Merge pull request #313 from JoseEspinosa/updates

Apply review suggestions

CHANGELOG.md

@@ -21,15 +21,14 @@ 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.
 - [[#278](https://github.com/nf-core/atacseq/issues/278)] - Make genome fasta file available when `IGV` process is run.
 - [[#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
 

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