From 31eedaa033a782461689190f54839e3fe79aac85 Mon Sep 17 00:00:00 2001
From: Murray Wham <murray.wham@ed.ac.uk>
Date: Wed, 23 Oct 2024 15:35:47 +0100
Subject: [PATCH] Adding conda directove to encryption step. Defaulting publish
mode to symlink - makes sense for large uploads, and FTP/Aspera can deal with
symlinks anyway
---
modules/local/ega/encrypt/main.nf | 1 +
nextflow.config | 2 +-
2 files changed, 2 insertions(+), 1 deletion(-)
diff --git a/modules/local/ega/encrypt/main.nf b/modules/local/ega/encrypt/main.nf
index 657ada3..25b9f14 100644
--- a/modules/local/ega/encrypt/main.nf
+++ b/modules/local/ega/encrypt/main.nf
@@ -4,6 +4,7 @@
*/
process EGA_ENCRYPT {
tag "$sample"
+ conda "${moduleDir}/environment.yml"
input:
tuple val(sample), path(reads)
diff --git a/nextflow.config b/nextflow.config
index 1dcc4e6..75513ae 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -38,7 +38,7 @@ process {
publishDir = [
path: { params.outdir },
- mode: 'copy',
+ mode: 'symlink',
pattern: '*.{gpg,md5}',
enabled: params.ega_user == null || params.ega_user == ''
]
--
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