Preparation of the config file

[JihedC]

Hi @ftabaro ,

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

I have obtained this, which seems to be similar to the example document:

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

I tried a dry run with snakemake -np and got the following error message:

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

Do you have any idea what can be wrong here?

Thanks in advance,

Jihed

[ftabaro]

If you are not using the provided wrapper script you will need to run Snakemake with --configfile because no default is provided inside the Snakefile.

In fact, my wrapper run_snakemake.sh should throw an error if not run as run_snakemake.sh path/to/config.yaml.

[JihedC]

So I can't make a dry run ?

[ftabaro]

You can make a dry run but you need to add the path to the config file:

snakemake -n -p --configfile path/to/config.yaml

[JihedC]

Thanks! It worked :)
I have got this error message now.

WildcardError in line 221 of /exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1/Snakefile:
Wildcards in params cannot be determined from output files. Note that you have to use a function to deactivate automatic wildcard expansion in params strings, e.g., `lambda wildcards: '{test}'`. Also see https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules:
'diff'

Do I need to define a contrast in the config file?

[ftabaro]

I pushed a fix, please, update your repositoty. Thanks for pointing out!

[JihedC]

Thanks the pipeline is now running. Note that I used the release 1.1.1 on a slurm computer.
I changed the Snakefile directly to make it work.

Thanks a lot! I hope to not have to bother you again! I learned a lot about Snakemake just by reading your pipeline!