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Chouaref
Snakemake_ATAC_2020
Commits
fcde192a
Commit
fcde192a
authored
Nov 17, 2020
by
WJH58
Browse files
bowtiw2 version changed again
parent
954d4052
Changes
2
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ATAC-seq_pipeline/envs/samtools_bowtie.yaml
View file @
fcde192a
channels
:
-
bioconda
dependencies
:
-
bowtie2=2.3.
2
-
bowtie2=2.3.
5
ATAC-seq_pipeline/snakefile
View file @
fcde192a
...
...
@@ -46,6 +46,8 @@ wildcard_constraints:
FASTQC = expand(RESULT_DIR + "fastqc/{samples}_{R}_2000reads_fastqc.html", samples = SAMPLES, R=['R1', 'R2']),
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']),
rule all:
input:
...
...
@@ -55,7 +57,8 @@ rule all:
WORKING_DIR + "genome.rev.1.bt2",
WORKING_DIR + "genome.rev.2.bt2",
FORWARD_READS,
REVERSE_READS
REVERSE_READS,
TRIMMED_FASTQC,
message : "Analysis is complete!"
shell:""
...
...
@@ -131,7 +134,6 @@ rule trimmed_fastqc:
shell:
"fastqc --outdir={params} {input.forward_reads} {input.reverse_reads} &>{log}"
rule fastqc:
input:
fwd = expand(DATA_DIR + "{samples}_R1_2000reads.fq.gz", samples = SAMPLES),
...
...
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