Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Chouaref
Snakemake_ATAC_2020
Commits
954d4052
Commit
954d4052
authored
Nov 17, 2020
by
WJH58
Browse files
bowtie2 version changed
parent
60251e93
Changes
2
Hide whitespace changes
Inline
Side-by-side
ATAC-seq_pipeline/envs/samtools_bowtie.yaml
View file @
954d4052
channels
:
-
bioconda
dependencies
:
-
bowtie2=2.
4
.2
-
bowtie2=2.
3
.2
ATAC-seq_pipeline/snakefile
View file @
954d4052
...
...
@@ -118,6 +118,19 @@ rule trimmomatic:
SLIDINGWINDOW:4:15 \
MINLEN:40 &>{log}
"""
rule trimmed_fastqc:
input:
forward_reads = WORKING_DIR + "trimmed/{samples}_forward.fastq.gz",
reverse_reads = WORKING_DIR + "trimmed/{samples}_reverse.fastq.gz"
output:
RESULT_DIR + "fastqc/{samples}_{R}_trimmed_fastqc.html"
params:
RESULT_DIR + "fastqc/"
conda:
"envs/fastqc.yaml"
shell:
"fastqc --outdir={params} {input.forward_reads} {input.reverse_reads} &>{log}"
rule fastqc:
input:
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment