From 99d43b48b997c7ab878a399a8dc392ee3126489a Mon Sep 17 00:00:00 2001 From: Neil Horner Date: Fri, 16 Jun 2023 10:08:48 +0000 Subject: [PATCH] Standardise parameters in readme --- README.md | 27 ++++++++++++++++----------- docs/quickstart.md | 27 ++++++++++++++++----------- 2 files changed, 32 insertions(+), 22 deletions(-) diff --git a/README.md b/README.md index 7c9a535..6a59627 100644 --- a/README.md +++ b/README.md @@ -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). diff --git a/docs/quickstart.md b/docs/quickstart.md index fed5d5c..392ea2e 100644 --- a/docs/quickstart.md +++ b/docs/quickstart.md @@ -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).