diff --git a/.github/workflows/containers_config.yml b/.github/workflows/containers_config.yml
new file mode 100644
index 000000000..034e96fe6
--- /dev/null
+++ b/.github/workflows/containers_config.yml
@@ -0,0 +1,53 @@
+name: Container Configs
+
+on:
+  push:
+    branches: [main, dev]
+    paths: ['modules.json']
+  pull_request:
+    branches: [main, dev]
+    paths: ['modules.json']
+  release:
+    types: [published]
+  # TODO workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    env:
+      FORCE_COLOR: 1
+    steps:
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        with:
+          token: ${{ secrets.nf_core_bot_auth_token }}
+          ref: ${{ github.head_ref }}
+      - uses: nf-core/setup-nextflow@v2
+        with:
+          version: "25.04.7"
+      - name: Snapshot containers
+        run: |
+          mkdir -p conf/containers
+          # TODO: Re-enable singularity builds once singularity image issues are resolved
+          # https://github.com/nf-core/rnaseq/pull/1515#pullrequestreview-3201429623
+          for container in docker; do # singularity
+            for arch in amd64 arm64; do
+              if [ "$arch" = "arm64" ]; then
+                profile="wave,$container,arm64"
+              else
+                profile="wave,$container"
+              fi
+              nextflow inspect . -profile $profile -format config > conf/containers/containers_${container}_${arch}.config
+              echo "Created conf/containers/containers_${container}_${arch}.config"
+              sort -o conf/containers/containers_${container}_${arch}.config conf/containers/containers_${container}_${arch}.config
+            done
+          done
+      - name: Commit & push changes
+        id: commit-and-push
+        run: |
+          git config user.email "core@nf-co.re"
+          git config user.name "nf-core-bot"
+          git config push.default upstream
+          git add conf/containers/.
+          git status
+          git commit -m "[automated] Update container configs"
+          git push
diff --git a/conf/arm.config b/conf/arm.config
deleted file mode 100644
index bb5b222c3..000000000
--- a/conf/arm.config
+++ /dev/null
@@ -1,273 +0,0 @@
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Nextflow config file for running the pipeline with ARM architecture
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Defines custom containers and Conda definitions required to run pipeline with ARM.
-
-    Use as follows:
-        nextflow run nf-core/rnaseq -profile <docker/singularity>,arm <OTHER_PARAMETERS>
-
-----------------------------------------------------------------------------------------
-*/
-
-process {
-
-    //
-    // Tools that have native Conda builds for AMD and ARM
-    //
-
-    withName: 'BBMAP_BBSPLIT' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/63ca91c8bf7285296777de219e5d5a71d2a7de47599cbc94441aced7868a4f83/data' : 'community.wave.seqera.io/library/bbmap:39.10--908996c2fb304bec' }
-    }
-
-    withName: 'BEDTOOLS_GENOMECOV' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/51/519a920dacc643078823740486c40d30b9f555c493217d9f72db04901350e009/data' : 'community.wave.seqera.io/library/bedtools:2.31.1--efd79503b8c63422' }
-    }
-
-    withName: 'BRACKEN_BRACKEN' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/64/648fd6bc2805481aa60db7ee9e37d41d7643eaaabd92f21bf1019f8b3f0879a6/data' : 'community.wave.seqera.io/library/bracken:3.1--0b6ab6dde7667f60' }
-    }
-
-    withName: 'CAT_FASTQ' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/38/38d3638640600b355110f9bca56c514e3cc068bf96b8b68f98cba2a59a053505/data' : 'community.wave.seqera.io/library/coreutils:9.5--3931e2d27d9884e5' }
-    }
-
-    withName: 'CUSTOM_CATADDITIONALFASTA' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c1/c17acd739990ad12c06583f57b097014c2bde5a91d0977fd102864a82f95e136/data' : 'community.wave.seqera.io/library/python:3.12.2--0d47e6fe32e00784' }
-    }
-
-    withName: 'CUSTOM_GETCHROMSIZES' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' }
-    }
-
-    withName: 'CUSTOM_TX2GENE' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/60/6029f43341dc0bea31d14c2ce4c779d7a48dfed6ecb29ce1630b8378c560c490/data' : 'community.wave.seqera.io/library/python:3.10.4--d0dc5eb8ea72fa82' }
-    }
-
-    withName: 'DESEQ2_QC' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/70/70a3d17733d2c21cff464c31a7a57438cea528bea84c675b7c474eaa7f075f57/data' : 'community.wave.seqera.io/library/r-base_r-optparse_r-ggplot2_r-rcolorbrewer_pruned:8bd3e9db55b129d7' }
-    }
-
-    withName: 'DUPRADAR' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/10/10141f8fd43964316d04214a5f7d99a62e11cdbab5bd2fcd4f7c3c06eca9f2f6/data' : 'community.wave.seqera.io/library/bioconductor-dupradar:1.32.0--f75495d6abf45328' }
-    }
-
-    withName: 'FASTP' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/7e/7ec6234f24305b9694b89de0352fff942ce1d68f840184020b0b9135bc54bda1/data' : 'community.wave.seqera.io/library/fastp:0.23.4--c1051f83dcae53f5' }
-    }
-
