Fix to be able to execute qmap config file specifying cores or memory for a single job

[dmartmillan]

It seems that when we want to execute a qmap script specifying the number of cores or the memory to use for a paarticular job it doesn't run it with them and it runs with the general parameters. Here, it's an example of a jobs file:

[pre]
. "/home/$USER/miniconda3/etc/profile.d/conda.sh"
conda activate biomarkers

[params]
cores = 7
memory = 32G

[jobs]
python $PWD/launch_pad/engine2/get_cnv-features.py
python $PWD/launch_pad/engine2/get_hla-features.py
python $PWD/launch_pad/engine2/get_somatic-features.py ## cores=40

The code that it gets the parameters is this one:

qmap/qmap/manager.py

Lines 328 to 333 in c73c355

	for i, c in job.items():
	cmd = c.split('##')
	params = None
	if len(cmd) > 1: # if the job has specific _params
	params = jobs_file.parse_inline_parameters(cmd[1]) # job specific _params
	job_list.append((i, SubmittedJob(i, self.out_folder, cmd[0].strip(), params, pre_commands=pre, post_commands=post)))

It generates the .env file for the specific job but it seems that it isn't running accordingly the parameters. Also, it generates the .bash file but it doesn't get the right .env. An exampe of a .bash file generated:

#!/bin/bash
#SBATCH --no-requeue
set -e

source "/home/dmartinezm/hartwig_biomarkers/fire_engine2_20220530/execution.env"
if [ -f "/home/dmartinezm/hartwig_biomarkers/fire_engine2_20220530/1.env" ]; then
	source "/home/dmartinezm/hartwig_biomarkers/fire_engine2_20220530/1.env"
fi

. "/home/$USER/miniconda3/etc/profile.d/conda.sh"
conda activate biomarkers
python $PWD/launch_pad/engine2/get_hla-features.py

[CarlosLopezElorduy]

Does anybody know if this is this still happening?