diff --git a/README.md b/README.md index d1180f3..e008b1a 100644 --- a/README.md +++ b/README.md @@ -186,45 +186,6 @@ sample-01 └── sample-01_unicycler_short.log ``` -If the `--versioned_outdir` flag is used, then a sub-directory will be created below each sample, named with the pipeline name and minor version: - -``` -sample-01 - └── routine-assembly-v0.4-output - ├── sample-01_20220216172238_provenance.yml - ├── sample-01_fastp.csv - ├── sample-01_fastp.json - ├── sample-01_unicycler_short.fa - ├── sample-01_unicycler_short.log - ├── sample-01_unicycler_short_prokka.gbk - ├── sample-01_unicycler_short_prokka.gff - └── sample-01_unicycler_short_quast.csv -``` - -This is provided as a way of combining outputs of several different pipelines or re-analysis with future versions of this pipeline: - -``` -sample-01 - └── routine-assembly-v0.4-output - │ ├── sample-01_20220216172238_provenance.yml - │ ├── sample-01_fastp.csv - │ ├── sample-01_fastp.json - │ ├── sample-01_unicycler_short.fa - │ ├── sample-01_unicycler_short.log - │ ├── sample-01_unicycler_short_prokka.gbk - │ ├── sample-01_unicycler_short_prokka.gff - │ └── sample-01_unicycler_short_quast.csv - └── routine-assembly-v0.5-output - ├── sample-01_20220612091224_provenance.yml - ├── sample-01_fastp.csv - ├── sample-01_fastp.json - ├── sample-01_unicycler_short.fa - ├── sample-01_unicycler_short.log - ├── sample-01_unicycler_short_prokka.gbk - ├── sample-01_unicycler_short_prokka.gff - └── sample-01_unicycler_short_quast.csv -``` - ### Provenance files For each pipeline invocation, each sample will produce a `provenance.yml` file with the following contents: