From 677371a8d0beb4ea3810c7c95e29dbc05ccfcdaa Mon Sep 17 00:00:00 2001
From: Victoria Carr <vc11@sanger.ac.uk>
Date: Wed, 12 Apr 2023 11:43:57 +0100
Subject: [PATCH 1/3] Update README.md

---
 README.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index d354710..dac054d 100755
--- a/README.md
+++ b/README.md
@@ -42,11 +42,11 @@ For each sample, palidis produces two output files: **1. FASTA file of insertion
 - Install [Docker](https://www.docker.com/) if using own machine or install [Singularity](https://sylabs.io/singularity/)/load a singularity module if using a shared HPC
 - Clone this repo:
 ```bash
-git clone --recursive -j8 https://github.com/blue-moon22/palidis.git
-cd palidis
+git clone --recursive -j8 https://github.com/blue-moon22/palidis4.git
+cd palidis4
 ```
 Note: You may be warned to first call `git config --global --add safe.directory`.
-</br>If you have already cloned this repo with `git clone https://github.com/blue-moon22/palidis.git`, you also need to get the submodules `git submodule update --init --recursive`
+</br>If you have already cloned this repo with `git clone https://github.com/blue-moon22/palidis4.git`, you also need to get the submodules `git submodule update --init --recursive`
 
 <a name="usage"></a>
 ## Usage

From e3d91ae1636999979bc8be730e38b9a5b8e8277f Mon Sep 17 00:00:00 2001
From: Victoria Carr <vc11@sanger.ac.uk>
Date: Wed, 12 Apr 2023 11:46:13 +0100
Subject: [PATCH 2/3] Update README.md

---
 README.md | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index dac054d..c44f628 100755
--- a/README.md
+++ b/README.md
@@ -1,7 +1,6 @@
 
-[![DOI](https://zenodo.org/badge/293755884.svg)](https://zenodo.org/badge/latestdoi/293755884)
-[![GitHub release (latest by date)](https://img.shields.io/github/v/release/blue-moon22/palidis)](https://github.com/blue-moon22/palidis/releases)
-![GitHub Workflow Status](https://img.shields.io/github/workflow/status/blue-moon22/palidis/test)
+[![GitHub release (latest by date)](https://img.shields.io/github/v/release/blue-moon22/palidis)](https://github.com/blue-moon22/palidis4/releases)
+![GitHub Workflow Status](https://img.shields.io/github/workflow/status/blue-moon22/palidis4/test)
 
 <img src="img/logo.png" alt="logo" width="400"/>
 
@@ -42,7 +41,7 @@ For each sample, palidis produces two output files: **1. FASTA file of insertion
 - Install [Docker](https://www.docker.com/) if using own machine or install [Singularity](https://sylabs.io/singularity/)/load a singularity module if using a shared HPC
 - Clone this repo:
 ```bash
-git clone --recursive -j8 https://github.com/blue-moon22/palidis4.git
+git clone --recursive -j8 git@github.com:blue-moon22/palidis4.git
 cd palidis4
 ```
 Note: You may be warned to first call `git config --global --add safe.directory`.

From 3d2becd25caf912ab7ca379b9dcac1dd2acad4fd Mon Sep 17 00:00:00 2001
From: Victoria Carr <vc11@sanger.ac.uk>
Date: Mon, 24 Jul 2023 12:29:53 +0100
Subject: [PATCH 3/3] Add singularity profile

---
 README.md       |  2 ++
 nextflow.config | 10 +++++++---
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index c44f628..3527378 100755
--- a/README.md
+++ b/README.md
@@ -54,6 +54,8 @@ Note: You may be warned to first call `git config --global --add safe.directory`
 nextflow palidis.nf --manifest <manifest_file> --batch_name <batch_name> -c configs/conf/<name_of_config>.config
 ```
 
+If you are using a cluster and it uses singularity instead of docker, please add `-profile standard,singularity`
+
 ### Mandatory arguments
 #### `<batch_name>`
 
diff --git a/nextflow.config b/nextflow.config
index c63b1eb..8f928be 100755
--- a/nextflow.config
+++ b/nextflow.config
@@ -24,9 +24,6 @@ params {
 profiles {
 
         standard {
-                docker {
-                        enabled = true
-                }
                 process {
                         container = 'bluemoon222/palidis_dependencies:0.0.22'
                         cpus = 1
@@ -145,4 +142,11 @@ profiles {
                         }
                 }
         }
+        singularity {
+                singularity {
+                        enabled = true
+                        autoMounts = true
+                        cacheDir = "$projectDir/singularity"
+                }
+        }
 }