diff --git a/docs/guides/usage.md b/docs/guides/usage.md index 6d2dc52..e539005 100644 --- a/docs/guides/usage.md +++ b/docs/guides/usage.md @@ -92,13 +92,14 @@ for the download of sequencing libraries from the Sequence Read Archive and conversion into FASTQ. The workflow expects the following parameters in the configuration file: -* `samples`, a sample table (tsv) with column *sample* containing *SRR* + +- `samples`, a sample table (tsv) with column *sample* containing *SRR* identifiers (ERR and DRR are also supported), as in this example [samples.tsv](https://github.com/zavolanlab/zarp/blob/dev/tests/input_files/sra_samples.tsv) file. -* `outdir`, an output directory -* `samples_out`, a pointer to a modified sample table with the locations of +- `outdir`, an output directory +- `samples_out`, a pointer to a modified sample table with the locations of the corresponding FASTQ files -* `cluster_log_dir`, the cluster log directory. +- `cluster_log_dir`, the cluster log directory. For executing the example with Conda environments, one can use the following command (from within the activated `zarp` Conda environment): @@ -137,11 +138,12 @@ from snakemake, which is called with [resources.tmpdir]. The workflow expects the following config: -* `samples`, a sample table (tsv) with column *sample* containing sample identifiers, as well as columns *fq1* and *fq2* containing the paths to the input fastq files + +- `samples`, a sample table (tsv) with column *sample* containing sample identifiers, as well as columns *fq1* and *fq2* containing the paths to the input fastq files see example [here](https://github.com/zavolanlab/zarp/blob/dev/tests/input_files/samples_htsinfer.tsv). If the table contains further ZARP compatible columns (see [pipeline documentation](https://github.com/zavolanlab/zarp/blob/dev/pipeline_documentation.md)), the values specified there by the user are given priority over htsinfer's results. -* `outdir`, an output directory -* `samples_out`, path to a modified sample table with inferred parameters -* `records`, set to 100000 per default +- `outdir`, an output directory +- `samples_out`, path to a modified sample table with inferred parameters +- `records`, set to 100000 per default For executing the example one can use the following (with activated *zarp* environment):