Merge branch 'release/1.1.5'

Author: rhshah

.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

cwl-commandlinetools

@@ -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
+
+rm $filename

cwl_subworkflows

@@ -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