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A Snakemake pipeline for RRBS data analysis

License: GNU General Public License v3.0

Python 44.42% Shell 4.28% R 51.30%

bioinformatics-pipeline methylation rrbs-data-analysis rrbs-pipeline snakemake

methylsnake's Introduction

Hi there 👋

🔭 I’m currently working on large genomics dataset at the European Molecular Biology Laboratory in Rome (Italy). I analyze genomics dataset and develop tools to automate such tasks.
🌱 I’m currently learning Snakemake 🐍 and Nextflow ⏭️. In my free time I am experimenting with Nix and NixOS.
👯 I’m looking to collaborate on image processing!
💬 Ask me about data visualization, genomics data analysis and the weather 😇
📫 How to reach me: [email protected]
😄 Pronouns: he/him/his

methylsnake's People

Contributors

Stargazers

Watchers

Forkers

balharbi nykterlab reettanatkin saimmomin12 ctl3120 zm-git-dev cvn001 elisabethgoldman

methylsnake's Issues

Preparation of the config file

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

Add automatic pooling of multi-lane samples

Extend the pipeline with an optional step to pool samples from different lanes. Config file should have a flag to enable this, the flag should be turned on if the sample sheet has some special column (named "pool" maybe?).

Validate treatment

The make_config.py script should validate the treatment column and throw and error if no control sample(s) are detected. Should also validate treatments as numeric values.

Problem with singularity

Hi @ftabaro ,

Thank you for your pipeline it seems very nice. I would like to try it but I have some issue with singularity.

I believe that before running the pipeline I need to perform a pull of the singularity container with:
singularity pull library://ftabaro/default/methylsnake

However when I do it I get the following error message:
ERROR: pull is only supported for shub URIs

I use singularity 3.6.1.

I have found your container here. But the pull command throws the same error.

I don't have administrator rights on the cluster computer I work on so the commands to compile the container won't work either.

sudo singularity build base.sif Singularity.base
sudo singularity build methylkit.sif Singularity.methylkit

Do you have suggestions to solve this issue? Can I install all the required packages via conda?

Thanks for your help!

Automate folder hierarchy generation

During the configuration phase, generate the folder hierarchy. The config script should take as input only the root (working directory) and generate all folders under it automatically.
This will simplify a lot the command line interface of the config script.

Missing R package genomation

Hi,
The pipeline worked fine until the rule run_methylkit_analysis where I got this:

[Fri Feb  5 08:19:44 2021]
Job 0: Performing methylKit analysis...

Rscript /exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1/.snakemake/scripts/tmpc5gro0mj.methylkit_analysis.R
#################################
## Starting methylKit analysis ##
#################################
Error in library(genomation) : there is no package called ‘genomation’
Calls: suppressPackageStartupMessages -> withCallingHandlers -> library
Execution halted
[Fri Feb  5 08:20:06 2021]
Error in rule run_methylkit_analysis:
    jobid: 0
    output: /exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1/log/methylkit_analysis0.01_15.0.done

Genomation package is missing. I am installing it at the moment.

Best regards,

Jihed

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