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Commit 5f511263 authored by Maciej Bak's avatar Maciej Bak
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refactor: remove old ALFA unit test

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1 merge request!99ci: clean old comments
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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
#!/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"
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