config.yaml

# samples_file: /lustre/bmt-data/genomics/projects/glioma_cellline_rrbs/samples.txt
wd: /lustre/bmt-data/genomics/projects/glioma_cellline_rrbs

tmp_folder: /scratch/ft413468

log_folder: /lustre/bmt-data/genomics/projects/glioma_cellline_rrbs/src/snakemake/logs
environments_folder: /lustre/bmt-data/genomics/projects/glioma_cellline_rrbs/src/snakemake/environments

raw_reads_folder: /lustre/bmt-data/genomics/projects/glioma_cellline_rrbs/reads

trimmed_reads_folder: /lustre/bmt-data/genomics/projects/glioma_cellline_rrbs/trimmed_reads

alignments_folder: /lustre/bmt-data/genomics/projects/glioma_cellline_rrbs/alignments

reports_folder: /lustre/bmt-data/genomics/projects/glioma_cellline_rrbs/bismark_reports

nucleotide_stats_folder: /lustre/bmt-data/genomics/projects/glioma_cellline_rrbs/nucleotide_stats

genome_fasta: /bmt-data/genomics/reference/hg19/hg19.fa

bismark_index_path: /bmt-data/genomics/reference/bismark/hg19

ensembl_root: "/bmt-data/genomics/reference/Ensembl"

ensembl_version: "grch37/release-97"

methylkitdb_folder: /lustre/bmt-data/genomics/projects/glioma_cellline_rrbs/methylDB

RData_folder: /lustre/bmt-data/genomics/projects/glioma_cellline_rrbs/R_data

pictures_folder: /lustre/bmt-data/genomics/projects/glioma_cellline_rrbs/pictures
tables_folder: /lustre/bmt-data/genomics/projects/glioma_cellline_rrbs/tables

dmr_window_size: 500
dmr_step_size: 500
dmr_difference: 25
dmr_qvalue: 0.01

samples:
    - SRR4048940
    - SRR4048941
    - SRR4048942
    - SRR4048943
    - SRR4048944
    - SRR4048945
    - SRR4048946
    - SRR4048947
    - SRR4048948
    - SRR4048949
    - SRR4048950
    - SRR4048951
    - SRR4048952
    - SRR4048953
    - SRR4048954
    - SRR4048955
    - SRR4048956
    - SRR4048957
    - SRR4048958
    - SRR4048959
    - TMP34p14_FRBS190660163-1a_HLKMYDSXX_L3
    - TMP34p14_FRBS190660163-1a_HLLW5DSXX_L4
    - TMP45p18_FRBS190660164-1a_HLKLYDSXX_L4
    - TMP45p18_FRBS190660164-1a_HLLW5DSXX_L4
    - TMP46p8_FRBS190660165-1a_HLKMYDSXX_L3
    - TMP46p8_FRBS190660165-1a_HLLW5DSXX_L4
    - TMP51p11_FRBS190660166-1a_HLFYCDSXX_L3
    - TMP51p11_FRBS190660166-1a_HLLW5DSXX_L4
    - TMP55p9_FRBS190660167-1a_HLFYCDSXX_L3
    - TMP55p9_FRBS190660167-1a_HLLL7DSXX_L3