project_name : "test"
project_dir : "test/test_project/"
sequencing_runs :
- name : "Run1"
version : 'v1'
dir : "test/seq_runs/run_v1_single_file"
fastq_path : "{read}.fastq.gz"
library_name : "test_lib0"
- name : "Run2"
version : 'v2'
dir : "test/seq_runs/run_v2_single_file"
fastq_path : "{read}.fastq.gz"
library_name : "test_lib1"
- name : "Run3"
version : 'v2'
dir : "test/seq_runs/run_v2_split"
fastq_path : "{library_prefix}_{split_affix}_{read}_001.fastq.gz"
split_affixes : ["L001", "L002"]
libraries :
- {library_name: "test_lib1", library_prefix: "lib1"}
- {library_name: "test_lib2", library_prefix: "lib2"}
- name : 'Run4'
version : 'v3'
dir : "test/seq_runs/run_v3"
fastq_path : "Undetermined_S0_{split_affix}_{read}_001.fastq.gz"
split_affixes : ["L001", "L002"]
libraries :
- {library_name: "test_lib3", library_index: "ATAGAG"}
- {library_name: "test_lib4", library_index: "AGAGGA"}
paths :
bowtie_index : "/Users/averes/Projects/Melton/grch38_test/Homo_sapiens.GRCh38.85.annotated"
python_dir : "/Users/averes/miniconda3/envs/py27/bin/"
samtools_dir : "/Users/averes/software/samtools-1.3.1/bin/"
rsem_dir : ""
java_dir : ""
parameters : # OPTIONAL PARAMETERS
# umi_quantification_arguments:
# m : 10 #Ignore reads with more than M alignments, after filtering on distance from transcript end.
# u : 1 #Ignore counts from UMI that should be split among more than U genes.
# d : 600 #Maximal distance from transcript end, NOT INCLUDING THE POLYA TAIL
# split-ambigs: False #If umi is assigned to m genes, add 1/m to each gene's count (instead of 1)
# min_non_polyA: 15 #Require reads to align to this much non-polyA sequence. (Set to 0 to disable filtering on this parameter.)
# output_arguments:
# output_unaligned_reads_to_other_fastq: False
# low_complexity_mask: False
# bowtie_arguments:
# m : 200
# n : 1
# l : 15
# e : 1000
trimmomatic_arguments:
LEADING: "28"
SLIDINGWINDOW: "4:20"
MINLEN: "16"
