# tab-separated file of the samples
samples: samples.tsv

# pipeline file locations
result_dir: ./results  # where to store results
genome_dir: ../genomes  # where to look for or download the genomes
fastq_dir: ../fastq_dir  # where to look for or download the fastqs


# contact info for multiqc report and trackhub
email: Jsmits@science.ru.nl
ignore_strandedness: True

# produce a UCSC trackhub?
create_trackhub: False

# how to handle replicates
technical_replicates: merge    # change to "keep" to not combine them

# which trimmer to use
trimmer: fastp

# which quantifier to use
quantifier: htseq  # or salmon or featurecounts

##### aligner and filter options are not used for the gene counts matrix if the quantifier is Salmon

# which aligner to use
aligner: star

# filtering after alignment
remove_blacklist: True
min_mapping_quality: 255  # (only keep uniquely mapped reads from STAR alignments)
only_primary_align: True

##### differential gene expression analysis (optional) #####

#deseq2:
#  multiple_testing_procedure: BH
#  alpha_value: 0.1
#  shrinkage_estimator: apeglm

#contrasts:
#  - 'celltype_KC_LSC'