-    withName: 'FASTQC' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fd/fd39534bf298698cbe3ee4d4a6f1e73330ec4bca44c38dd9a4d06cb5ea838017/data' : 'community.wave.seqera.io/library/fastqc:0.12.1--df99cb252670875a' }
-    }
-
-    withName: 'FQ_SUBSAMPLE' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b0/b00189d4f7eed55199354a3dff8a9a535e1dfb3a2f4c97f5d0bf9e388105795e/data' : 'community.wave.seqera.io/library/fq:0.12.0--ad6857b304869ce9' }
-    }
-
-    withName: 'GFFREAD' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9e/9e6db95013607b07689e38ee37a654d029236de77fdfde97fe1866f45d01e064/data' : 'community.wave.seqera.io/library/gffread:0.12.7--1577aa7c95340d9f' }
-    }
-
-    withName: 'GTF2BED' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/89/896a3e55b2f664def0f8707420e1f53b4c447adb99fd6a1432a155c3403b9199/data' : 'community.wave.seqera.io/library/perl:5.26.2--2a6adf51d600e047' }
-    }
-
-    withName: 'GTF_FILTER' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f0/f012a4fe624e7965c4c52fe1eb1b591a3d97cee5c16c5c0d654aa86ee1c0c801/data' : 'community.wave.seqera.io/library/python:3.9.5--d54415978b031ba5' }
-    }
-
-    withName: 'GUNZIP' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4b/4bcb36d5e1fb90c8af0171a83b792ada446b04feb4ac3f26d0ce550d3c678383/data' : 'community.wave.seqera.io/library/grep_sed_tar:4b2523b1c76a5494' }
-    }
-
-    withName: 'HISAT2_ALIGN' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/95/95a04506094435ef9cbd94b479d5cd713cd1d106d5e5718bf4410686c3d19f15/data' : 'community.wave.seqera.io/library/hisat2_samtools:aaedc5f7a0ece7e8' }
-    }
-
-    withName: 'HISAT2_BUILD|HISAT2_EXTRACTSPLICESITES' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/95/95a04506094435ef9cbd94b479d5cd713cd1d106d5e5718bf4410686c3d19f15/data' : 'community.wave.seqera.io/library/hisat2_samtools:aaedc5f7a0ece7e8' }
-    }
-
-    withName: 'KALLISTO_INDEX' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/24/24655791b5db39ffdfffa8e5aeabfd11dda4553b5311ddb22e724c38b1591e8d/data' : 'community.wave.seqera.io/library/kallisto:0.51.1--58dde61fc91c371b' }
-    }
-
-    withName: 'KALLISTO_QUANT' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/24/24655791b5db39ffdfffa8e5aeabfd11dda4553b5311ddb22e724c38b1591e8d/data' : 'community.wave.seqera.io/library/kallisto:0.51.1--58dde61fc91c371b' }
-    }
-
-    withName: 'KRAKEN2_KRAKEN2' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/be/beba752dd6b17d3dd79b9a71dd2c1c46d09fa1e28212b6aef7c6119d68804f4a/data' : 'community.wave.seqera.io/library/kraken2_coreutils_pigz:2a28cee7c0427b32' }
-    }
-
-    withName: 'MULTIQC' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6e/6e97dcafc5915f90f863e70153f96bbe47963ebfd08383454d8bcd7263696e4e/data' : 'community.wave.seqera.io/library/multiqc:1.25.1--4062a515975cacba' }
-    }
-
-    withName: 'MULTIQC_CUSTOM_BIOTYPE' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f0/f012a4fe624e7965c4c52fe1eb1b591a3d97cee5c16c5c0d654aa86ee1c0c801/data' : 'community.wave.seqera.io/library/python:3.9.5--d54415978b031ba5' }
-    }
-
-    withName: 'PICARD_MARKDUPLICATES' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c0/c0d4bbb10417a70d137a28da09329d9f9fbdf964a1cfeda24b05b618cae6b16f/data' : 'community.wave.seqera.io/library/picard:3.1.1--c28da730a329ab3c' }
-    }
-
-    withName: 'PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4a/4ad78019c37ff4ab22c0dff6ab1af655c6438562ef644d0323861a97971d7694/data' : 'community.wave.seqera.io/library/sed:4.7--978821297d2b6677' }
-    }
-
-    withName: 'PRESEQ_LCEXTRAP' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5ab535d5b4c88dc4837cab00919d4d5ea66dd4d6dc837d841886bef72145f435/data' : 'community.wave.seqera.io/library/preseq:3.2.0--80c9d2ffee38d3ac' }
-    }
-
-    withName: 'QUALIMAP_RNASEQ' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/7a/7aa0998788d327c6e7104c2c1e7bea2e8bb8fb7076ec5de3fdab4027e501b9a9/data' : 'community.wave.seqera.io/library/qualimap:2.3--8375b60bba97a2a6' }
-    }
-
-    withName: 'RSEM_CALCULATEEXPRESSION' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/eb/eb5a2993bc13825b1b2443f740248c56ce0730a29553683392ce6388b7a2afe3/data' : 'community.wave.seqera.io/library/rsem_star:0dc50db916f3de8f' }
-    }
-
-    withName: 'RSEM_MERGE_COUNTS' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4a/4ad78019c37ff4ab22c0dff6ab1af655c6438562ef644d0323861a97971d7694/data' : 'community.wave.seqera.io/library/sed:4.7--978821297d2b6677' }
-    }
-
-    withName: 'RSEM_PREPAREREFERENCE' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/eb/eb5a2993bc13825b1b2443f740248c56ce0730a29553683392ce6388b7a2afe3/data' : 'community.wave.seqera.io/library/rsem_star:0dc50db916f3de8f' }
-    }
-
-    withName: 'RSEQC_BAMSTAT' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' }
-    }
-
-    withName: 'RSEQC_INFEREXPERIMENT' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' }
-    }
-
-    withName: 'RSEQC_INNERDISTANCE' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' }
-    }
-
-    withName: 'RSEQC_JUNCTIONANNOTATION' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' }
-    }
-
