example_config.yaml

# data
indir: /data/akhtar/sequencing_data/180412_J00182_0077_AHV23YBBXX_lanes1_4/Project_370_Semplicio_Akhtar/Sample_18L005768

R1_path: /data/akhtar/sequencing_data/180412_J00182_0077_AHV23YBBXX_lanes1_4/Project_370_Semplicio_Akhtar/Sample_18L005768/MAPCap_I_R1.fastq.gz
R2_path: /data/akhtar/sequencing_data/180412_J00182_0077_AHV23YBBXX_lanes1_4/Project_370_Semplicio_Akhtar/Sample_18L005768/MAPCap_I_R2.fastq.gz
## paired-end read name
reads: [MAPCap_I_R1, MAPCap_I_R2]

expname: MAPCap
sampleinfo: /data/processing4/jana/mapcap_pipeline/sampleInfo.tsv

# Trimming
cutadapt_path: /package/anaconda3/envs/cutadapt-1.16/bin/
trim_options:
trim_galore_path: /package/trim_galore_v0.4.4/

# Mapping
mapping_prg: STAR
star_index: /data/repository/organisms/dm6_ensembl/STARIndex/
star_path: /package/STAR-2.5.3a/bin/
star_options:
paired: True
hisat_index: /data/repository/organisms/GRCh38_ensembl/HISAT2Index/genome
subread_index: /data/processing4/jana/mapcap_pipeline/dm6_subread_index/dm6
genes_gtf: /data/repository/organisms/dm6_ensembl/ensembl/release-79/genes.gtf
map_spike: TRUE
spike_index_star: /data/repository/organisms/GRCh38_ensembl/STARIndex/
spike_index_subread: /data/processing4/jana/mapcap_pipeline/hg38_subread_index/hg38
spikeIn_prefix: "_human"

# R
R_libs_path:  /data/processing4/R_LIB/3.5
R_path: /package/R-3.5.0/bin
demult: /data/processing4/jana/mapcap_pipeline/rscript/demult.R
removedup: /data/processing4/jana/mapcap_pipeline/rscript/removeduplicate.R
tssdetection: /data/processing4/jana/mapcap_pipeline/rscript/tssdetection.R
tss_annotation: /data/processing4/jana/mapcap_pipeline/rscript/tss_annotation.R
plotscripts: /data/processing4/jana/mapcap_pipeline/rscript/plotReadStats.R

# TSS
fold_change: "5"
plotFile: "NA"
GTFfile: "/data/processing4/jana/mapcap_pipeline/dm6_existing_annotations/dmel-all-r6.21.gtf"
enhancer_file: "/data/processing4/jana/mapcap_pipeline/dm6_existing_annotations/starkLab_enhancers.bed"
repeat_file: "/data/processing4/jana/mapcap_pipeline/dm6_existing_annotations/dm6_repeatPositions.bed"
dhs_file: "NA"