From 84a5d81ad1756032178a3c717d4aee495875ee9a Mon Sep 17 00:00:00 2001 From: aclum Date: Tue, 23 Jul 2024 09:23:10 -0700 Subject: [PATCH 1/4] Create wdl_linter.yml --- .../.github/workflows/wdl_linter.yml | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 .github/workflows/.github/workflows/wdl_linter.yml diff --git a/.github/workflows/.github/workflows/wdl_linter.yml b/.github/workflows/.github/workflows/wdl_linter.yml new file mode 100644 index 0000000..01fb4a1 --- /dev/null +++ b/.github/workflows/.github/workflows/wdl_linter.yml @@ -0,0 +1,27 @@ +name: MiniWDL linter CI + +on: + pull_request: + branches: master + +jobs: + run-miniwdl: + runs-on: ubuntu-latest + + steps: + - name: Checkout repository + uses: actions/checkout@v2 + + - name: Set up Python + uses: actions/setup-python@v2 + with: + python-version: '3.8' # specify the Python version you need + + - name: Install MiniWDL + run: | + python -m pip install --upgrade pip + pip install miniwdl + - name: Run MiniWDL + run: | + # Add the commands to run your MiniWDL workflow + miniwdl check --suppress UnknownRuntimeKey ReadbasedAnalysis.wdl From 13356cacfd92e773ccf92e8cd0d482983c2fd314 Mon Sep 17 00:00:00 2001 From: aclum Date: Tue, 23 Jul 2024 09:25:30 -0700 Subject: [PATCH 2/4] moving wdl_linter.yml to correct directory --- .github/workflows/{.github/workflows => }/wdl_linter.yml | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename .github/workflows/{.github/workflows => }/wdl_linter.yml (100%) diff --git a/.github/workflows/.github/workflows/wdl_linter.yml b/.github/workflows/wdl_linter.yml similarity index 100% rename from .github/workflows/.github/workflows/wdl_linter.yml rename to .github/workflows/wdl_linter.yml From 5fd2b7700bf237bae3cc1919376e5c9fd175918c Mon Sep 17 00:00:00 2001 From: aclum Date: Tue, 23 Jul 2024 09:30:47 -0700 Subject: [PATCH 3/4] fix duplicate input variable for make_info_file and patch version bump --- ReadbasedAnalysis.wdl | 1 - version.txt | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/ReadbasedAnalysis.wdl b/ReadbasedAnalysis.wdl index 839d06c..0d229dc 100755 --- a/ReadbasedAnalysis.wdl +++ b/ReadbasedAnalysis.wdl @@ -61,7 +61,6 @@ workflow ReadbasedAnalysis { enabled_tools_gottcha2 = enabled_tools_gottcha2, enabled_tools_kraken2 = enabled_tools_kraken2, enabled_tools_centrifuge = enabled_tools_centrifuge, - docker = docker, db_gottcha2 = db_gottcha2, db_kraken2 = db_kraken2, db_centrifuge = db_centrifuge, diff --git a/version.txt b/version.txt index cbe8779..14b34a4 100644 --- a/version.txt +++ b/version.txt @@ -1 +1 @@ -v1.0.7 +v1.0.8 From 5027f19fabd26a44072bf2c048b874b3f0ccb93f Mon Sep 17 00:00:00 2001 From: aclum Date: Tue, 23 Jul 2024 09:34:58 -0700 Subject: [PATCH 4/4] fixes another duplicate variable issue --- ReadbasedAnalysis.wdl | 1 - 1 file changed, 1 deletion(-) diff --git a/ReadbasedAnalysis.wdl b/ReadbasedAnalysis.wdl index 0d229dc..91be086 100755 --- a/ReadbasedAnalysis.wdl +++ b/ReadbasedAnalysis.wdl @@ -67,7 +67,6 @@ workflow ReadbasedAnalysis { docker = docker, gottcha2_info = profilerGottcha2.info, gottcha2_report_tsv = profilerGottcha2.report_tsv, - gottcha2_info = profilerGottcha2.info, centrifuge_report_tsv = profilerCentrifuge.report_tsv, centrifuge_info = profilerCentrifuge.info, kraken2_report_tsv = profilerKraken2.report_tsv,