-    withName: 'RSEQC_JUNCTIONSATURATION' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' }
-    }
-
-    withName: 'RSEQC_READDISTRIBUTION' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' }
-    }
-
-    withName: 'RSEQC_READDUPLICATION' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' }
-    }
-
-    withName: 'RSEQC_TIN' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' }
-    }
-
-    withName: 'SALMON_INDEX' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b8/b8e3bcb1daa42497d0159cd5ae3b6d164b4470a972dd72d9d10b365fa166e5a4/data' : 'community.wave.seqera.io/library/salmon:1.10.3--dc33937abc5bffd1' }
-    }
-
-    withName: 'SALMON_QUANT' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b8/b8e3bcb1daa42497d0159cd5ae3b6d164b4470a972dd72d9d10b365fa166e5a4/data' : 'community.wave.seqera.io/library/salmon:1.10.3--dc33937abc5bffd1' }
-    }
-
-    withName: 'SAMTOOLS_FLAGSTAT' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' }
-    }
-
-    withName: 'SAMTOOLS_IDXSTATS' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' }
-    }
-
-    withName: 'SAMTOOLS_INDEX' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' }
-    }
-
-    withName: 'SAMTOOLS_SORT' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' }
-    }
-
-    withName: 'SAMTOOLS_STATS' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' }
-    }
-
-    withName: 'STAR_ALIGN' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/40/40d803371e50330de0773c7cc50315e2c3b4b41dcf123823adeb0a07d71654c1/data' : 'community.wave.seqera.io/library/htslib_samtools_star_gawk:ae438e9a604351a4' }
-    }
-
-    withName: 'STAR_GENOMEGENERATE' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/40/40d803371e50330de0773c7cc50315e2c3b4b41dcf123823adeb0a07d71654c1/data' : 'community.wave.seqera.io/library/htslib_samtools_star_gawk:ae438e9a604351a4' }
-    }
-
-    withName: 'STRINGTIE_STRINGTIE' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9e/9ebc6b1a27262420a5739330d369086b0d8c941a43b81d3fd0f741045bb3d46f/data' : 'community.wave.seqera.io/library/stringtie:2.2.3--77d8df3265c94ba1' }
-    }
-
-    withName: 'SUBREAD_FEATURECOUNTS' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/2a/2a81571bc8c4ac812adb76c51045a245041d7cc8923a2d7cc34a866588fead0c/data' : 'community.wave.seqera.io/library/subread:2.0.6--df9c6b502b57bb9c' }
-    }
-
-    withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a7/a7d1ef576617b9790973bc9d178c4ef136a52b6337260c536cff6cd68f103b45/data' : 'community.wave.seqera.io/library/bioconductor-summarizedexperiment:1.32.0--859858039875a2a5' }
-    }
-
-    withName: 'TRIMGALORE' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/10/10e7b91ef06bdf5790120809afc8cf36aac0261b618d810c952d5afd60dd5ed2/data' : 'community.wave.seqera.io/library/cutadapt_trim-galore:2aa2fc797328573b' }
-    }
-
-    withName: 'TXIMETA_TXIMPORT' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f8/f89ab1fef6e38e572ad1844d06f6d3d334d2b19a70c9e5d87bfc862b88728c23/data' : 'community.wave.seqera.io/library/bioconductor-tximeta:1.20.1--3b0ca8a1710e2b2b' }
-    }
-
-    withName: 'UCSC_BEDCLIP' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5f/5f559cabdfda8b2937c4213d3a53547eb882b2fc8cc36ebfeff07481fa47823a/data' : 'community.wave.seqera.io/library/ucsc-bedclip:377--489576e83f1992e0' }
-    }
-
-    withName: 'UCSC_BEDGRAPHTOBIGWIG' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/38/389312a4a6022c5f5d2510dfa9bedb0491b36c8a27e8d842c05de00bc3b5be76/data' : 'community.wave.seqera.io/library/ucsc-bedgraphtobigwig:469--1db18e1b19f8e5f1' }
-    }
-
-    withName: 'UMITOOLS_DEDUP' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ba/ba7c02244236db73a56ff1eb880b16c2dd53679834e1b72bb096e1f633e35644/data' : 'community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' }
-    }
-
-    withName: 'UMITOOLS_EXTRACT' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ba/ba7c02244236db73a56ff1eb880b16c2dd53679834e1b72bb096e1f633e35644/data' : 'community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' }
-    }
-
-    withName: 'UMITOOLS_PREPAREFORRSEM' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ba/ba7c02244236db73a56ff1eb880b16c2dd53679834e1b72bb096e1f633e35644/data' : 'community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' }
-    }
-
-    withName: 'UNTAR' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4b/4bcb36d5e1fb90c8af0171a83b792ada446b04feb4ac3f26d0ce550d3c678383/data' : 'community.wave.seqera.io/library/grep_sed_tar:4b2523b1c76a5494' }
-    }
-
-    // SortMeRNA does not yet have aarch64 builds conda forge. Working on it, using builds from Seqera channel for now
-    // See https://github.com/conda-forge/conda-forge-pinning-feedstock/pull/7454
-
-    withName: 'SORTMERNA' {
-        conda = 'seqera::sortmerna=4.3.7'
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f1/f161ea3d4083b7d8fcbf8524cb5ab69f386b4e36b771bb5abf9ccf8ab29e9775/data' : 'community.wave.seqera.io/library/sortmerna:4.3.7--4cc83a7bffbaaa61' }
-    }
-
-    //
-    // Tools that do not have native Conda builds for AMD and ARM. Required custom builds in 'seqera' Conda channel.
