INNER CODE UNIT · Python

nFolders

franciscozorrilla/metaGEM · workflow/metaGEM.sh:140

nFolders=$(ls -d */|wc -l)
if [[ "$nFolders" -le 20 ]]; then
    while true; do
        read -p "Some folders appear to be missing, do you wish to run the createFolders Snakefile rule? (y/n)" yn
        case $yn in
            [Yy]* ) echo "Running the createFolders snakefile rule ... " && snakemake createFolders -j1; break;;
            [Nn]* ) echo "Skipping folder creation ... "; break;;
            * ) echo "Please answer yes or no.";;
        esac
    done
fi

# search for folders and files with .gz extension within dataset folder
count_files=$(find dataset -name "*.gz"|wc -l)
count_samp=$(ls dataset|grep -v gz|wc -l)
if [[ "$count_files" -eq 0 ]]; then
    echo -e "\nThere are no sequencing files (*.gz) in the dataset folder!"
    echo -e "Please download or move your paired end files into sample specific subfolders within the dataset folder.\n"

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