kfukuta/wf-transcriptomes-v202
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Merge branch 'CW-2209-docs' into 'dev'

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CW-2209 docs remove =

Closes CW-2209

See merge request epi2melabs/workflows/wf-transcriptomes!114
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Sarah Griffiths 2023-07-25 09:51:34 +00:00
commit 805c15297e
3 changed files with 29 additions and 26 deletions
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3
CHANGELOG.md
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@ -8,6 +8,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Changed
- Any sample aliases that contain spaces will be replaced with underscores.
### Fixed
- Documentation parameter examples corrected.
## [v0.2.0]
### Changed
- GitHub issue templates

26
README.md
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@ -153,24 +153,24 @@ Below are some commonly used parameters in the format used in config files.
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 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).
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:
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'`
- `--minimap2_opts '-uf --splice-flank=no'`
- 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'`
- 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'`
- nhmmscan `--pychopper opts '-m phmm'`
- edlib `--pychopper opts '-m edlib'`
__Note__: edlib is set by default in the config as it's quite a lot faster. However, it may be less sensitive than nhmmscan.
@ -199,8 +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 = reference_genome_name` optional (default: `hg38`)
`jaffal_annotation = jaffal_annotation_prefix` 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).

26
docs/quickstart.md
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@ -63,24 +63,24 @@ Below are some commonly used parameters in the format used in config files.
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 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).
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:
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'`
- `--minimap2_opts '-uf --splice-flank=no'`
- 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'`
- 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'`
- nhmmscan `--pychopper opts '-m phmm'`
- edlib `--pychopper opts '-m edlib'`
__Note__: edlib is set by default in the config as it's quite a lot faster. However, it may be less sensitive than nhmmscan.
@ -109,8 +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 = reference_genome_name` optional (default: `hg38`)
`jaffal_annotation = jaffal_annotation_prefix` 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).