-    //
-
-    withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' {
-        conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0'
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/18/18b787cb710e54b55e04d8df4f5d363b3581c0f6008a908d7ab7de03275dfedb/data' : 'community.wave.seqera.io/library/star_samtools_gawk:c0246261b9d809e1' }
-    }
-
-    withName: 'STAR_GENOMEGENERATE_IGENOMES' {
-        conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0'
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/18/18b787cb710e54b55e04d8df4f5d363b3581c0f6008a908d7ab7de03275dfedb/data' : 'community.wave.seqera.io/library/star_samtools_gawk:c0246261b9d809e1' }
-    }
-
-}
diff --git a/conf/containers/containers_docker_amd64.config b/conf/containers/containers_docker_amd64.config
new file mode 100644
index 000000000..aca76f390
--- /dev/null
+++ b/conf/containers/containers_docker_amd64.config
@@ -0,0 +1,64 @@
+process { withName: 'BBMAP_BBSPLIT' { container = 'community.wave.seqera.io/library/bbmap:39.10--168578230ff6490a' } }
+process { withName: 'BEDTOOLS_GENOMECOV' { container = 'community.wave.seqera.io/library/bedtools:2.31.1--7c4ce4cb07c09ee4' } }
+process { withName: 'BRACKEN_BRACKEN' { container = 'community.wave.seqera.io/library/bracken:2.9--3d5af74ed6966fc1' } }
+process { withName: 'CAT_FASTQ' { container = 'community.wave.seqera.io/library/coreutils:9.5--ae99c88a9b28c264' } }
+process { withName: 'CUSTOM_CATADDITIONALFASTA' { container = 'community.wave.seqera.io/library/python:3.12.2--8aba3d9ac529ff19' } }
+process { withName: 'CUSTOM_GETCHROMSIZES' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } }
+process { withName: 'CUSTOM_TX2GENE' { container = 'community.wave.seqera.io/library/python:3.10.4--a643e28963f01eef' } }
+process { withName: 'DESEQ2_QC' { container = 'community.wave.seqera.io/library/r-base_r-optparse_r-ggplot2_r-rcolorbrewer_pruned:d06fadc02f8422a2' } }
+process { withName: 'DUPRADAR' { container = 'community.wave.seqera.io/library/bioconductor-dupradar:1.32.0--dcb3a3be56be6612' } }
+process { withName: 'FASTP' { container = 'community.wave.seqera.io/library/fastp:0.23.4--f8cefc1e5f7a782e' } }
+process { withName: 'FASTQC' { container = 'community.wave.seqera.io/library/fastqc:0.12.1--af7a5314d5015c29' } }
+process { withName: 'FQ_LINT' { container = 'community.wave.seqera.io/library/fq:0.12.0--45ea0ea1c4d20daa' } }
+process { withName: 'FQ_SUBSAMPLE' { container = 'community.wave.seqera.io/library/fq:0.12.0--45ea0ea1c4d20daa' } }
+process { withName: 'GFFREAD' { container = 'community.wave.seqera.io/library/gffread:0.12.7--33b95f1cfcc0e572' } }
+process { withName: 'GTF2BED' { container = 'community.wave.seqera.io/library/perl:5.26.2--e6570c5f08d3e12c' } }
+process { withName: 'GTF_FILTER' { container = 'community.wave.seqera.io/library/python:3.9.5--0ee01a3faebf676a' } }
+process { withName: 'GUNZIP' { container = 'community.wave.seqera.io/library/grep_sed_tar:4f61255d5eff93dc' } }
+process { withName: 'HISAT2_ALIGN' { container = 'community.wave.seqera.io/library/hisat2_samtools:9ef5e68250d2aa60' } }
+process { withName: 'HISAT2_BUILD' { container = 'community.wave.seqera.io/library/hisat2:2.2.1--df34d2bb25ac6de5' } }
+process { withName: 'HISAT2_EXTRACTSPLICESITES' { container = 'community.wave.seqera.io/library/hisat2:2.2.1--df34d2bb25ac6de5' } }
+process { withName: 'KALLISTO_INDEX' { container = 'community.wave.seqera.io/library/kallisto:0.51.1--b63691b6841c7a52' } }
+process { withName: 'KALLISTO_QUANT' { container = 'community.wave.seqera.io/library/kallisto:0.51.1--b63691b6841c7a52' } }
+process { withName: 'KRAKEN2_KRAKEN2' { container = 'community.wave.seqera.io/library/kraken2_coreutils_pigz:0892e153c7954635' } }
+process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.27--b0d1ffb40dfd9e97' } }
+process { withName: 'MULTIQC_CUSTOM_BIOTYPE' { container = 'community.wave.seqera.io/library/python:3.9.5--0ee01a3faebf676a' } }
+process { withName: 'PICARD_MARKDUPLICATES' { container = 'community.wave.seqera.io/library/picard:3.1.1--bae6cd265e6bf3d3' } }
+process { withName: 'PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' { container = 'community.wave.seqera.io/library/sed:4.7--c9d1b71422302845' } }
+process { withName: 'PRESEQ_LCEXTRAP' { container = 'community.wave.seqera.io/library/preseq:3.2.0--2789d8b704b33613' } }
+process { withName: 'QUALIMAP_RNASEQ' { container = 'community.wave.seqera.io/library/qualimap:2.3--c1797c2253925b3a' } }
+process { withName: 'RSEM_CALCULATEEXPRESSION' { container = 'community.wave.seqera.io/library/rsem_star:5acb4e8c03239c32' } }
+process { withName: 'RSEM_MERGE_COUNTS' { container = 'community.wave.seqera.io/library/sed:4.7--c9d1b71422302845' } }
