refactor: remove old ALFA unit test

tests/test_alfa/expected_output.md5

-90e42aa46890e9cd0a47800428699fbf  results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.stranded.ALFA_index
-ccc3cf5a57fddb0d469e597d4376b1bf  results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.unstranded.ALFA_index
-e5959524a2daf35da9249fb313920315  results/samples/paired_end_R1_on_minus_antisense/ALFA/Unique/paired_end_R1_on_minus_antisense.ALFA_feature_counts.tsv
-c406c1800d3690dd774aaa7e3c190523  results/samples/paired_end_R1_on_minus_sense/ALFA/Unique/paired_end_R1_on_minus_sense.ALFA_feature_counts.tsv
-c406c1800d3690dd774aaa7e3c190523  results/samples/paired_end_R1_on_plus_antisense/ALFA/Unique/paired_end_R1_on_plus_antisense.ALFA_feature_counts.tsv
-e5959524a2daf35da9249fb313920315  results/samples/paired_end_R1_on_plus_sense/ALFA/Unique/paired_end_R1_on_plus_sense.ALFA_feature_counts.tsv
-e5959524a2daf35da9249fb313920315  results/samples/paired_end_R1_on_minus_antisense/ALFA/UniqueMultiple/paired_end_R1_on_minus_antisense.ALFA_feature_counts.tsv
-c406c1800d3690dd774aaa7e3c190523  results/samples/paired_end_R1_on_minus_sense/ALFA/UniqueMultiple/paired_end_R1_on_minus_sense.ALFA_feature_counts.tsv
-c406c1800d3690dd774aaa7e3c190523  results/samples/paired_end_R1_on_plus_antisense/ALFA/UniqueMultiple/paired_end_R1_on_plus_antisense.ALFA_feature_counts.tsv
-e5959524a2daf35da9249fb313920315  results/samples/paired_end_R1_on_plus_sense/ALFA/UniqueMultiple/paired_end_R1_on_plus_sense.ALFA_feature_counts.tsv
-5e90c760710980f4f4866dbe9aa32c6c  results/samples/paired_end_R1_on_minus_antisense/ALFA/UniqueMultiple/paired_end_R1_on_minus_antisense.UniqueMultiple.minus.bg
-8e23d52d7f635d927e292174f33168eb  results/samples/paired_end_R1_on_minus_antisense/ALFA/UniqueMultiple/paired_end_R1_on_minus_antisense.UniqueMultiple.plus.bg
-8e23d52d7f635d927e292174f33168eb  results/samples/paired_end_R1_on_minus_sense/ALFA/UniqueMultiple/paired_end_R1_on_minus_sense.UniqueMultiple.minus.bg
-5e90c760710980f4f4866dbe9aa32c6c  results/samples/paired_end_R1_on_minus_sense/ALFA/UniqueMultiple/paired_end_R1_on_minus_sense.UniqueMultiple.plus.bg
-8e23d52d7f635d927e292174f33168eb  results/samples/paired_end_R1_on_plus_antisense/ALFA/UniqueMultiple/paired_end_R1_on_plus_antisense.UniqueMultiple.minus.bg
-5e90c760710980f4f4866dbe9aa32c6c  results/samples/paired_end_R1_on_plus_antisense/ALFA/UniqueMultiple/paired_end_R1_on_plus_antisense.UniqueMultiple.plus.bg
-5e90c760710980f4f4866dbe9aa32c6c  results/samples/paired_end_R1_on_plus_sense/ALFA/UniqueMultiple/paired_end_R1_on_plus_sense.UniqueMultiple.minus.bg
-8e23d52d7f635d927e292174f33168eb  results/samples/paired_end_R1_on_plus_sense/ALFA/UniqueMultiple/paired_end_R1_on_plus_sense.UniqueMultiple.plus.bg
-5e90c760710980f4f4866dbe9aa32c6c  results/samples/paired_end_R1_on_minus_antisense/ALFA/Unique/paired_end_R1_on_minus_antisense.Unique.minus.bg
-8e23d52d7f635d927e292174f33168eb  results/samples/paired_end_R1_on_minus_antisense/ALFA/Unique/paired_end_R1_on_minus_antisense.Unique.plus.bg
-8e23d52d7f635d927e292174f33168eb  results/samples/paired_end_R1_on_minus_sense/ALFA/Unique/paired_end_R1_on_minus_sense.Unique.minus.bg
-5e90c760710980f4f4866dbe9aa32c6c  results/samples/paired_end_R1_on_minus_sense/ALFA/Unique/paired_end_R1_on_minus_sense.Unique.plus.bg
-8e23d52d7f635d927e292174f33168eb  results/samples/paired_end_R1_on_plus_antisense/ALFA/Unique/paired_end_R1_on_plus_antisense.Unique.minus.bg
-5e90c760710980f4f4866dbe9aa32c6c  results/samples/paired_end_R1_on_plus_antisense/ALFA/Unique/paired_end_R1_on_plus_antisense.Unique.plus.bg
-5e90c760710980f4f4866dbe9aa32c6c  results/samples/paired_end_R1_on_plus_sense/ALFA/Unique/paired_end_R1_on_plus_sense.Unique.minus.bg
-8e23d52d7f635d927e292174f33168eb  results/samples/paired_end_R1_on_plus_sense/ALFA/Unique/paired_end_R1_on_plus_sense.Unique.plus.bg
-5e90c760710980f4f4866dbe9aa32c6c  results/samples/paired_end_R1_on_minus_antisense/STAR_coverage/paired_end_R1_on_minus_antisense_Signal.UniqueMultiple.str1.out.bg
-8e23d52d7f635d927e292174f33168eb  results/samples/paired_end_R1_on_minus_antisense/STAR_coverage/paired_end_R1_on_minus_antisense_Signal.UniqueMultiple.str2.out.bg
-5e90c760710980f4f4866dbe9aa32c6c  results/samples/paired_end_R1_on_minus_antisense/STAR_coverage/paired_end_R1_on_minus_antisense_Signal.Unique.str1.out.bg
-8e23d52d7f635d927e292174f33168eb  results/samples/paired_end_R1_on_minus_antisense/STAR_coverage/paired_end_R1_on_minus_antisense_Signal.Unique.str2.out.bg
-5e90c760710980f4f4866dbe9aa32c6c  results/samples/paired_end_R1_on_minus_sense/STAR_coverage/paired_end_R1_on_minus_sense_Signal.UniqueMultiple.str1.out.bg
-8e23d52d7f635d927e292174f33168eb  results/samples/paired_end_R1_on_minus_sense/STAR_coverage/paired_end_R1_on_minus_sense_Signal.UniqueMultiple.str2.out.bg
-5e90c760710980f4f4866dbe9aa32c6c  results/samples/paired_end_R1_on_minus_sense/STAR_coverage/paired_end_R1_on_minus_sense_Signal.Unique.str1.out.bg
-8e23d52d7f635d927e292174f33168eb  results/samples/paired_end_R1_on_minus_sense/STAR_coverage/paired_end_R1_on_minus_sense_Signal.Unique.str2.out.bg
-8e23d52d7f635d927e292174f33168eb  results/samples/paired_end_R1_on_plus_antisense/STAR_coverage/paired_end_R1_on_plus_antisense_Signal.UniqueMultiple.str1.out.bg
-5e90c760710980f4f4866dbe9aa32c6c  results/samples/paired_end_R1_on_plus_antisense/STAR_coverage/paired_end_R1_on_plus_antisense_Signal.UniqueMultiple.str2.out.bg
-8e23d52d7f635d927e292174f33168eb  results/samples/paired_end_R1_on_plus_antisense/STAR_coverage/paired_end_R1_on_plus_antisense_Signal.Unique.str1.out.bg
-5e90c760710980f4f4866dbe9aa32c6c  results/samples/paired_end_R1_on_plus_antisense/STAR_coverage/paired_end_R1_on_plus_antisense_Signal.Unique.str2.out.bg
-8e23d52d7f635d927e292174f33168eb  results/samples/paired_end_R1_on_plus_sense/STAR_coverage/paired_end_R1_on_plus_sense_Signal.UniqueMultiple.str1.out.bg
-5e90c760710980f4f4866dbe9aa32c6c  results/samples/paired_end_R1_on_plus_sense/STAR_coverage/paired_end_R1_on_plus_sense_Signal.UniqueMultiple.str2.out.bg
-8e23d52d7f635d927e292174f33168eb  results/samples/paired_end_R1_on_plus_sense/STAR_coverage/paired_end_R1_on_plus_sense_Signal.Unique.str1.out.bg
-5e90c760710980f4f4866dbe9aa32c6c  results/samples/paired_end_R1_on_plus_sense/STAR_coverage/paired_end_R1_on_plus_sense_Signal.Unique.str2.out.bg

