Rule to find files/samples
Like find -max_depth
Alternately, instead of sample_rule use sample_glob to find files. Glob does not differentiate between files and directories.
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
No change - previously by sample outdir
Preface outdir with sample
outdir/ rule1 rule2 outdir/ Sample_01/ rule1 rule2
This is our actual list of samples
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.
Infiles to be processed