Delete folders from a directory once it's sbatch`ed in a for loop?

If I understand correctly, what you want to do is:

1. Submit one cellranger job to Slurm for each of your fastq directories.
2. Delete the directory.

However, that isn't what your script is doing. You have

    cmd="cellranger count \
    [. . . ]

And then you have:

    sbatch --nodes=1 \
         -J cellranger_count <<EOF
         [. . . ]
   cmd="rm -r $fastq_dir"

So in the job you are actually passing to sbatch, $cmd is just rm -rf $fastq_dir and not cellrangercount....

In any case, I suspect that the rm -rf "$fastq_dir" won't work anyway, not unless the sbatch is running in the same directory, so you might want to use the full path in the for loop. For example, if your fastq_first/ is actually /home/echo94/data/fastq_first, then you should change your for to be like this:

for fastq_dir in /home/echo94/data/fastq_first/*; do

Also, since you only want directories, you can add a slash to ensure that no files will be selected by the for loop:

for fastq_dir in /home/echo94/data/fastq_first/*/; do

You now have the full path to each directory so you can rm $fastq_dir from anywhere on the system. Putting all this together, this script is probably what you need:

for fastq_dir in /home/echo94/data/fastq_first/*/; do
    barcode=`basename "$fastq_dir"`

    cmd="cellranger count \
        --id=${barcode} \
        --fastqs= ${fastq_dir}   \
        --sample=${barcode} \
        --transcriptome=${reference_dir} \
        --localcores=32 \
        --localmem=92"

    sbatch --nodes=1 \
        --cpus-per-task=32 \
        --mem=96G \
        --time=2880 \
        -o cellranger_count.%j.out \
        -e cellranger_count.%j.err \
        -J cellranger_count <<EOF
#!/bin/bash
set -ue
echo "Start Cell Ranger count `date`"
echo "$cmd" 
eval "$cmd"
echo "Done "`date` 
cellranger count --version
rm -r "$fastq_dir"
EOF

done