+process { withName: 'RSEM_PREPAREREFERENCE' { container = 'community.wave.seqera.io/library/rsem_star:5acb4e8c03239c32' } }
+process { withName: 'RSEQC_BAMSTAT' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } }
+process { withName: 'RSEQC_INFEREXPERIMENT' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } }
+process { withName: 'RSEQC_INNERDISTANCE' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } }
+process { withName: 'RSEQC_JUNCTIONANNOTATION' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } }
+process { withName: 'RSEQC_JUNCTIONSATURATION' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } }
+process { withName: 'RSEQC_READDISTRIBUTION' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } }
+process { withName: 'RSEQC_READDUPLICATION' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } }
+process { withName: 'RSEQC_TIN' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } }
+process { withName: 'SALMON_INDEX' { container = 'community.wave.seqera.io/library/salmon:1.10.3--fcd0755dd8abb423' } }
+process { withName: 'SALMON_QUANT' { container = 'community.wave.seqera.io/library/salmon:1.10.3--fcd0755dd8abb423' } }
+process { withName: 'SAMTOOLS_FLAGSTAT' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } }
+process { withName: 'SAMTOOLS_IDXSTATS' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } }
+process { withName: 'SAMTOOLS_INDEX' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } }
+process { withName: 'SAMTOOLS_SORT' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } }
+process { withName: 'SAMTOOLS_STATS' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } }
+process { withName: 'SORTMERNA' { container = 'community.wave.seqera.io/library/sortmerna:4.3.7--6502243397c065ba' } }
+process { withName: 'STAR_ALIGN' { container = 'community.wave.seqera.io/library/htslib_samtools_star_gawk:311d422a50e6d829' } }
+process { withName: 'STAR_ALIGN_IGENOMES' { container = 'community.wave.seqera.io/library/star_samtools_gawk:bef5708b1c54889a' } }
+process { withName: 'STAR_GENOMEGENERATE' { container = 'community.wave.seqera.io/library/htslib_samtools_star_gawk:311d422a50e6d829' } }
+process { withName: 'STAR_GENOMEGENERATE_IGENOMES' { container = 'community.wave.seqera.io/library/star_samtools_gawk:bef5708b1c54889a' } }
+process { withName: 'STRINGTIE_STRINGTIE' { container = 'community.wave.seqera.io/library/stringtie:2.2.3--3c30041821e5a79a' } }
+process { withName: 'SUBREAD_FEATURECOUNTS' { container = 'community.wave.seqera.io/library/subread:2.0.6--1968a7457b0ed34e' } }
+process { withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { container = 'community.wave.seqera.io/library/bioconductor-summarizedexperiment:1.32.0--13051b66560c2065' } }
+process { withName: 'TRIMGALORE' { container = 'community.wave.seqera.io/library/cutadapt_trim-galore_pigz:a98edd405b34582d' } }
+process { withName: 'TXIMETA_TXIMPORT' { container = 'community.wave.seqera.io/library/bioconductor-tximeta:1.20.1--cd025af46d4ef23a' } }
+process { withName: 'UCSC_BEDCLIP' { container = 'community.wave.seqera.io/library/ucsc-bedclip:377--41de764ea1c26af4' } }
+process { withName: 'UCSC_BEDGRAPHTOBIGWIG' { container = 'community.wave.seqera.io/library/ucsc-bedgraphtobigwig:469--f66c00635e28f216' } }
+process { withName: 'UMICOLLAPSE' { container = 'community.wave.seqera.io/library/umicollapse:1.1.0--74864b350c72f3a0' } }
+process { withName: 'UMITOOLS_DEDUP' { container = 'community.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60' } }
+process { withName: 'UMITOOLS_EXTRACT' { container = 'community.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60' } }
+process { withName: 'UMITOOLS_PREPAREFORRSEM' { container = 'community.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60' } }
+process { withName: 'UNTAR' { container = 'community.wave.seqera.io/library/grep_sed_tar:4f61255d5eff93dc' } }
diff --git a/conf/containers/containers_docker_arm64.config b/conf/containers/containers_docker_arm64.config
new file mode 100644
index 000000000..f4e5fa426
--- /dev/null
+++ b/conf/containers/containers_docker_arm64.config
@@ -0,0 +1,64 @@
+process { withName: 'BBMAP_BBSPLIT' { container = 'community.wave.seqera.io/library/bbmap:39.10--908996c2fb304bec' } }
+process { withName: 'BEDTOOLS_GENOMECOV' { container = 'community.wave.seqera.io/library/bedtools:2.31.1--efd79503b8c63422' } }
+process { withName: 'BRACKEN_BRACKEN' { container = 'community.wave.seqera.io/library/bracken:2.9--e06b532ae215c74d' } }
+process { withName: 'CAT_FASTQ' { container = 'community.wave.seqera.io/library/coreutils:9.5--3931e2d27d9884e5' } }
+process { withName: 'CUSTOM_CATADDITIONALFASTA' { container = 'community.wave.seqera.io/library/python:3.12.2--0d47e6fe32e00784' } }
+process { withName: 'CUSTOM_GETCHROMSIZES' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } }
