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Chouaref
Snakemake_ATAC_2020
Commits
a35f703d
Commit
a35f703d
authored
Nov 17, 2020
by
WJH58
Browse files
put comments on trimmomatic
parent
c6afcd22
Changes
1
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ATAC-seq_pipeline/snakefile
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a35f703d
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@@ -47,8 +47,8 @@ FASTQC = expand(RESULT_DIR + "fastqc/{samples}_{R}_2000reads_fastqc.htm
FORWARD_READS = expand(WORKING_DIR + "trimmed/{samples}_forward.fastq.gz", samples = SAMPLES),
REVERSE_READS = expand(WORKING_DIR + "trimmed/{samples}_reverse.fastq.gz", samples = SAMPLES),
TRIMMED_FASTQC = expand(RESULT_DIR + "fastqc/{samples}_{R}_trimmed_fastqc.html", samples = SAMPLES, R=['R1', 'R2']),
MAPPED = expand(WORKING_DIR + "mapped/{samples}.bam", samples = SAMPLES),
UNMAPPED = [WORKING_DIR + "unmapped/{samples}.fq." + str(i) +".gz" for i in range(1,2)],
#
MAPPED = expand(WORKING_DIR + "mapped/{samples}.bam", samples = SAMPLES),
#
UNMAPPED = [WORKING_DIR + "unmapped/{samples}.fq." + str(i) +".gz" for i in range(1,2)],
rule all:
input:
...
...
@@ -152,26 +152,26 @@ rule fastqc:
shell:
"fastqc --outdir={params} {input.fwd} {input.rev} &>{log}"
rule mapping:
input:
foward = WORKING_DIR + "trimmed/{samples}_forward.fastq.gz",
reverse = WORKING_DIR + "trimmed/{samples}_reverse.fastq.gz",
forwardUnpaired = WORKING_DIR + "trimmed/{samples}_forward_unpaired.fastq.gz",
reverseUnpaired = WORKING_DIR + "trimmed/{samples}_reverse_unpaired.fastq.gz",
index = [WORKING_DIR + "genome." + str(i) + ".bt2" for i in range(1,4)]
output:
mapped = WORKING_DIR + "mapped/{samples}.bam",
unmapped = [WORKING_DIR + "unmapped/{samples}.fq." + str(i) +".gz" for i in range(1,2)],
params:
bowtie = " ".join(config["bowtie2"]["params"].values()), #take argument separated as a list separated with a space
index = WORKING_DIR + "genome",
unmapped = WORKING_DIR + "unmapped/{samples}.fq.gz"
threads: 10
conda:
"../envs/samtools_bowtie.yaml"
log:
RESULT_DIR + "logs/bowtie/{samples}.log"
shell:
"""
bowtie2 {params.bowtie} --threads {threads} -x {params.index} -1 {input.forward} -2 {input.reverse} -U {input.forwardUnpaired},{input.reverseUnpaired} --un-conc-gz {params.unmapped} | samtools view -Sb - > {output.mapped} 2>{log}
"""
#
rule mapping:
#
input:
#
foward = WORKING_DIR + "trimmed/{samples}_forward.fastq.gz",
#
reverse = WORKING_DIR + "trimmed/{samples}_reverse.fastq.gz",
#
forwardUnpaired = WORKING_DIR + "trimmed/{samples}_forward_unpaired.fastq.gz",
#
reverseUnpaired = WORKING_DIR + "trimmed/{samples}_reverse_unpaired.fastq.gz",
#
index = [WORKING_DIR + "genome." + str(i) + ".bt2" for i in range(1,4)]
#
output:
#
mapped = WORKING_DIR + "mapped/{samples}.bam",
#
unmapped = [WORKING_DIR + "unmapped/{samples}.fq." + str(i) +".gz" for i in range(1,2)],
#
params:
#
bowtie = " ".join(config["bowtie2"]["params"].values()), #take argument separated as a list separated with a space
#
index = WORKING_DIR + "genome",
#
unmapped = WORKING_DIR + "unmapped/{samples}.fq.gz"
#
threads: 10
#
conda:
#
"../envs/samtools_bowtie.yaml"
#
log:
#
RESULT_DIR + "logs/bowtie/{samples}.log"
#
shell:
#
"""
#
bowtie2 {params.bowtie} --threads {threads} -x {params.index} -1 {input.forward} -2 {input.reverse} -U {input.forwardUnpaired},{input.reverseUnpaired} --un-conc-gz {params.unmapped} | samtools view -Sb - > {output.mapped} 2>{log}
#
"""
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