sample_rule

Rule to find files/samples

maxdepth

Like find -max_depth

sample_glob

Alternately, instead of sample_rule use sample_glob to find files. Glob does not differentiate between files and directories.

find_sample_bydir

#Previous find_by_dir

Use this option when you sample names are by directory The default is to find samples by filename

    /SAMPLE1
        SAMPLE1_r1.fastq.gz
        SAMPLE1_r2.fastq.gz
    /SAMPLE2
        SAMPLE2_r1.fastq.gz
        SAMPLE2_r2.fastq.gz

by_sample_outdir

No change - previously by sample outdir

Preface outdir with sample

Instead of

  outdir/
    rule1
    rule2

  outdir/
    Sample_01/
      rule1
      rule2

samples

This is our actual list of samples

resample

Boolean value get new samples based on indir/sample_rule or no

Samples are found at the beginning of the workflow, based on the global indir variable and the file_find.

Chances are you don't want to set resample to true. These files probably won't exist outside of the indirectory until the pipeline is run.

One example of doing so, shown in the gemini.yml in the examples directory, is looking for uncompressed files, .vcf extension, compressing them, and then resampling based on the .vcf.gz extension.

sample_files

Infiles to be processed