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KoesGroup / Snakemake_ChIPseq_PE

Pipeline for the analysis of PE ChIP-seq data
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Fastqc #1

Closed JihedC closed 6 years ago

JihedC commented 6 years ago

Add rule fastqc to the snakemake pipeline Generates .zip and .html file for the fastq after trimming.

JihedC commented 6 years ago

I have added wget in the environnement file because on my local computer it asked for it

JihedC commented 6 years ago

I spotted 1 mistake I made, the shell command doesn't output the log of the QC to the folder/files created by snakemake. This is because I remove the 2> {log} at the end of the shell directive.

mgalland commented 6 years ago

Everything works except on genseq for some obscure reason (java configuration). An improvement for later is to use singularity with a docker image. By writing in a Snakefile: singularity: "docker://continuumio/miniconda3:4.4.10" for instance. See here for more info: https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#combining-conda-package-management-with-containers

JihedC commented 6 years ago

Thanks, then I will merge it !