The samples file used for this run:

sample assembly technical_replicates descriptivate_name
HSCD12_DMSO_1bio GRCh38.p13 DMSO_1 HSCD12_DMSO_1bio
HSCD12_DMSO_1tec GRCh38.p13 DMSO_1 HSCD12_DMSO_1tec
HSCD12_DMSO_2bio GRCh38.p13 DMSO_2 HSCD12_DMSO_2bio
HSCD12_DMSO_2tec GRCh38.p13 DMSO_2 HSCD12_DMSO_2tec
HSCD12_DMSO_3bio GRCh38.p13 DMSO_3 HSCD12_DMSO_3bio
HSCD12_DMSO_3tec GRCh38.p13 DMSO_3 HSCD12_DMSO_3tec
HSCD12_RU1uM_1bio GRCh38.p13 RU1uM_1 HSCD12_RU1uM_1bio
HSCD12_RU1uM_1tec GRCh38.p13 RU1uM_1 HSCD12_RU1uM_1tec
HSCD12_RU1uM_2bio GRCh38.p13 RU1uM_2 HSCD12_RU1uM_2bio
HSCD12_RU1uM_2tec GRCh38.p13 RU1uM_2 HSCD12_RU1uM_2tec
HSCD12_RU1uM_3bio GRCh38.p13 RU1uM_3 HSCD12_RU1uM_3bio
HSCD12_RU1uM_3tec GRCh38.p13 RU1uM_3 HSCD12_RU1uM_3tec
HSCD12_RU1uMTA100nM_1bio GRCh38.p13 RU1uMTA100nM_1 HSCD12_RU1uMTA100nM_1bio
HSCD12_RU1uMTA100nM_1tec GRCh38.p13 RU1uMTA100nM_1 HSCD12_RU1uMTA100nM_1tec
HSCD12_RU1uMTA100nM_2bio GRCh38.p13 RU1uMTA100nM_2 HSCD12_RU1uMTA100nM_2bio
HSCD12_RU1uMTA100nM_2tec GRCh38.p13 RU1uMTA100nM_2 HSCD12_RU1uMTA100nM_2tec
HSCD12_RU1uMTA100nM_3bio GRCh38.p13 RU1uMTA100nM_3 HSCD12_RU1uMTA100nM_3bio
HSCD12_RU1uMTA100nM_3tec GRCh38.p13 RU1uMTA100nM_3 HSCD12_RU1uMTA100nM_3tec
HSCD12_RU1uMTA1uM_1bio GRCh38.p13 RU1uMTA1uM_1 HSCD12_RU1uMTA1uM_1bio
HSCD12_RU1uMTA1uM_1tec GRCh38.p13 RU1uMTA1uM_1 HSCD12_RU1uMTA1uM_1tec
HSCD12_RU1uMTA1uM_2bio GRCh38.p13 RU1uMTA1uM_2 HSCD12_RU1uMTA1uM_2bio
HSCD12_RU1uMTA1uM_2tec GRCh38.p13 RU1uMTA1uM_2 HSCD12_RU1uMTA1uM_2tec
HSCD12_RU1uMTA1uM_3bio GRCh38.p13 RU1uMTA1uM_3 HSCD12_RU1uMTA1uM_3bio
HSCD12_RU1uMTA1uM_3tec GRCh38.p13 RU1uMTA1uM_3 HSCD12_RU1uMTA1uM_3tec
HSCD12_TA100nM_1bio GRCh38.p13 TA100nM_1 HSCD12_TA100nM_1bio
HSCD12_TA100nM_1tec GRCh38.p13 TA100nM_1 HSCD12_TA100nM_1tec
HSCD12_TA100nM_2bio GRCh38.p13 TA100nM_2 HSCD12_TA100nM_2bio
HSCD12_TA100nM_2tec GRCh38.p13 TA100nM_2 HSCD12_TA100nM_2tec
HSCD12_TA100nM_3bio GRCh38.p13 TA100nM_3 HSCD12_TA100nM_3bio
HSCD12_TA100nM_3tec GRCh38.p13 TA100nM_3 HSCD12_TA100nM_3tec
HSCD12_TA1uM_1bio GRCh38.p13 TA1uM_1 HSCD12_TA1uM_1bio
HSCD12_TA1uM_1tec GRCh38.p13 TA1uM_1 HSCD12_TA1uM_1tec
HSCD12_TA1uM_2bio GRCh38.p13 TA1uM_2 HSCD12_TA1uM_2bio
HSCD12_TA1uM_2tec GRCh38.p13 TA1uM_2 HSCD12_TA1uM_2tec
HSCD12_TA1uM_3bio GRCh38.p13 TA1uM_3 HSCD12_TA1uM_3bio
HSCD12_TA1uM_3tec GRCh38.p13 TA1uM_3 HSCD12_TA1uM_3tec
NP_Day12_supernatant_DMSO_1 GRCh38.p13 DMSO_4 NP_Day12_supernatant_DMSO_1
NP_Day12_supernatant_DMSO_2 GRCh38.p13 DMSO_4 NP_Day12_supernatant_DMSO_2
NP_Day12_supernatant_DMSO_3 GRCh38.p13 DMSO_4 NP_Day12_supernatant_DMSO_3
NP_Day12_supernatant_TA_1 GRCh38.p13 TA_1 NP_Day12_supernatant_TA_1
NP_Day12_supernatant_TA_2 GRCh38.p13 TA_1 NP_Day12_supernatant_TA_2
NP_Day12_supernatant_TA_3 GRCh38.p13 TA_1 NP_Day12_supernatant_TA_3
NP_Day1_adherentcells_DMSO_1 GRCh38.p13 day_1_dmso NP_Day1_adherentcells_DMSO_1
NP_Day1_adherentcells_DMSO_2 GRCh38.p13 day_1_dmso NP_Day1_adherentcells_DMSO_2
NP_Day1_adherentcells_DMSO_3 GRCh38.p13 day_1_dmso NP_Day1_adherentcells_DMSO_3
NP_Day1_adherentcells_TA_1 GRCh38.p13 day_1_TA NP_Day1_adherentcells_TA_1
NP_Day1_adherentcells_TA_2 GRCh38.p13 day_1_TA NP_Day1_adherentcells_TA_2
NP_Day1_adherentcells_TA_3 GRCh38.p13 day_1_TA NP_Day1_adherentcells_TA_3

The config file used for this run: 
# tab-separated file of the samples
samples: samples.tsv

# pipeline file locations
result_dir: ./results  # where to store results
genome_dir: /ceph/rimlsfnwi/data/genomes/
fastq_dir: /home/slrinzema/ceph/ghe/samples


# contact info for multiqc report and trackhub
email: slrinzema@science.ru.nl

# produce a UCSC trackhub?
create_trackhub: true

# 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: salmon

# which aligner to use
aligner: star

# how to sort bam
bam_sorter:
  samtools:
    coordinate

# filtering after alignment
remove_blacklist: true
only_primary_align: true
min_mapping_quality: 255 # instead of 30
remove_dups: false