+process { withName: 'CUSTOM_TX2GENE' { container = 'community.wave.seqera.io/library/python:3.10.4--d0dc5eb8ea72fa82' } }
+process { withName: 'DESEQ2_QC' { container = 'community.wave.seqera.io/library/r-base_r-optparse_r-ggplot2_r-rcolorbrewer_pruned:8bd3e9db55b129d7' } }
+process { withName: 'DUPRADAR' { container = 'community.wave.seqera.io/library/bioconductor-dupradar:1.32.0--f75495d6abf45328' } }
+process { withName: 'FASTP' { container = 'community.wave.seqera.io/library/fastp:0.23.4--c1051f83dcae53f5' } }
+process { withName: 'FASTQC' { container = 'community.wave.seqera.io/library/fastqc:0.12.1--df99cb252670875a' } }
+process { withName: 'FQ_LINT' { container = 'community.wave.seqera.io/library/fq:0.12.0--ad6857b304869ce9' } }
+process { withName: 'FQ_SUBSAMPLE' { container = 'community.wave.seqera.io/library/fq:0.12.0--ad6857b304869ce9' } }
+process { withName: 'GFFREAD' { container = 'community.wave.seqera.io/library/gffread:0.12.7--1577aa7c95340d9f' } }
+process { withName: 'GTF2BED' { container = 'community.wave.seqera.io/library/perl:5.26.2--2a6adf51d600e047' } }
+process { withName: 'GTF_FILTER' { container = 'community.wave.seqera.io/library/python:3.9.5--d54415978b031ba5' } }
+process { withName: 'GUNZIP' { container = 'community.wave.seqera.io/library/grep_sed_tar:4b2523b1c76a5494' } }
+process { withName: 'HISAT2_ALIGN' { container = 'community.wave.seqera.io/library/hisat2_samtools:16f4ce5d5c83f6ec' } }
+process { withName: 'HISAT2_BUILD' { container = 'community.wave.seqera.io/library/hisat2:2.2.1--722945b3f185af3d' } }
+process { withName: 'HISAT2_EXTRACTSPLICESITES' { container = 'community.wave.seqera.io/library/hisat2:2.2.1--722945b3f185af3d' } }
+process { withName: 'KALLISTO_INDEX' { container = 'community.wave.seqera.io/library/kallisto:0.51.1--58dde61fc91c371b' } }
+process { withName: 'KALLISTO_QUANT' { container = 'community.wave.seqera.io/library/kallisto:0.51.1--58dde61fc91c371b' } }
+process { withName: 'KRAKEN2_KRAKEN2' { container = 'community.wave.seqera.io/library/kraken2_coreutils_pigz:efede2ece83f7a32' } }
+process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.27--7cf5785022026d98' } }
+process { withName: 'MULTIQC_CUSTOM_BIOTYPE' { container = 'community.wave.seqera.io/library/python:3.9.5--d54415978b031ba5' } }
+process { withName: 'PICARD_MARKDUPLICATES' { container = 'community.wave.seqera.io/library/picard:3.1.1--c28da730a329ab3c' } }
+process { withName: 'PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' { container = 'community.wave.seqera.io/library/sed:4.7--978821297d2b6677' } }
+process { withName: 'PRESEQ_LCEXTRAP' { container = 'community.wave.seqera.io/library/preseq:3.2.0--80c9d2ffee38d3ac' } }
+process { withName: 'QUALIMAP_RNASEQ' { container = 'community.wave.seqera.io/library/qualimap:2.3--8375b60bba97a2a6' } }
+process { withName: 'RSEM_CALCULATEEXPRESSION' { container = 'community.wave.seqera.io/library/rsem_star:871666abaeb8fb01' } }
+process { withName: 'RSEM_MERGE_COUNTS' { container = 'community.wave.seqera.io/library/sed:4.7--978821297d2b6677' } }
+process { withName: 'RSEM_PREPAREREFERENCE' { container = 'community.wave.seqera.io/library/rsem_star:871666abaeb8fb01' } }
+process { withName: 'RSEQC_BAMSTAT' { container = 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } }
+process { withName: 'RSEQC_INFEREXPERIMENT' { container = 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } }
+process { withName: 'RSEQC_INNERDISTANCE' { container = 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } }
+process { withName: 'RSEQC_JUNCTIONANNOTATION' { container = 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } }
+process { withName: 'RSEQC_JUNCTIONSATURATION' { container = 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } }
+process { withName: 'RSEQC_READDISTRIBUTION' { container = 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } }
+process { withName: 'RSEQC_READDUPLICATION' { container = 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } }
+process { withName: 'RSEQC_TIN' { container = 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } }
+process { withName: 'SALMON_INDEX' { container = 'community.wave.seqera.io/library/salmon:1.10.3--dc33937abc5bffd1' } }
+process { withName: 'SALMON_QUANT' { container = 'community.wave.seqera.io/library/salmon:1.10.3--dc33937abc5bffd1' } }
+process { withName: 'SAMTOOLS_FLAGSTAT' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } }
+process { withName: 'SAMTOOLS_IDXSTATS' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } }
+process { withName: 'SAMTOOLS_INDEX' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } }
+process { withName: 'SAMTOOLS_SORT' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } }
