Faster snakemake files

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write as many snakemake files and with much faster iterations and completely from the single files or from the list of the files with the path appended. This will make your writing the snakemake easier

#!/usr/bin/env bash
# -*- coding:  utf-8 -*-
# Universität Potsdam, Germany
# Author: Gaurav Sablok
# date: 2024-2-8
# a indexed based and brace expansion based way of writing
# the snakemake files for computing the below version is
# for if you have some files.
read -r -p "please provide the rule name:" rule
read -r -p "please provide the shell command:" command
read -r -p "please provide the input file directory:" inputdirectory
read -r -p "please provide the output file directory:" outputdirectory
declare -a snakeinput=()
while true; do
    read -r -p "please provide me the input name:" inputname
    if [[ "${inputname}" == "" ]]; then
        break
    fi
    snakeinput+=("${inputdirectory}"\"${inputname}\"\,)
done
declare -a snakeoutput=()
while true; do
    read -r -p "please provide me the output name:" outputname
    if [[ "${outputname}" == "" ]]; then
        break
    fi
    snakeoutput+=("${outputdirectory}"\"${outputname}\"\,)
done
for i in "${snakeinput[*]}"; do
    echo "rule ${rule}:"
    echo "  ""input: ${i}"
    echo "  ""output:${snakeoutput[*]}"
    echo "  ""shell: ${command} ${snakeinput[*]} ${snakeoutput[*]}"
done
#!/usr/bin/env bash
# -*- coding:  utf-8 -*-
# Universität Potsdam, Germany
# Author: Gaurav Sablok
# date: 2024-2-8
# a indexed based and brace expansion based way of writing
# the snakemake files for computing the below version is
# for if you have some files.
read -r -p "please provide the rule name:" rule
read -r -p "please provide the shell command:" command
read -r -p "please provide the input file directory:" inputdirectory
read -r -p "please provide the output file directory:" outputdirectory
read -r -p "please provide the input text file:" inputtextfile
read -r -p "please provide the output text file:" outputtextfile
if [[ ! -f "${inputtextfile}" && ! -f "${outputtextfile}" ]]
then
declare -a snakeinput=()
while true; do
    read -r -p "please provide me the input name:" inputname
    if [[ "${inputname}" == "" ]]; then
        break
    fi
    snakeinput+=("${inputdirectory}"\"${inputname}\"\,)
done
declare -a snakeoutput=()
while true; do
    read -r -p "please provide me the output name:" outputname
    if [[ "${outputname}" == "" ]]; then
        break
    fi
    snakeoutput+=("${outputdirectory}"\"${outputname}\"\,)
done
for i in "${snakeinput[*]}"; do
    echo "rule ${rule}:"
    echo "  ""input: ${i}"
    echo "  ""output:${snakeoutput[*]}"
    echo "  ""shell: ${command} ${snakeinput[*]} ${snakeoutput[*]}"
done
fi
if [[ -f "${inputtextfile}" && -f "${outputtextfile}" ]]
then
declare -a inputtext=()
for i in $(cat "${inputtextfile}" | cut -f 1 -d " ")
do
    inputtext+=("${inputdirectory}"\"${i}\"\,)
done
    echo "the number of the files added to the input snakemake: {#inputtext[@]}"
    echo "the files added to the input array are: ${inputtext[*]}"
declare -r outputtext=()
for i in $(cat "${outputtextfile}" | cut -f 1 -d " ")
do 
    outputtext+=("${outputdirectory}"\"${i}\"\,)
done
    echo "the number of the files added to the output snakemake: {#outputtext[@]}"
    echo "the files added to the input array are: ${outputtext[*]}"
    echo "rule ${rule}:"
    echo "  ""input: ${inputtext[*]}"
    echo "  ""output:${outputtext[*]}"
    echo "  ""shell: ${command} ${inputtext[*]} ${outputtext[*]}"
fi
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