软著字第1402752号
Copy snakefile and cluster.json to your raw data directory. Modify the LIBRARY, BARCODE_NAME to your project.
The raw data filename must be "{LIBRARY}.R1.fastq.gz and {LIBRARY}.R2.fastq.gz"
LIBRARY = "H16A28P250-1"
run the shell:
export PATH=/home/xujm/soft/Anaconda/anaconda3/bin:$PATH
source activate snakemake
snakemake -j 80 --cluster-config cluster.json -c "qsub -cwd -l vf={cluster.vf} -e {cluster.err} -o {cluster.std}" --jn {params.job_name}{jobid} -T
The same flow has two type inner barcode ITS miseq and hiseq
Fastqfilter sample name error bug
Cant execute fastqc when there is no clean.fq data, so the flow cant to finish for reporting
Support repeat barcode between ITS and 16S
support fuzzy search for barcode
Sample name has '_' letter will cause report sample name mistake
add nifH data type
It can only read gz file now, I will upgrade the rule to support read uncompressed fastq file for flow input
Support repeat barcode between ITS and 16S
Read the column 5 of the giving 'sam_barcode.all' file for multiple primer support in the same flow
/bin/sh: fastqc: command not found when running flow, the workflow will crash when run fastqc without fastqc installed
set F_PRIMER == "none" and R_PRIMER == "none"
store raw data reads number for report speed up
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