Commit fcde192a authored by WJH58's avatar WJH58
Browse files

bowtiw2 version changed again

parent 954d4052
channels:
- bioconda
dependencies:
- bowtie2=2.3.2
- bowtie2=2.3.5
......@@ -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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