bump skylab demo script

Author: mlin

test_corpi/HumanCellAtlas/skylab

@@ -22,8 +22,8 @@ $miniwdl check --no-shellcheck \
     "$SOURCE_DIR/test_corpi/HumanCellAtlas/skylab/pipelines/optimus/Optimus.wdl" > optimus.out
 is "$?" "0" "check Optimus.wdl"
 is "$(grep UnusedDeclaration optimus.out | wc -l)" "2" "Optimus.wdl UnusedDeclaration"
-is "$(grep NameCollision optimus.out | wc -l)" "2" "Optimus.wdl NameCollision"
-is "$(cat optimus.out | wc -l)" "73" "Optimus.wdl output"
+is "$(grep NameCollision optimus.out | wc -l)" "3" "Optimus.wdl NameCollision"
+is "$(cat optimus.out | wc -l)" "77" "Optimus.wdl output"
 
 $miniwdl check --no-shellcheck \
     --path "$SOURCE_DIR/test_corpi/HumanCellAtlas/skylab/library/tasks" \
@@ -32,7 +32,7 @@ $miniwdl check --no-shellcheck \
     > optimus_smartseq2.out
 is "$?" "0" "check Optimus.wdl and SmartSeq2SingleSample.wdl"
 is "$(grep UnusedDeclaration optimus_smartseq2.out | wc -l)" "3" "UnusedDeclaration in Optimus.wdl and SmartSeq2SingleSample.wdl"
-is "$(cat optimus_smartseq2.out | wc -l)" "105" "Optimus.wdl and SmartSeq2SingleSample.wdl output"
+is "$(cat optimus_smartseq2.out | wc -l)" "109" "Optimus.wdl and SmartSeq2SingleSample.wdl output"
 
 cat << EOF > lex_error.wdl
 # comment

tests/check.t

@@ -38,6 +38,7 @@ def rw(v, index=None):
         "test/bulk_rna_pipeline/pr/test_bulk_rna_pipeline_PR.wdl",
         "test/optimus/pr/test_optimus_PR.wdl",
         "test/smartseq2_single_sample/pr/test_smartseq2_single_sample_PR.wdl",
+        "test/smartseq2_single_sample_unpaired/pr/test_smartseq2_single_sample_unpaired_PR.wdl",
     ]
     for wdl in test_wdl:
         wdl = os.path.join(skylab_dir, wdl)
@@ -53,6 +54,7 @@ def rw(v, index=None):
                 "-p", os.path.join(skylab_dir, "pipelines/bulk_rna_pipeline"),
                 "-p", os.path.join(skylab_dir, "pipelines/optimus"),
                 "-p", os.path.join(skylab_dir, "pipelines/smartseq2_single_sample"),
+                "-p", os.path.join(skylab_dir, "pipelines/smartseq2_single_sample_unpaired"),
                 "-p", os.path.join(skylab_dir, "pipelines/snap-atac"),
                 "-i", "staged_test_inputs.json",
                 "--verbose", "--no-quant-check"

tests/skylab.py

@@ -123,7 +123,7 @@ class HCAskylab_task(unittest.TestCase):
 @test_corpus(
     ["test_corpi/HumanCellAtlas/skylab/pipelines/**"],
     path=[["test_corpi/HumanCellAtlas/skylab/library/tasks"]],
-    expected_lint={'UnusedDeclaration': 12, 'NameCollision': 2, 'UnknownRuntimeKey': 3, 'StringCoercion': 5, 'MixedIndentation': 1, 'FileCoercion': 1}
+    expected_lint={'UnusedDeclaration': 12, 'NameCollision': 3, 'UnknownRuntimeKey': 3, 'StringCoercion': 5, 'MixedIndentation': 1, 'FileCoercion': 1}
 )
 class HCAskylab_workflow(unittest.TestCase):
     pass