Commit fcde192a authored by WJH58's avatar WJH58
Browse files

bowtiw2 version changed again

parent 954d4052
channels: channels:
- bioconda - bioconda
dependencies: dependencies:
- bowtie2=2.3.2 - bowtie2=2.3.5
...@@ -46,6 +46,8 @@ wildcard_constraints: ...@@ -46,6 +46,8 @@ wildcard_constraints:
FASTQC = expand(RESULT_DIR + "fastqc/{samples}_{R}_2000reads_fastqc.html", samples = SAMPLES, R=['R1', 'R2']), 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), FORWARD_READS = expand(WORKING_DIR + "trimmed/{samples}_forward.fastq.gz", samples = SAMPLES),
REVERSE_READS = expand(WORKING_DIR + "trimmed/{samples}_reverse.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: rule all:
input: input:
...@@ -55,7 +57,8 @@ rule all: ...@@ -55,7 +57,8 @@ rule all:
WORKING_DIR + "genome.rev.1.bt2", WORKING_DIR + "genome.rev.1.bt2",
WORKING_DIR + "genome.rev.2.bt2", WORKING_DIR + "genome.rev.2.bt2",
FORWARD_READS, FORWARD_READS,
REVERSE_READS REVERSE_READS,
TRIMMED_FASTQC,
message : "Analysis is complete!" message : "Analysis is complete!"
shell:"" shell:""
...@@ -131,7 +134,6 @@ rule trimmed_fastqc: ...@@ -131,7 +134,6 @@ rule trimmed_fastqc:
shell: shell:
"fastqc --outdir={params} {input.forward_reads} {input.reverse_reads} &>{log}" "fastqc --outdir={params} {input.forward_reads} {input.reverse_reads} &>{log}"
rule fastqc: rule fastqc:
input: input:
fwd = expand(DATA_DIR + "{samples}_R1_2000reads.fq.gz", samples = SAMPLES), fwd = expand(DATA_DIR + "{samples}_R1_2000reads.fq.gz", samples = SAMPLES),
......
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