Revision 31052e7c
Added by Chloe Quignot 6 months ago
| demo_advanced/codes/Snakefile | ||
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fq="data/{sample}.fastq.gz",
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idxFile=rules.bowtieIndex.output,
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output:
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bam=report(
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pipe("result/bowtie/{sample}.sam"),
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caption="report/bowtie2.rst",
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category="Step 2 Bowtie2",
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),
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# not a good idea because bam files are heavy
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bam=pipe("result/bowtie/{sample}.sam"),
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log:
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bwtout="result/logs/bowtie/{sample}_align.txt",
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stderr="result/logs/bowtie/{sample}_align.stderr",
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| ... | ... | |
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shell:
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"""
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bowtie2 -x {params.idx} -U {input.fq} -p {threads} {params.extra} \
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2> {log.bwtout} > {output}
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2> {log.bwtout} > {output}
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"""
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| ... | ... | |
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input:
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"result/bowtie/{sample}.sam",
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output:
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protected("result/bowtie/{sample}.bam"),
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report(
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protected("result/bowtie/{sample}.bam"),
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caption="report/bowtie2.rst",
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category="Step 2 Bowtie2",
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),
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# not a good idea because bam files are heavy
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log:
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"result/logs/samtools/{sample}.txt",
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benchmark:
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| demo_advanced/runRnaseq.sh | ||
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cd /path/to/the/project/
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snakemake --executor cluster-generic --cluster-generic-submit-cmd "qsub -V -l walltime={resources.time_min} -l select=1:ncpus={threads}:mem={resources.mem}" --snakefile codes/Snakefile --profile codes/profile --configfile configfile.yaml &> smkpipeline.txt
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# create directory for the pbs logs
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mkdir pbs
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snakemake --executor cluster-generic --cluster-generic-submit-cmd "qsub -V -l walltime={resources.time_min} -l select=1:ncpus={threads}:mem={resources.mem}" --snakefile codes/Snakefile --profile codes/profile --configfile configfile.yaml --report smkRnaseq_report.html
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snakemake --executor cluster-generic --cluster-generic-submit-cmd "qsub -V -l walltime={resources.time_min} -l select=1:ncpus={threads}:mem={resources.mem} -e pbs/{name}_$PBS_JOBID.err -o pbs/{name}_$PBS_JOBID.out" --snakefile codes/Snakefile --profile codes/profile --configfile configfile.yaml &> smkpipeline.txt
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snakemake --executor cluster-generic --cluster-generic-submit-cmd "qsub -V -l walltime={resources.time_min} -l select=1:ncpus={threads}:mem={resources.mem}" --snakefile codes/Snakefile --profile codes/profile --configfile configfile.yaml --report smkRnaseq_report.html
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Also available in: Unified diff
add Emilie's changes from other repo: change report from bowtie2 to samtoolsSort