+process { withName: 'SAMTOOLS_STATS' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } }
+process { withName: 'SORTMERNA' { container = 'community.wave.seqera.io/library/sortmerna:4.3.7--4cc83a7bffbaaa61' } }
+process { withName: 'STAR_ALIGN' { container = 'community.wave.seqera.io/library/htslib_samtools_star_gawk:de8c848656c2c4c5' } }
+process { withName: 'STAR_ALIGN_IGENOMES' { container = 'community.wave.seqera.io/library/star_samtools_gawk:6ae64d775f2cb855' } }
+process { withName: 'STAR_GENOMEGENERATE' { container = 'community.wave.seqera.io/library/htslib_samtools_star_gawk:de8c848656c2c4c5' } }
+process { withName: 'STAR_GENOMEGENERATE_IGENOMES' { container = 'community.wave.seqera.io/library/star_samtools_gawk:6ae64d775f2cb855' } }
+process { withName: 'STRINGTIE_STRINGTIE' { container = 'community.wave.seqera.io/library/stringtie:2.2.3--77d8df3265c94ba1' } }
+process { withName: 'SUBREAD_FEATURECOUNTS' { container = 'community.wave.seqera.io/library/subread:2.0.6--df9c6b502b57bb9c' } }
+process { withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { container = 'community.wave.seqera.io/library/bioconductor-summarizedexperiment:1.32.0--859858039875a2a5' } }
+process { withName: 'TRIMGALORE' { container = 'community.wave.seqera.io/library/cutadapt_trim-galore_pigz:d0b730b6770575ef' } }
+process { withName: 'TXIMETA_TXIMPORT' { container = 'community.wave.seqera.io/library/bioconductor-tximeta:1.20.1--3b0ca8a1710e2b2b' } }
+process { withName: 'UCSC_BEDCLIP' { container = 'community.wave.seqera.io/library/ucsc-bedclip:377--489576e83f1992e0' } }
+process { withName: 'UCSC_BEDGRAPHTOBIGWIG' { container = 'community.wave.seqera.io/library/ucsc-bedgraphtobigwig:469--1db18e1b19f8e5f1' } }
+process { withName: 'UMICOLLAPSE' { container = 'community.wave.seqera.io/library/umicollapse:1.1.0--d406900dbf84ec60' } }
+process { withName: 'UMITOOLS_DEDUP' { container = 'community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' } }
+process { withName: 'UMITOOLS_EXTRACT' { container = 'community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' } }
+process { withName: 'UMITOOLS_PREPAREFORRSEM' { container = 'community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' } }
+process { withName: 'UNTAR' { container = 'community.wave.seqera.io/library/grep_sed_tar:4b2523b1c76a5494' } }
diff --git a/conf/containers/containers_singularity_amd64.config b/conf/containers/containers_singularity_amd64.config
new file mode 100644
index 000000000..5c5b57da7
--- /dev/null
+++ b/conf/containers/containers_singularity_amd64.config
@@ -0,0 +1,64 @@
+process { withName: 'BBMAP_BBSPLIT' { container = 'docker://community.wave.seqera.io/library/bbmap:39.10--168578230ff6490a' } }
+process { withName: 'BEDTOOLS_GENOMECOV' { container = 'docker://community.wave.seqera.io/library/bedtools:2.31.1--7c4ce4cb07c09ee4' } }
+process { withName: 'BRACKEN_BRACKEN' { container = 'docker://community.wave.seqera.io/library/bracken:2.9--3d5af74ed6966fc1' } }
+process { withName: 'CAT_FASTQ' { container = 'docker://community.wave.seqera.io/library/coreutils:9.5--ae99c88a9b28c264' } }
+process { withName: 'CUSTOM_CATADDITIONALFASTA' { container = 'docker://community.wave.seqera.io/library/python:3.12.2--8aba3d9ac529ff19' } }
+process { withName: 'CUSTOM_GETCHROMSIZES' { container = 'docker://community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } }
+process { withName: 'CUSTOM_TX2GENE' { container = 'docker://community.wave.seqera.io/library/python:3.10.4--a643e28963f01eef' } }
+process { withName: 'DESEQ2_QC' { container = 'docker://community.wave.seqera.io/library/r-base_r-optparse_r-ggplot2_r-rcolorbrewer_pruned:d06fadc02f8422a2' } }
+process { withName: 'DUPRADAR' { container = 'docker://community.wave.seqera.io/library/bioconductor-dupradar:1.32.0--dcb3a3be56be6612' } }
+process { withName: 'FASTP' { container = 'docker://community.wave.seqera.io/library/fastp:0.23.4--f8cefc1e5f7a782e' } }
+process { withName: 'FASTQC' { container = 'docker://community.wave.seqera.io/library/fastqc:0.12.1--af7a5314d5015c29' } }
+process { withName: 'FQ_LINT' { container = 'docker://community.wave.seqera.io/library/fq:0.12.0--45ea0ea1c4d20daa' } }
+process { withName: 'FQ_SUBSAMPLE' { container = 'docker://community.wave.seqera.io/library/fq:0.12.0--45ea0ea1c4d20daa' } }
+process { withName: 'GFFREAD' { container = 'docker://community.wave.seqera.io/library/gffread:0.12.7--33b95f1cfcc0e572' } }
+process { withName: 'GTF2BED' { container = 'docker://community.wave.seqera.io/library/perl:5.26.2--e6570c5f08d3e12c' } }
+process { withName: 'GTF_FILTER' { container = 'docker://community.wave.seqera.io/library/python:3.9.5--0ee01a3faebf676a' } }
+process { withName: 'GUNZIP' { container = 'docker://community.wave.seqera.io/library/grep_sed_tar:4f61255d5eff93dc' } }
