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@ -21,13 +21,13 @@ export NXF_TEMP=/scratch/tmp
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export NXF_SINGULARITY_CACHEDIR=/projects/dan1/people/${USER}/cache/singularity-images
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```
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create nextflow directories if they dont exist:
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Create the user-specific nextflow directories if they don't exist yet:
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```
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mkdir $NXF_SINGULARITY_CACHEDIR
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mkdir $NXF_HOME
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```
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Finally, download and test the pipeline of choice using the `-profile ku_sund_dangpu`. Note that normally you would run resource-intensive commands with slurm, but in case of nf-core pipelines you do not have to do this: we have pre-configured slurm as resource manager within the `ku_sund_dangpu profile`. Just make sure that the pipeline is run within a tmux session.
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Finally, download and test the pipeline of choice using the `-profile ku_sund_dangpu`. Note that normally you would run resource-intensive commands with slurm, but in case of nf-core pipelines you do not have to do this: we have pre-configured slurm to be the resource manager within the `ku_sund_dangpu profile`. Just make sure that the pipeline is run within a tmux session.
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```
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nextflow run nf-core/rnaseq -profile test,ku_sund_dangpu
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