From 94a2e2c28c02ea413314b909d54b8f6ff197fb8a Mon Sep 17 00:00:00 2001 From: Neil Horner Date: Fri, 24 Feb 2023 16:49:28 +0000 Subject: [PATCH] Update docs to remove JAFFAL install instructions --- README.md | 47 ++++++++++++----------------------- docs/quickstart.md | 47 ++++++++++++----------------------- download_jaffal_references.sh | 5 ---- 3 files changed, 32 insertions(+), 67 deletions(-) delete mode 100644 download_jaffal_references.sh diff --git a/README.md b/README.md index bc35fa5..34570e9 100644 --- a/README.md +++ b/README.md @@ -172,48 +172,33 @@ __Note__: edlib is set by default in the config as it's quite a lot faster. Howe ### Fusion detection 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** - -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), +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) do: ```shell mkdir 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 ```` - -To use alternative genome and annotation files, they should be prepared as described -[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 +Then the path to the directory containing the downloaded reference data must be specified with +`--jaffal_refBase`. -**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 -files `--jaffal_genome` should be set to `hg38_chr20` and `--jaffal_annotation` to `genCode22` +These should be prepared as described +[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__: -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` +__Note__: JAFFAL is not currently working on Mac M1 (osx-arm64 architecture). ### Differential Expression diff --git a/docs/quickstart.md b/docs/quickstart.md index 4adb6b2..a1fdce3 100644 --- a/docs/quickstart.md +++ b/docs/quickstart.md @@ -82,48 +82,33 @@ __Note__: edlib is set by default in the config as it's quite a lot faster. Howe ### Fusion detection 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** - -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), +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) do: ```shell mkdir 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 ```` - -To use alternative genome and annotation files, they should be prepared as described -[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 +Then the path to the directory containing the downloaded reference data must be specified with +`--jaffal_refBase`. -**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 -files `--jaffal_genome` should be set to `hg38_chr20` and `--jaffal_annotation` to `genCode22` +These should be prepared as described +[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__: -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` +__Note__: JAFFAL is not currently working on Mac M1 (osx-arm64 architecture). ### Differential Expression diff --git a/download_jaffal_references.sh b/download_jaffal_references.sh deleted file mode 100644 index ec12648..0000000 --- a/download_jaffal_references.sh +++ /dev/null @@ -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 \ No newline at end of file