          exclude_if_any: "0xF04"
+          include_if_any: "03"
+          exclude_if_all: "" # empty string should trigger a fail
+    assertions:
+      should_fail: true