Modify check_tab_delimited to ignore headers starting with # (#30)

* Modify check_tab_delimited to ignore headers starting with # * Use the most recent annotated tag in releases * Bump version --------- Co-authored-by: Heather Ward <[email protected]>
DNAstack · Jun 12, 2023 · 866db31 · 866db31
1 parent bccdcf4
commit 866db31
Show file tree

Hide file tree

Showing 5 changed files with 14 additions and 13 deletions.
diff --git a/.github/workflows/docker-build-push.yml b/.github/workflows/docker-build-push.yml
@@ -16,7 +16,7 @@ jobs:
         id: prep
         run: |
           IMAGE="dnastack/wdl-ci"
-          VERSION_TAG=`git describe --tags`
+          VERSION_TAG=`git describe --tags --abbrev=0`
           LONG_VERSION_TAG=`git describe --tags --long --always`
           LATEST_TAG="latest"
           ALL_TAGS="${IMAGE}:${VERSION_TAG},${IMAGE}:${LONG_VERSION_TAG},${IMAGE}:${LATEST_TAG}"

diff --git a/README.md b/README.md
@@ -15,7 +15,7 @@ If any step of the action fails, the check will fail; however if some task tests
 # GitHub action usage
 
 ```yaml
-- uses: dnastack/[email protected].8
+- uses: dnastack/[email protected].9
   with:
     # Configuration file where tests can be found
     # Default: wdl-ci.config.json
@@ -86,7 +86,7 @@ jobs:
         with:
           submodules: true
       - name: wdl-ci
-        uses: dnastack/[email protected].8
+        uses: dnastack/[email protected].9
         with:
           wallet-url: ${{ secrets.WALLET_URL }}
           wallet-client-id: ${{ secrets.WALLET_CLIENT_ID }}
@@ -114,7 +114,7 @@ jobs:
           repository: ${{ github.event.pull_request.head.repo.full_name }}
           ref: ${{ github.event.pull_request.head.ref }}
       - name: wdl-ci
-        uses: dnastack/[email protected].8
+        uses: dnastack/[email protected].9
         with:
           wallet-url: ${{ secrets.WALLET_URL }}
           wallet-client-id: ${{ secrets.WALLET_CLIENT_ID }}
@@ -144,7 +144,7 @@ jobs:
           repository: ${{ github.event.pull_request.head.repo.full_name }}
           ref: ${{ github.event.pull_request.head.ref }}
       - name: wdl-ci
-        uses: dnastack/[email protected].8
+        uses: dnastack/[email protected].9
         with:
           wallet-url: ${{ secrets.WALLET_URL }}
           wallet-client-id: ${{ secrets.WALLET_CLIENT_ID }}

diff --git a/action.yml b/action.yml
@@ -50,19 +50,19 @@ runs:
           echo "WDL_CI_CUSTOM_TEST_WDL_DIR"=${{ inputs.wdl_ci_custom_test_wdl_dir }} >> $GITHUB_ENV
         fi
     - name: lint
-      uses: docker://dnastack/wdl-ci:v0.1.8
+      uses: docker://dnastack/wdl-ci:v0.1.9
       with:
         args: lint
     - name: detect-changes
-      uses: docker://dnastack/wdl-ci:v0.1.8
+      uses: docker://dnastack/wdl-ci:v0.1.9
       with:
         args: detect-changes
     - name: submit
-      uses: docker://dnastack/wdl-ci:v0.1.8
+      uses: docker://dnastack/wdl-ci:v0.1.9
       with:
         args: submit
     - name: monitor
-      uses: docker://dnastack/wdl-ci:v0.1.8
+      uses: docker://dnastack/wdl-ci:v0.1.9
       with:
         args: monitor --update-digests
       # If a test fails, still update task digests for any tests that succeeded
@@ -76,6 +76,6 @@ runs:
         default_author: github_actions
     - name: cleanup
       if: always()
-      uses: docker://dnastack/wdl-ci:v0.1.8
+      uses: docker://dnastack/wdl-ci:v0.1.9
       with:
         args: cleanup
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,7 +1,7 @@
 [project]
 name = "wdl-testing-cli"
 description = "DNAstack WDL testing CLI"
-version = "v0.1.8"
+version = "v0.1.9"
 authors = [
     { name = "DNAstack", email = "[email protected]" }
 ]

diff --git a/src/wdlci/wdl_tests/check_tab_delimited.wdl b/src/wdlci/wdl_tests/check_tab_delimited.wdl
@@ -28,11 +28,12 @@ task check_tab_delimited {
 		# Validated dir path in input block vs. command block is different
 		validated_dir_path=$(dirname ~{validated_output})
 
-		if ! awk '{exit !/\t/}' "${validated_dir_path}/$(basename ~{validated_output} .gz)"; then
+		# Disregard headers starting with `#`
+		if ! sed '/^#/d' "${validated_dir_path}/$(basename ~{validated_output} .gz)" | awk '{exit !/\t/}'; then
 			err "Validated file: [~{basename(validated_output)}] is not tab-delimited"
 			exit 1
 		else
-			if awk '{exit !/\t/}' ~{current_run_output_unzipped}; then
+			if sed '/^#/d' ~{current_run_output_unzipped} | awk '{exit !/\t/}'; then
 				echo "Current run file: [~{basename(current_run_output)}] is tab-delimited"
 			else
 				err "Current run file: [~{basename(current_run_output)}] is not tab-delimited"