diff --git a/.github/workflows/test_nucleo_qc.yaml b/.github/workflows/test_nucleo_qc.yaml index 9d3f56d..78d9d77 100644 --- a/.github/workflows/test_nucleo_qc.yaml +++ b/.github/workflows/test_nucleo_qc.yaml @@ -22,12 +22,12 @@ jobs: python-version: [3.10.8] steps: - name: Checkout - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: ref: ${{ github.head_ref }} submodules: recursive - name: Set up Python - uses: actions/setup-python@v3 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name : Set up NodeJS diff --git a/cwl-commandlinetools b/cwl-commandlinetools index cf66cd5..24accf3 160000 --- a/cwl-commandlinetools +++ b/cwl-commandlinetools @@ -1 +1 @@ -Subproject commit cf66cd5f0269b5a51adceda97c4f5cf046b31133 +Subproject commit 24accf3747b8698a66b3ec262dc44f9a18231e8d diff --git a/cwl_subworkflows b/cwl_subworkflows index d9bbc74..275a628 160000 --- a/cwl_subworkflows +++ b/cwl_subworkflows @@ -1 +1 @@ -Subproject commit d9bbc743d68baae2a0372358abaf82e465976b88 +Subproject commit 275a62872353456a2e39ce0605bc90dc101cfd6e diff --git a/install_data.sh b/install_data.sh index 70b3580..f8f8975 100644 --- a/install_data.sh +++ b/install_data.sh @@ -1,18 +1,27 @@ #!/usr/bin/env bash - # Test data is hosted on Google Drive at: # https://drive.google.com/u/0/uc?id=1i1GA4AZhuw6Si8RmPFPJxmejIUt3ZZ1D +fileid=1i1GA4AZhuw6Si8RmPFPJxmejIUt3ZZ1D + filename=test_nucleo_qc.tar.gz -# Note: Drive seems to change somewhat frequently how it handles endpoints for large files -# add confirm parameter to link for this to work -# previously used another wget scheme and gdown -wget -O $filename "https://drive.google.com/u/0/uc?id=1i1GA4AZhuw6Si8RmPFPJxmejIUt3ZZ1D&export=download&confirm=t" +foldername=test_data + +# Skip if already have test data +[[ -f $filename ]] && exit 0 +[[ -d $foldername ]] && exit 0 + +#curl -c ./cookie -s -k -L "https://drive.google.com/uc?export=download&id=$fileid" > /dev/null +#curl -k -Lb ./cookie "https://drive.google.com/uc?export=download&confirm=`awk '/download/ {print $NF}' ./cookie`&id=${fileid}" -o ${filename} +cd tests/inputs || exit +curl -L "https://drive.usercontent.google.com/download?id=${fileid}&confirm=xxx" -o ${filename} + # Suppress linux warnings for MacOS tar.gz files if [[ "$OSTYPE" == "linux-gnu" ]]; then - tar --warning=no-unknown-keyword -xzvf $filename -C tests/inputs/ + tar --warning=no-unknown-keyword -xzvf $filename elif [[ "$OSTYPE" == "darwin"* ]]; then - tar -xzvf $filename -C tests/inputs/ + tar -xzvf $filename fi -rm $filename \ No newline at end of file + +rm $filename diff --git a/nucleo_aggregate_visualize.cwl b/nucleo_aggregate_visualize.cwl index 0a1213a..3bb681e 100644 --- a/nucleo_aggregate_visualize.cwl +++ b/nucleo_aggregate_visualize.cwl @@ -178,7 +178,7 @@ steps: source: config out: - id: aggregate_parsed_stats - run: cwl-commandlinetools/cci_utils/0.3.1/general_stats_parse.cwl + run: cwl-commandlinetools/cci_utils/0.3.2/general_stats_parse.cwl label: general_stats_parse 'sbg:x': 870.1131591796875 'sbg:y': 520.0625