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Standardise parameters in readme

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This commit is contained in:
Neil Horner 2023-06-16 10:08:48 +00:00
parent cb73e0a6cd
commit 99d43b48b9
2 changed files with 32 additions and 22 deletions
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27
README.md
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@ -147,22 +147,27 @@ nextflow run . --fastq test_data/fastq \
-w ${OUTPUT}/workspace \
--sample sample_id
```
A full list of options can be seen in nextflow_schema.json. Below are some commonly used ones.
A full list of options can be seen in nextflow_schema.json.
Parameters can be specified either in a config like `parameter = value` or on the command line like `--parameter value`.
Below are some commonly used parameters in the format used in config files.
- Threshold for including isoforms into interactive table `transcript_table_cov_thresh = 50`
- Run the denovo pipeline `denovo = true` (default false)
- To run the workflow with direct RNA reads `--direct_rna` (this just skips the pychopper step).
Select how the transcriptome used for analysis should be prepared:
- To create a reference transcriptome using an existing reference genome `transcriptome_source = reference-guided` (default)
- Use a a supplied transcriptome `transcriptome_source = precomputed"`
- Gnerate transcriptome via the denovo pipeline `transcriptome_source = denovo"`
To run the workflow with direct RNA reads `direct_rna = false` (this just skips the pychopper step).
Pychopper and minimap2 can take options via `minimap2_opts` and `pychopper_opts`, for example:
- When using the SIRV synthetic test data
- `minimap2_opts = '-uf --splice-flank=no'`
- pychopper needs to know which cDNA synthesis kit used
- SQK-PCS109: use `pychopper_opts = '-k PCS109'` (default)
- SQK-PCS110: use `pychopper_opts = '-k PCS110'`
- SQK-PCS111: use `pychopper_opts = '-k PCS111'`
- pychopper needs to know which cDNA synthesis kit used, which can be specified with
- SQK-PCS109: `pychopper_opts = '-k PCS109'` (default)
- SQK-PCS110: `pychopper_opts = '-k PCS110'`
- SQK-PCS111: `pychopper_opts = '-k PCS111'`
- pychopper can use one of two available backends for identifying primers in the raw reads
- nhmmscan `pychopper opts = '-m phmm'`
- edlib `pychopper opts = '-m edlib'`
@ -194,8 +199,8 @@ These should be prepared as described
The resulting JAFFAL reference files will look something like `hg38_genCode22.fa`. The following options enable JAFFAL to find these
files:
`--jaffal_genome` optional (default: `hg38`)
`--jaffal_annotation` optional (default: `genCode22`)
`jaffal_genome = reference_genome_name` optional (default: `hg38`)
`jaffal_annotation = jaffal_annotation_prefix` optional (default: `genCode22`)
__Note__: JAFFAL is not currently working on Mac M1 (osx-arm64 architecture).

27
docs/quickstart.md
View File

@ -57,22 +57,27 @@ nextflow run . --fastq test_data/fastq \
-w ${OUTPUT}/workspace \
--sample sample_id
```
A full list of options can be seen in nextflow_schema.json. Below are some commonly used ones.
A full list of options can be seen in nextflow_schema.json.
Parameters can be specified either in a config like `parameter = value` or on the command line like `--parameter value`.
Below are some commonly used parameters in the format used in config files.
- Threshold for including isoforms into interactive table `transcript_table_cov_thresh = 50`
- Run the denovo pipeline `denovo = true` (default false)
- To run the workflow with direct RNA reads `--direct_rna` (this just skips the pychopper step).
Select how the transcriptome used for analysis should be prepared:
- To create a reference transcriptome using an existing reference genome `transcriptome_source = reference-guided` (default)
- Use a a supplied transcriptome `transcriptome_source = precomputed"`
- Gnerate transcriptome via the denovo pipeline `transcriptome_source = denovo"`
To run the workflow with direct RNA reads `direct_rna = false` (this just skips the pychopper step).
Pychopper and minimap2 can take options via `minimap2_opts` and `pychopper_opts`, for example:
- When using the SIRV synthetic test data
- `minimap2_opts = '-uf --splice-flank=no'`
- pychopper needs to know which cDNA synthesis kit used
- SQK-PCS109: use `pychopper_opts = '-k PCS109'` (default)
- SQK-PCS110: use `pychopper_opts = '-k PCS110'`
- SQK-PCS111: use `pychopper_opts = '-k PCS111'`
- pychopper needs to know which cDNA synthesis kit used, which can be specified with
- SQK-PCS109: `pychopper_opts = '-k PCS109'` (default)
- SQK-PCS110: `pychopper_opts = '-k PCS110'`
- SQK-PCS111: `pychopper_opts = '-k PCS111'`
- pychopper can use one of two available backends for identifying primers in the raw reads
- nhmmscan `pychopper opts = '-m phmm'`
- edlib `pychopper opts = '-m edlib'`
@ -104,8 +109,8 @@ These should be prepared as described
The resulting JAFFAL reference files will look something like `hg38_genCode22.fa`. The following options enable JAFFAL to find these
files:
`--jaffal_genome` optional (default: `hg38`)
`--jaffal_annotation` optional (default: `genCode22`)
`jaffal_genome = reference_genome_name` optional (default: `hg38`)
`jaffal_annotation = jaffal_annotation_prefix` optional (default: `genCode22`)
__Note__: JAFFAL is not currently working on Mac M1 (osx-arm64 architecture).