From 3a9045af5ca2b174077606dca8afae4ef3f6d940 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Thu, 5 Dec 2024 21:05:41 -0600
Subject: [PATCH] feat: Add pigz to trimgalore

https://github.com/nf-core/atacseq/issues/394
https://github.com/FelixKrueger/TrimGalore/issues/16#issuecomment-458557103
https://github.com/FelixKrueger/TrimGalore/blob/master/CHANGELOG.md#version-060-release-on-1-mar-2019
---
 modules/nf-core/trimgalore/environment.yml | 2 +-
 modules/nf-core/trimgalore/main.nf         | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/trimgalore/environment.yml b/modules/nf-core/trimgalore/environment.yml
index 622407edadf..b1efd94c4a0 100644
--- a/modules/nf-core/trimgalore/environment.yml
+++ b/modules/nf-core/trimgalore/environment.yml
@@ -1,7 +1,7 @@
 channels:
   - conda-forge
   - bioconda
-
 dependencies:
   - bioconda::cutadapt=4.9
   - bioconda::trim-galore=0.6.10
+  - conda-forge::pigz=2.8
diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf
index 8a2fc54b33d..fcd09efa7ab 100644
--- a/modules/nf-core/trimgalore/main.nf
+++ b/modules/nf-core/trimgalore/main.nf
@@ -4,8 +4,8 @@ process TRIMGALORE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/trim-galore%3A0.6.10--hdfd78af_1' :
-        'biocontainers/trim-galore:0.6.10--hdfd78af_1' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9b/9becad054093ad4083a961d12733f2a742e11728fe9aa815d678b882b3ede520/data' :
+        'community.wave.seqera.io/library/cutadapt_trim-galore_pigz:a98edd405b34582d' }"
 
     input:
     tuple val(meta), path(reads)
@@ -24,7 +24,7 @@ process TRIMGALORE {
     script:
     def args = task.ext.args ?: ''
     // Calculate number of --cores for TrimGalore based on value of task.cpus
-    // See: https://github.com/FelixKrueger/TrimGalore/blob/master/Changelog.md#version-060-release-on-1-mar-2019
+    // See: https://github.com/FelixKrueger/TrimGalore/blob/master/CHANGELOG.md#version-060-release-on-1-mar-2019
     // See: https://github.com/nf-core/atacseq/pull/65
     def cores = 1
     if (task.cpus) {