pipeline.cfg

[DEFAULT]
output_dir = /pstore/home/zhangj83/projects/2019-01-LowInputRNASeq/analysis/QiagenSinglecellRnaOutdir
cell_index_file = /pstore/home/zhangj83/projects/2019-01-LowInputRNASeq/analysis/QiagenInformation/cell-index.list4.96.txt
vector_sequence = AAGCAGTGGTATCAACGCAGAGTAC
isolator = ACG
mt_len = 12
num_cores = 4
num_errors = 3
editdist = 0  
cell_indices_used = C1,C13,C25,C37,C49,C61,C73,C85,C47,C27,C28,C29,C30,C31,C32,C33,C34 

[ExtractMultiplexRegion]

[DeMultiplexer]

[Alignment]
cell_fastq = 
cell_num = 
cell_index = 

[CountMT]
cell_fastq = 
cell_num = 
cell_index = 

[JoinCountFiles]

[CombineSamples]

[ClusteringAnalysis]

[WriteExcelSheet]

[config]
star = /pstore/apps/STAR/2.5.2a-goolf-1.7.20/bin/STAR
star_params = --runMode alignReads --genomeLoad NoSharedMemory --runThreadN 4 --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMprimaryFlag AllBestScore --outSAMmultNmax 1 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0
star_load_params = --genomeLoad NoSharedMemory 
star_exit_params = --genomeLoad Exit
genome_dir = /pstore/data/bi/apps/genomes/human/hg38/star_ensembl/
seqtype = wts
primer_file =
annotation_gtf = /pstore/data/bi/apps/genomes/human/hg38/gtf/ensembl/ensembl.gtf
ercc_bed = /pstore/data/biomics/_pre_portfolio/_platform_evaluation/7788_LowInputEvaluation_3UPXQiagen/3UPXQiagenTest_19.12.2018/QiagenInformation/ERCC-mix2.bed
is_low_input = 1
species = human
catalog_number = polyA-human

[core]
log_level = INFO

[retcode]
already_running = 10
missing_data = 20
not_run = 25
task_failed = 30
scheduling_error = 35
unhandled_exception = 40