tests/test_alfa/results/star_indexes/homo_sapiens/75/STAR_index/chrNameLength.txt

-Chr1	1500

tests/test_alfa/test.sh

-#!/bin/bash
-
-# Tear down test environment
-cleanup () {
-    rc=$?
-    rm -rf .java/
-    rm -rf .snakemake/
-    rm -rf logs/
-    rm -rfv results/alfa_indexes/
-    rm -rfv results/*/*/ALFA/
-    rm -rfv results/*/*/STAR_coverage/
-    rm -rfv results/ALFA/
-    cd $user_dir
-    echo "Exit status: $rc"
-}
-trap cleanup EXIT
-
-# Set up test environment
-set -eo pipefail  # ensures that script exits at first command that exits with non-zero status
-set -u  # ensures that script exits when unset variables are used
-set -x  # facilitates debugging by printing out executed commands
-user_dir=$PWD
-script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd)"
-cd $script_dir
-
-# Run tests
-snakemake \
-    --snakefile="../../Snakefile" \
-    --configfile="../input_files/config_alfa.yaml" \
-    --cores=4 \
-    --printshellcmds \
-    --rerun-incomplete \
-    --use-singularity \
-    --singularity-args="--bind ${PWD}/../input_files,${PWD}/../../images" \
-    --verbose \
-    --notemp \
-    --no-hooks \
-    results/ALFA/ALFA_plots_mqc.png
-
-# Check md5 sum of some output files
-find results/ -type f -name \*\.gz -exec gunzip '{}' \;
-find results/ -type f -name \*\.zip -exec sh -c 'unzip -o {} -d $(dirname {})' \;
-md5sum --check "expected_output.md5"