Prepared by the eResearch Office, QUT.
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group,replicate,fastq_1,fastq_2,strandedness control,1,/path/to/fastq/control-1_R1.fastq.gz,/path/to/fastq/control-1_R2.fastq.gz,unstranded control,2,/path/to/fastq/control-2_R1.fastq.gz,/path/to/fastq/control-2_R2.fastq.gz,unstranded control,3,/path/to/fastq/control-3_R1.fastq.gz,/path/to/fastq/control-3_R2.fastq.gz,unstranded infected,1,/path/to/fastq/infected-1_R1.fastq.gz,/path/to/fastq/infected-1_R2.fastq.gz,unstranded infected,2,/path/to/fastq/infected-1_R1.fastq.gz,/path/to/fastq/infected-2_R2.fastq.gz,unstranded infected,3,/path/to/fastq/infected-1_R1.fastq.gz,/path/to/fastq/infected-3_R2.fastq.gz,unstranded |
Nex Index format for current version 3.3:
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In the folder you have created for this run create launch.pbs using a text editor (i.e., vim, nano)
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#!/bin/bash -l #PBS -N nfrna2 #PBS -l select=1:ncpus=2:mem=4gb #PBS -l walltime=24:00:00 cd $PBS_O_WORKDIR module load java NXF_OPTS='-Xms1g -Xmx4g' nextflow run nf-core/rnaseq -profile singularity -r 3.3 --input samplesheetindex.csv --genome GRCm38 --aligner star_rsem --min_mapped_reads 5 salmon |
Additional options:
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#!/bin/bash -l
#PBS -N nfrna2
#PBS -l select=1:ncpus=2:mem=4gb
#PBS -l walltime=24:00:00
#work on current directory (folder)
cd $PBS_O_WORKDIR
#load java and set up memory settings to run nextflow
module load java
NXF_OPTS='-Xms1g -Xmx4g'
#run the rnaseq pipeline
#with-dag can output files in .png, .pdf, .svg or .html
nextflow run nf-core/rnaseq -profile conda --input samplesheet.csv \
--genome GRCm38 \
--aligned star_rsem \
--min_mapped_reads 5 \
--clip_r1 10 \
--clip_r2 10 \
--three_prime_clip_r1 2 \
--three_prime_clip_r2 2 \
--remove_ribo_rna \
-dump-channels \
-with-dag flowchart.png |
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You can use the command
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qstat -u $USER |
Alternatively use the following command:
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qjobs |
To check on the jobs you are running. Nextflow will launch additional jobs during the run.
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