diff --git a/CHANGELOG.md b/CHANGELOG.md
index e3ebdac5..badcbb04 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -21,8 +21,6 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 
 - [[#226](https://github.com/nf-core/atacseq/issues/262)] - Add `ataqv_mito_reference` parameter.
 - Optional support of control data analog to nf-core/chipseq.
-- Updated pipeline template to [nf-core/tools 2.8](https://github.com/nf-core/tools/releases/tag/2.8)
-- Add public_aws_ecr profile for using containers hosted on ECR.
 - [[#277](https://github.com/nf-core/atacseq/issues/277)] - Fix error when using a gunziped fasta file.
 - [[#286](https://github.com/nf-core/atacseq/issues/286)] - Fix error when no `--mito_name parameter is provided.
 - [[#268](https://github.com/nf-core/atacseq/issues/268)] - Fix error when a bed file is provided using the `--blacklist` option.
@@ -30,6 +28,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [[#276](https://github.com/nf-core/atacseq/issues/276)] - Bump version 1.3.1 of ataqv to fix enrichment plots rendering.
 - [[#290](https://github.com/nf-core/atacseq/issues/290)] - Fix case-sensitivity issue while sorting bedGraph.
 - [[#295](https://github.com/nf-core/atacseq/issues/295)] - Enable downstream steps for bam files produced from paired-end reads by `chromap` after its upgrade.
+- Updated pipeline template to [nf-core/tools 2.9](https://github.com/nf-core/tools/releases/tag/2.9)
 - Make fasta index available for IGV session.
 - [[nf-core/chipseq#347](https://github.com/nf-core/chipseq/issues/347)] - Add read group tag to bam files processed by bowtie2
 
diff --git a/conf/public_aws_ecr.config b/conf/public_aws_ecr.config
deleted file mode 100644
index d308789c..00000000
--- a/conf/public_aws_ecr.config
+++ /dev/null
@@ -1,72 +0,0 @@
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    AWS ECR Config
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Config to set public AWS ECR images wherever possible
-    This improves speed when running on AWS infrastructure.
-    Use this as an example template when using your own private registry.
-----------------------------------------------------------------------------------------
-*/
-
-docker.registry = 'public.ecr.aws'
-podman.registry = 'public.ecr.aws'
-
-process {
-    withName: 'BAMTOOLS_FILTER' {
-        container = 'quay.io/biocontainers/mulled-v2-0560a8046fc82aa4338588eca29ff18edab2c5aa:5687a7da26983502d0a8a9a6b05ed727c740ddc4-0'
-    }
-    withName: 'BAM_REMOVE_ORPHANS' {
-        container = 'quay.io/biocontainers/mulled-v2-57736af1eb98c01010848572c9fec9fff6ffaafd:402e865b8f6af2f3e58c6fc8d57127ff0144b2c7-0'
-    }
-    withName: 'BOWTIE2_ALIGN' {
-        container = 'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0'
-    }
-    withName: 'BWA_MEM' {
-        container = 'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:219b6c272b25e7e642ae3ff0bf0c5c81a5135ab4-0'
-    }
-    withName: 'CHROMAP_CHROMAP' {
-        container = 'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:5b2e433ab8b3d1ef098fc944b567fd98caa23f56-0'
-    }
-    withName: 'DESEQ2_QC' {
-        container = 'quay.io/biocontainers/mulled-v2-8849acf39a43cdd6c839a369a74c0adc823e2f91:ab110436faf952a33575c64dd74615a84011450b-0'
-    }
-    withName: 'FRIP_SCORE' {
-        container = 'quay.io/biocontainers/mulled-v2-8186960447c5cb2faa697666dc1e6d919ad23f3e:3127fcae6b6bdaf8181e21a26ae61231030a9fcb-0'
-    }
-    withName: 'GET_AUTOSOMES' {
-        container = 'quay.io/biocontainers/python:3.8.3'
-    }
-    withName: 'GTF2BED' {
-        container = 'quay.io/biocontainers/perl:5.26.2'
-    }
-    withName: 'GUNZIP' {
-        container = 'quay.io/nf-core/ubuntu:20.04'
-    }
-    withName: 'IGV' {
-        container = 'quay.io/biocontainers/python:3.8.3'
-    }
-    withName: 'MACS2_CONSENSUS' {
-        container = 'quay.io/biocontainers/mulled-v2-2f48cc59b03027e31ead6d383fe1b8057785dd24:5d182f583f4696f4c4d9f3be93052811b383341f-0'
-    }
-    withName: 'MULTIQC_CUSTOM_PEAKS' {
-        container = 'quay.io/nf-core/ubuntu:20.04'
-    }
-    withName: 'PLOT_HOMER_ANNOTATEPEAKS' {
-        container = 'quay.io/biocontainers/mulled-v2-ad9dd5f398966bf899ae05f8e7c54d0fb10cdfa7:05678da05b8e5a7a5130e90a9f9a6c585b965afa-0'
-    }
-    withName: 'PLOT_MACS2_QC' {
-        container = 'quay.io/biocontainers/mulled-v2-ad9dd5f398966bf899ae05f8e7c54d0fb10cdfa7:05678da05b8e5a7a5130e90a9f9a6c585b965afa-0'
-    }
-    withName: 'SAMPLESHEET_CHECK' {
-        container = 'quay.io/biocontainers/python:3.8.3'
-    }
-    withName: 'STAR_GENOMEGENERATE' {
-        container = 'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0'
-    }
-    withName: 'TSS_EXTRACT' {
-        container = 'quay.io/nf-core/ubuntu:20.04'
-    }
-    withName: 'UNTAR' {
-        container = 'quay.io/nf-core/ubuntu:20.04'
-    }
-}
diff --git a/nextflow.config b/nextflow.config
index 10b44904..251cf88b 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -222,9 +222,6 @@ profiles {
         executor.cpus          = 16
         executor.memory        = 60.GB
     }
-    public_aws_ecr {
-        includeConfig 'conf/public_aws_ecr.config'
-    }
     test          { includeConfig 'conf/test.config'          }
     test_controls { includeConfig 'conf/test_controls.config' }
     test_full     { includeConfig 'conf/test_full.config'     }
@@ -264,12 +261,6 @@ env {
 // Capture exit codes from upstream processes when piping
 process.shell = ['/bin/bash', '-euo', 'pipefail']
 
-// Set default registry for Docker and Podman independent of -profile
-// Will not be used unless Docker / Podman are enabled
-// Set to your registry if you have a mirror of containers
-docker.registry = 'quay.io'
-podman.registry = 'quay.io'
-
 def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
 timeline {
     enabled = true