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fix: updated schemas and params docs
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‎.test/config/config.yml‎

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multiqc:
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config: "config/multiqc_config.yml"
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report:
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export_figures: True
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export_dir: "figures/"
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figure_width: 875
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figure_height: 500
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figure_resolution: 125

‎README.md‎

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This template workflow contains artifical sequencing data in `*.fastq.gz` format.
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The test data is located in `.test/data`. Input files are supplied with a mandatory table, whose location is indicated in the `config.yml` file (default: `.test/samples.tsv`). The sample sheet has the following layout:
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| sample | condition | replicate | data_folder | fq1 |
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| -------- | --------- | --------- | ----------- | ------------------------ |
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| RPF-RTP1 | RPF-RTP | 1 | data | RPF-RTP1_R1_001.fastq.gz |
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| RPF-RTP2 | RPF-RTP | 2 | data | RPF-RTP2_R1_001.fastq.gz |
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| sample | condition | replicate | read1 | read2 |
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| ------- | --------- | --------- | -------------------------- | -------------------------- |
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| sample1 | wild_type | 1 | sample1.bwa.read1.fastq.gz | sample1.bwa.read2.fastq.gz |
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| sample2 | wild_type | 2 | sample2.bwa.read1.fastq.gz | sample2.bwa.read2.fastq.gz |
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### Execution
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This table lists all parameters that can be used to run the workflow.
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| parameter | type | details | default |
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| ---------------------- | ---- | ------------------------------------------- | -------------------------------------------- |
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| **samplesheet** | | | |
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| path | str | path to samplesheet, mandatory | "config/samples.tsv" |
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| **cutadapt** | | | |
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| fivep_adapter | str | sequence of the 5' adapter | Null |
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| threep_adapter | str | sequence of the 3' adapter | `ATCGTAGATCGGAAGAGCACACGTCTGAA` |
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| default | str | additional options passed to `cutadapt` | [`-q 10 `, `-m 22 `, `-M 52`, `--overlap=3`] |
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| parameter | type | details | default |
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| ------------------ | ---- | --------------------------------------- | --------------------------------------------- |
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| **samplesheet** | | | |
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| path | str | path to samplesheet, mandatory | "config/samples.tsv" |
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| **get_genome** | | | |
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| database | str | one of `manual`, `ncbi` | `ncbi` |
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| assembly | str | RefSeq ID | `GCF_000006785.2` |
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| fasta | str | optional path to fasta file | Null |
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| gff | str | optional path to gff file | Null |
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| gff_source_type | str | list of name/value pairs for GFF source | see config file |
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| **simulate_reads** | | | |
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| read_length | num | | 100 |
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| read_number | | | 100000 |
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| random_freq | | | 0.01 |
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| **cutadapt** | | | |
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| threep_adapter | str | sequence of the 3' adapter | `-a ATCGTAGATCGG` |
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| fivep_adapter | str | sequence of the 5' adapter | `-A GATGGCGATAGG` |
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| default | str | additional options passed to `cutadapt` | [`-q 10 `, `-m 25 `, `-M 100`, `--overlap=5`] |
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| **multiqc** | | | |
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| config | str | path to multiqc config | `config/multiqc_config.yml` |
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## Authors
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‎config/config.yml‎

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multiqc:
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config: "config/multiqc_config.yml"
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report:
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export_figures: True
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export_dir: "figures/"
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figure_width: 875
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figure_height: 500
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figure_resolution: 125

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