how_to_run_this.txt

#First, create the index with the command following, or just exectute this script, also be sure to have installed parallel and moreutils for running in parallel for every core a job.
#Also make sure to have downloaded the right cdna file and have it in .fa format and rename it as index.fa or call the command with the name wanted.

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kallisto index --make-unique -i index.fa.idx index.fa
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#Next step will be calling the script with the files for the paths and the jobscript which will be created 
#To create the list, use the trick ls -1 *.fastq.gz and save it > editme, later modify it. adding at the beggining the sample_names... and launch the script. ls -1 *.fastq.gz > editme


#Create the list of files positioning in the folder and run: 

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echo "$(ls $PWD/Sample_*/*.gz | sort -V)" >> fastq_files_paths.txt
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add the number of sample at the begginig of the file to recognize the files later.

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awk 'BEGIN{count=1; OFS="\t"}{print "sample"count++, $0}' fastq_files_paths.txt >> fastq_files_paths_samples.txt

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#Run the script.

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bash Make_job_list_kallisto.sh fastq_files_paths_samples.txt job_list_for_parallel.txt
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#And run the parallel task and the script log.
#Notice the final tee.

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parallel --progress --jobs 4 --joblog kallisto_joblog.txt < job_list_for_parallel.txt 2>&1 | tee final_report.txt
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