From 08de000d1283534d3fb7037e5395105273a551bd Mon Sep 17 00:00:00 2001 From: Sarah Griffiths Date: Tue, 25 Jul 2023 09:51:34 +0000 Subject: [PATCH] CW-2209 docs remove = --- CHANGELOG.md | 3 +++ README.md | 26 +++++++++++++------------- docs/quickstart.md | 26 +++++++++++++------------- 3 files changed, 29 insertions(+), 26 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 80469d8..8225d14 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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 diff --git a/README.md b/README.md index 7ed3a34..6a2ec58 100644 --- a/README.md +++ b/README.md @@ -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). diff --git a/docs/quickstart.md b/docs/quickstart.md index 9ef5b36..9d92026 100644 --- a/docs/quickstart.md +++ b/docs/quickstart.md @@ -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).