28 lines
873 B
Bash
28 lines
873 B
Bash
#!/bin/bash
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#SBATCH --job-name=FastQC.for.alveolar_type_2
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#SBATCH --comment=FastQC.for.alveolar_type_2
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#SBATCH --time=48:00:00
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#SBATCH --mincpus=2
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#SBATCH --mem=20G
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#SBATCH --qos=priority
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# For 173 samples, it will take about 24 hrs to run with about 15Gb of memory.
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# Should probably parallelize the perl script/make it a bash/slurm script.
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module purge
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module load Perl/5.26.2-foss-2015b-bare
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module load BioPerl/1.6.924-foss-2015b-Perl-5.22.0
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module load Java/11.0.2
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module load FastQC/0.11.7-Java-1.8.0_144-unlimited_JCE
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# Please see
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# https://www.youtube.com/watch?v=0Rj_xNuyOyQ
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cd /groups/umcg-griac/tmp04/projects/umcg-rbults/alveolar_type2_fastq/
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perl scripts/00_fastqc.pl
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mkdir rene_FastQC.results
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find . -maxdepth 1 -type d -iname "*_R[123]" -exec mv {} ./rene_FastQC.results/ \;
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#find . -maxdepth 1 -type f -iname "*.htm*" -exec mv {} ./FastQC.results/ \;
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