Merge branch 'cifix' into 'dev'

ci: clean old comments

See merge request !99

tests/test_scripts_prepare_inputs_table/expected_output.md5

-40bd0f0fcecdd0d9bc932f63c2811478  config.yaml
-d8fb1773e3b83b6fab0a0d44c9fa71e6  samples.tsv
\ No newline at end of file

tests/test_scripts_prepare_inputs_table/input_table.tsv

-Mate2_5p_Adapter	Condition_Name	Name_Quality_Control_File_Mate1	Disease_Short_Name	Single_Paired	Gender	Entry_Date	Disease_Description	Strain_Isolate_Breed_Ecotype	Genotype_Description	Mate1_File	Source_Tissue_Name	Developmental_Stage	Mate1_Direction	Quality_Control_Flag	Genotype_Short_Name	Strain_Isolate_Breed_Ecotype_ID	Fragment_Length_Mean	Organism	Contaminant_Sequences	TaxonID	Documentation	Prepared_By	_labkeyurl_Entry_Date	Molecule	Mate2_Direction	Library_preparation_kit	Checksum_Raw_FASTQ_Mate1	Cycles	Fragment_Length_SD	Sample_Name	Passage_Number	Mate1_5p_Adapter	Mate2_3p_Adapter	Path_Fastq_Files	Mate1_3p_Adapter	Treatment_Short_Name	Age	Sequencing_Date	Checksum_Raw_FASTQ_Mate2	Biomaterial_Provider	Treatment_Description	Sample_Preparation_Date	BioAnalyzer_File	Sequencing_Instrument	Additional_Tissue_Description	Protocol_File	Name_Quality_Control_File_Mate2	Tissue_Code	File_Name_Metadata_File	Mate2_File
-	synthetic_10_reads_paired	xxx	xxx	PAIRED	xxx	Fri Dec 20 00:00:00 CET 2019	xxx	xxx	xxx	synthetic.mate_1.fastq.gz	xxx	xxx	SENSE	xxx	xxx	xxx	250.0	Homo sapiens	xxx	9606	xxx	xxx	/labkey/Zavolan%20Group/Test_labkey/list-details.view?listId=9&pk=../input_files/project1	xxx	ANTISENSE	xxx	xxx	xxx	100.0	synthetic_10_reads_paired	xxx		AGATCGGAAGAGCGT	../input_files/project1	AGATCGGAAGAGCACA	xxx	xxx	xxx	xxx	xxx	xxx	xxx	xxx	xxx	xxx	xxx	xxx	xxx	xxx	synthetic.mate_2.fastq.gz
-	synthetic_10_reads_mate_1	xxx	xxx	SINGLE	xxx	Fri Dec 20 00:00:00 CET 2019	xxx	xxx	xxx	synthetic.mate_1.fastq.gz	xxx	xxx	SENSE	xxx	xxx	xxx	250.0	Homo sapiens	xxx	9606	xxx	xxx	/labkey/Zavolan%20Group/Test_labkey/list-details.view?listId=9&pk=../input_files/project2	xxx		xxx	xxx	xxx	100.0	synthetic_10_reads_mate_1	xxx			../input_files/project2	AGATCGGAAGAGCACA	xxx	xxx	xxx	xxx	xxx	xxx	xxx	xxx	xxx	xxx	xxx	xxx	xxx	xxx	

tests/test_scripts_prepare_inputs_table/test.sh

-#!/bin/bash
-
-# Tear down test environment
-cleanup () {
-    rc=$?
-    rm -rf .snakemake/
-    rm -rf config.yaml
-    rm -rf samples.tsv
-    rm -rf logs
-    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
-python "../../scripts/prepare_inputs.py" \
-    --input-to-output-mapping="../../scripts/prepare_inputs.dict.tsv" \
-    --resources-dir="../input_files" \
-    --output-table="samples.tsv" \
-    --config-file="config.yaml" \
-    --multimappers='10' \
-    --logo="../../images/logo.128px.png" \
-    --output-dir="" \
-    --no-process-paths \
-    "input_table.tsv"
-
-
-# Check if dry run completes
-snakemake \
-    --snakefile="../../workflow/Snakefile" \
-    --configfile="config.yaml" \
-    --dryrun \
-    --verbose
-
-md5sum --check "expected_output.md5"
-# MD5 sums obtained with command:
-# md5sum config.yaml samples.tsv > expected_output.md5