Merge branch 'CW-2209-docs' into 'dev'

CW-2209 docs remove =

Closes CW-2209

See merge request epi2melabs/workflows/wf-transcriptomes!114

Author: sarahjeeeze

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

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).

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).