##  pijpleiding configuration file. Run `pijplieding --help` for more help.
##
##  the pipe_run parameter decides whether to run the pipe segment or not.
##  the pipe_input_files (which can be multilined) is treated as multiple shell
##  patterns refering to existing files, so it is expanded and split accordingly,
##  and passed as 'input_files' to the pipe segment. The rest of the parameters
##  are passed as they are to the pipe segments, so check their description
##
##  nice -n 19 python2 pijpleiding.py /scratch/etanis/FRIEDL/220513/config_file_LW52-1.txt



[scythe_wrapper]
pipe_run = True

[bc_demultiplex]
pipe_run = True

bc_index_file= /ceph/rimlsfnwi/data/moldevbio/mulder/karjosukarso/LAURA/new_results/barcodes_umis.txt
sample_sheet= /scratch/etanis/FRIEDL/220513/sample_sheet_LW52_plate1.txt
pipe_input_files= /scratch/etanis/FRIEDL/210913/LW-52/FASTQ_RNA/INV_LW-52_plate1_CTCs_lane1_44_R1.fastq
fname_delimiter = _
lane_field = 4
index_field = 5
strand_field = 6
output_dir= /scratch/etanis/FRIEDL/220513/barcode_splitted_LW52
stats_file= stats.tab
min_bc_quality= 10
bc_length = 8
umi_length = 8
cut_length = 50

[bowtie_wrapper]
pipe_run = True

pipe_input_files= /scratch/etanis/FRIEDL/220513/barcode_splitted_LW52/L*.fastq
index_file= /ceph/rimlsfnwi/data/moldevbio/mulder/etanis/1_RAID/refs/bowtie2/mm_mCherry_blasticidin/mm10_mCherry_blast
output_dir= /scratch/etanis/FRIEDL/220513/sam_files_LW52
bowtie_report_name = bt_report_full.tab
number_of_threads = 3
extra_params = -k 3
procs = 10

[htseq_wrapper]
pipe_run = True

pipe_input_files= /scratch/etanis/FRIEDL/220513/sam_files_LW52/L*.sam
gff_file = /scratch/etanis/genome_ref/gencode.vM16.basic_ERCC_mcherry_mCherry-blast.gff3
output_dir= /scratch/etanis/FRIEDL/220513/COUNT_TABLES_LW52
umi= true
extra_params = -q
count_filename = COUNTS_LW52.tab

[clean_up]
pipe_run = False