Issue7: update README #10
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| @@ -159,17 +159,10 @@ For use on an HPC cluster (rosalind, aspen) the workflow can be run as a job by | |||
| module load nextflow | |||
| ``` | |||
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| 2) Prepare file `cdc.confing` with the necessary `sge` submission parameters, add it to sub-directory [./conf/](./conf), and include it in [nextflow.config](./nextflow.config) with: | |||
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@jessicarowell couldn't this be either or? user could add their own cdc.conf with includeConfig OR just specify the scicomp reference cdc.conf.
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Yes, it could be either-or. Just based on my conversations with scicomp, they'd rather people use the one they've preconfigured...and I think building one's own config file just adds unnecessary complexity. But I can add back that line if you wish!
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First copy mpxvgfa.sif to assets.
Then test with:
nextflow run main.nf --indir /scicomp/groups-pure/Projects/scbs_mpob/JRowell_ick4/mpox_testing/paired/ --outdir /scicomp/groups-pure/Projects/scbs_mpob/JRowell_ick4/mpox_testing/results/ --project_name test -config /scicomp/reference/nextflow/configs/cdc-dev.config -profile singularity,rosalind