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Hoffman2 nfCore RNA-seq Bash Script Generator

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Login to Hoffman2

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+ ssh your_username@hoffman2.idre.ucla.edu +
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Replace 'your_username' with your actual Hoffman2 username.

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Create Sample Sheet

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Create a CSV file with the following columns:

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  • sample: Unique sample identifier
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  • fastq_1: Path to first FASTQ file
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  • fastq_2: Path to second FASTQ file (for paired-end data)
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  • strandedness: RNA-seq strandedness (auto/forward/reverse/unstranded)
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Example sample sheet:

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sample,fastq_1,fastq_2,strandedness
+sample1,/path/to/sample1_R1.fastq.gz,/path/to/sample1_R2.fastq.gz,auto
+sample2,/path/to/sample2_R1.fastq.gz,/path/to/sample2_R2.fastq.gz,auto
+sample3,/path/to/sample3_R1.fastq.gz,/path/to/sample3_R2.fastq.gz,auto
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Tips:

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  • Save the file with a .csv extension
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  • Use full paths to FASTQ files
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  • Ensure all FASTQ files are accessible on Hoffman2
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  • If unsure about strandedness, use 'auto'
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  • Double-check that there are no spaces after commas
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Generate Bash Script

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Bash Script:

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