I have prepared a config.yaml file as suggested in your documentation.
#!/bin/sh
REFERENCE="/exports/humgen/jihed/rrbs_zbtb24/reference"
python scripts/make_config.py \
--config-path /exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1/config.yaml \
--wd /exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1 \
--genome-path /exports/humgen/jihed/rrbs_zbtb24/reference/mm10.reference.fa \
--bismark-index-path /exports/humgen/jihed/rrbs_zbtb24/reference \
--sample-sheet /exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1/sample_sheet.csv \
--annotation-file /exports/humgen/jihed/rrbs_zbtb24/genes.gtf \
--dmr-window-size 500 \
--dmr-difference 15 \
--dmr-qvalue 0.01 \
--min-per-group 2 \
--mate1-pattern _R1 \
--mate2-pattern _R2 \
--fastq-extension .fastq \
--genome-version mm10 \
--singularity-container /exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1/methylsnake_latest.sif \
--tmp-folder /exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1/temp \
--log-folder /exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1/log \
--reads-folder /exports/humgen/jihed/rrbs_zbtb24/fastq \
--trimmed-folder /exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1/trimmed \
--alignments-folder /exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1/bismark \
--reports-folder /exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1/reports/ \
--nucleotide-stats-folder /exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1/stats \
--methylkitdb-folder /exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1/methylkit \
--rdata-folder /exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1/rds \
--bed-folder /exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1/dmr \
--pictures-folder /exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1/pictures \
--tables-folder /exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1/tables \
--fastqc-folder /exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1/fastqc
alignments_folder: /exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1/bismark
annotation_file: /exports/humgen/jihed/rrbs_zbtb24/genes.gtf
bed_folder: /exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1/dmr
bismark_index_path: /exports/humgen/jihed/rrbs_zbtb24/reference
dmr_difference:
- 15.0
dmr_qvalue:
- 0.01
dmr_step_size: 500
dmr_window_size: 500
fastq_extension: .fastq
fastqc_folder: /exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1/fastqc
genome_path: /exports/humgen/jihed/rrbs_zbtb24/reference/mm10.reference.fa
genome_version: mm10
high_coverage_percentage: 99.9
log_folder: /exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1/log
low_coverage_count: 10
mate1_pattern: _R1
mate2_pattern: _R2
methylkitdb_folder: /exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1/methylkit
min_per_group: 2
nucleotide_stats_folder: /exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1/stats
pictures_folder: /exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1/pictures
rdata_folder: /exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1/rds
reads_folder: /exports/humgen/jihed/rrbs_zbtb24/fastq
reports_folder: /exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1/reports/
sample_sheet: /exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1/sample_sheet.csv
samples:
- WT1
- WT2
- KO1
- KO2
singularity_container: /exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1/methylsnake_latest.sif
tables_folder: /exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1/tables
tmp_folder: /exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1/temp
trimmed_folder: /exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1/trimmed
wd: /exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1
KeyError in line 3 of /exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1/Snakefile:
'singularity_container'
File "/exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1/Snakefile", line 3, in <module>
I don't understand the error here because I downloaded the container and added the path to the config file:
/exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1/methylsnake_latest.sif