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Merge branch 'jaffal_docs' into 'dev'

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Update docs to remove JAFFAL install instructions

See merge request epi2melabs/workflows/wf-transcriptomes!89
This commit is contained in:
Neil Horner 2023-02-24 16:49:28 +00:00
commit 5c0a93bc17
3 changed files with 32 additions and 67 deletions
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47
README.md
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@ -172,48 +172,33 @@ __Note__: edlib is set by default in the config as it's quite a lot faster. Howe
### Fusion detection ### Fusion detection
JAFFAL from the [JAFFA](https://github.com/Oshlack/JAFFA) JAFFAL from the [JAFFA](https://github.com/Oshlack/JAFFA)
package is used to identify potential fusion transcripts. To get this this working, there are a couple of things that need doing first. package is used to identify potential fusion transcripts.
**Install JAFFA** In order to use JAFFAL, reference files must first be downloaded.
To use pre-processed hg38 genome and GENCODE v22 annotation files (as used in the JAFFAL paper)
to install JAFFA and it's dependencies run the folllowing:
```shell
cd wf-transcriptomes/
./subworkflows/JAFFAL/install_jaffa.sh
```
**Prepare JAFFAL reference data**
To use pre-processed reference files for the hg38 genome and GENCODE v22 annotation (as used in the JFFAAL paper),
do: do:
```shell ```shell
mkdir jaffal_data_dir mkdir jaffal_data_dir
cd jaffal_data_dir/ cd jaffal_data_dir/
wf-transcriptomes/subworkflows/JAFFAL/load_jaffal_references.sh sh path/to/wf-transcriptomes/subworkflows/JAFFAL/download_jaffal_references.sh
```` ````
Then the path to the directory containing the downloaded reference data must be specified with
To use alternative genome and annotation files, they should be prepared as described `--jaffal_refBase`.
[here](https://github.com/Oshlack/JAFFA/wiki/FAQandTroubleshooting#how-can-i-generate-the-reference-files-for-a-non-supported-genome)
**Specifying the location of the JAFFA code and reference directories**
`--jaffal_dir`
Full path to the directory made by running install_jaffa.sh as shown above. eg: /home/wf-trnascriptomes/JAFFA
`--jaffal_refBase`
The directory containing the reference data prepared for use with JAFFAL
**JAFFAL annotation and genome files** **Using alternative genome and annotation files**
The prepared JAFFAL reference files will look something like `hg38_chr20_genCode22.fa`. To enable JAFFAL to find these These should be prepared as described
files `--jaffal_genome` should be set to `hg38_chr20` and `--jaffal_annotation` to `genCode22` [here](https://github.com/Oshlack/JAFFA/wiki/FAQandTroubleshooting#how-can-i-generate-the-reference-files-for-a-non-supported-genome).
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 Notes__: __Note__: JAFFAL is not currently working on Mac M1 (osx-arm64 architecture).
g++ must be installed. JAFFAL is not currently working on Mac M1 (osx-arm64 architecture). If there are no fusion transcripts
detected, the workflow will terminate with an error at the JAFFAL stage. If this happens,
skip the JAFFAL stage by omitting ` --jaffal_refBase`
### Differential Expression ### Differential Expression

47
docs/quickstart.md
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@ -82,48 +82,33 @@ __Note__: edlib is set by default in the config as it's quite a lot faster. Howe
### Fusion detection ### Fusion detection
JAFFAL from the [JAFFA](https://github.com/Oshlack/JAFFA) JAFFAL from the [JAFFA](https://github.com/Oshlack/JAFFA)
package is used to identify potential fusion transcripts. To get this this working, there are a couple of things that need doing first. package is used to identify potential fusion transcripts.
**Install JAFFA** In order to use JAFFAL, reference files must first be downloaded.
To use pre-processed hg38 genome and GENCODE v22 annotation files (as used in the JAFFAL paper)
to install JAFFA and it's dependencies run the folllowing:
```shell
cd wf-transcriptomes/
./subworkflows/JAFFAL/install_jaffa.sh
```
**Prepare JAFFAL reference data**
To use pre-processed reference files for the hg38 genome and GENCODE v22 annotation (as used in the JFFAAL paper),
do: do:
```shell ```shell
mkdir jaffal_data_dir mkdir jaffal_data_dir
cd jaffal_data_dir/ cd jaffal_data_dir/
wf-transcriptomes/subworkflows/JAFFAL/load_jaffal_references.sh sh path/to/wf-transcriptomes/subworkflows/JAFFAL/download_jaffal_references.sh
```` ````
Then the path to the directory containing the downloaded reference data must be specified with
To use alternative genome and annotation files, they should be prepared as described `--jaffal_refBase`.
[here](https://github.com/Oshlack/JAFFA/wiki/FAQandTroubleshooting#how-can-i-generate-the-reference-files-for-a-non-supported-genome)
**Specifying the location of the JAFFA code and reference directories**
`--jaffal_dir`
Full path to the directory made by running install_jaffa.sh as shown above. eg: /home/wf-trnascriptomes/JAFFA
`--jaffal_refBase`
The directory containing the reference data prepared for use with JAFFAL
**JAFFAL annotation and genome files** **Using alternative genome and annotation files**
The prepared JAFFAL reference files will look something like `hg38_chr20_genCode22.fa`. To enable JAFFAL to find these These should be prepared as described
files `--jaffal_genome` should be set to `hg38_chr20` and `--jaffal_annotation` to `genCode22` [here](https://github.com/Oshlack/JAFFA/wiki/FAQandTroubleshooting#how-can-i-generate-the-reference-files-for-a-non-supported-genome).
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 Notes__: __Note__: JAFFAL is not currently working on Mac M1 (osx-arm64 architecture).
g++ must be installed. JAFFAL is not currently working on Mac M1 (osx-arm64 architecture). If there are no fusion transcripts
detected, the workflow will terminate with an error at the JAFFAL stage. If this happens,
skip the JAFFAL stage by omitting ` --jaffal_refBase`
### Differential Expression ### Differential Expression

5
download_jaffal_references.sh
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@ -1,5 +0,0 @@
#!/bin/sh
#Download the data. We should we move the data out of Figshare?
wget -O JAFFA_REFERENCE_FILES_HG38_GENCODE22.V2.tar.gz https://figshare.com/ndownloader/files/25410494
tar -zxvf JAFFA_REFERENCE_FILES_HG38_GENCODE22.V2.tar.gz