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hwlim / BisKit-RNA

BisKit for CCHMC HPC users
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update config file & issue update #8

Closed hwlim closed 5 months ago

hwlim commented 5 months ago

Update by Lim:

@cahn20 Among the folder names, please move the top tier folders only, Not need to move RNA species folders since they can be implicit as subfolders for each samples.

  1. Move following parameters from Snakefile to config file

src_sampleInfo = "sample.tsv" chrRegex = "^chr[0-9XY]+$"

fastq_dir = "0.Fastq" # Directory containing fastq files trim_dir = "0.Fastq.Trim" # Directory for trimmed fastq files sample_dir = "1.Sample" plot_dir = "1.Sample_Plots" per_sample_plot_dir = "Plots" per_pairwise_plot_dir = "Plots" rRNA_dir = "1.rRNA" tRNA_dir = "2.tRNA" miRNA_dir = "3.miRNA" piRNA_dir = "4.piRNA" genome_dir = "5.genome" circRNA_dir = "6.circRNA" compare_dir = "2.Diff" combined_compare_dir = "3.combined_Diff" mqc_dir = "4.multiQC"

  1. Comment unclosed issues if they are completed/handled so that I can close.
cahn20 commented 5 months ago

Addressed in pull request #10