+process { withName: 'HISAT2_ALIGN' { container = 'docker://community.wave.seqera.io/library/hisat2_samtools:9ef5e68250d2aa60' } }
+process { withName: 'HISAT2_BUILD' { container = 'docker://community.wave.seqera.io/library/hisat2:2.2.1--df34d2bb25ac6de5' } }
+process { withName: 'HISAT2_EXTRACTSPLICESITES' { container = 'docker://community.wave.seqera.io/library/hisat2:2.2.1--df34d2bb25ac6de5' } }
+process { withName: 'KALLISTO_INDEX' { container = 'docker://community.wave.seqera.io/library/kallisto:0.51.1--b63691b6841c7a52' } }
+process { withName: 'KALLISTO_QUANT' { container = 'docker://community.wave.seqera.io/library/kallisto:0.51.1--b63691b6841c7a52' } }
+process { withName: 'KRAKEN2_KRAKEN2' { container = 'docker://community.wave.seqera.io/library/kraken2_coreutils_pigz:0892e153c7954635' } }
+process { withName: 'MULTIQC' { container = 'docker://community.wave.seqera.io/library/multiqc:1.27--b0d1ffb40dfd9e97' } }
+process { withName: 'MULTIQC_CUSTOM_BIOTYPE' { container = 'docker://community.wave.seqera.io/library/python:3.9.5--0ee01a3faebf676a' } }
+process { withName: 'PICARD_MARKDUPLICATES' { container = 'docker://community.wave.seqera.io/library/picard:3.1.1--bae6cd265e6bf3d3' } }
+process { withName: 'PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' { container = 'docker://community.wave.seqera.io/library/sed:4.7--c9d1b71422302845' } }
+process { withName: 'PRESEQ_LCEXTRAP' { container = 'docker://community.wave.seqera.io/library/preseq:3.2.0--2789d8b704b33613' } }
+process { withName: 'QUALIMAP_RNASEQ' { container = 'docker://community.wave.seqera.io/library/qualimap:2.3--c1797c2253925b3a' } }
+process { withName: 'RSEM_CALCULATEEXPRESSION' { container = 'docker://community.wave.seqera.io/library/rsem_star:5acb4e8c03239c32' } }
+process { withName: 'RSEM_MERGE_COUNTS' { container = 'docker://community.wave.seqera.io/library/sed:4.7--c9d1b71422302845' } }
+process { withName: 'RSEM_PREPAREREFERENCE' { container = 'docker://community.wave.seqera.io/library/rsem_star:5acb4e8c03239c32' } }
+process { withName: 'RSEQC_BAMSTAT' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } }
+process { withName: 'RSEQC_INFEREXPERIMENT' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } }
+process { withName: 'RSEQC_INNERDISTANCE' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } }
+process { withName: 'RSEQC_JUNCTIONANNOTATION' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } }
+process { withName: 'RSEQC_JUNCTIONSATURATION' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } }
+process { withName: 'RSEQC_READDISTRIBUTION' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } }
+process { withName: 'RSEQC_READDUPLICATION' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } }
+process { withName: 'RSEQC_TIN' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } }
+process { withName: 'SALMON_INDEX' { container = 'docker://community.wave.seqera.io/library/salmon:1.10.3--fcd0755dd8abb423' } }
+process { withName: 'SALMON_QUANT' { container = 'docker://community.wave.seqera.io/library/salmon:1.10.3--fcd0755dd8abb423' } }
+process { withName: 'SAMTOOLS_FLAGSTAT' { container = 'docker://community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } }
+process { withName: 'SAMTOOLS_IDXSTATS' { container = 'docker://community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } }
+process { withName: 'SAMTOOLS_INDEX' { container = 'docker://community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } }
+process { withName: 'SAMTOOLS_SORT' { container = 'docker://community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } }
+process { withName: 'SAMTOOLS_STATS' { container = 'docker://community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } }
+process { withName: 'SORTMERNA' { container = 'docker://community.wave.seqera.io/library/sortmerna:4.3.7--6502243397c065ba' } }
+process { withName: 'STAR_ALIGN' { container = 'docker://community.wave.seqera.io/library/htslib_samtools_star_gawk:311d422a50e6d829' } }
+process { withName: 'STAR_ALIGN_IGENOMES' { container = 'docker://community.wave.seqera.io/library/star_samtools_gawk:bef5708b1c54889a' } }
+process { withName: 'STAR_GENOMEGENERATE' { container = 'docker://community.wave.seqera.io/library/htslib_samtools_star_gawk:311d422a50e6d829' } }
+process { withName: 'STAR_GENOMEGENERATE_IGENOMES' { container = 'docker://community.wave.seqera.io/library/star_samtools_gawk:bef5708b1c54889a' } }
+process { withName: 'STRINGTIE_STRINGTIE' { container = 'docker://community.wave.seqera.io/library/stringtie:2.2.3--3c30041821e5a79a' } }
+process { withName: 'SUBREAD_FEATURECOUNTS' { container = 'docker://community.wave.seqera.io/library/subread:2.0.6--1968a7457b0ed34e' } }
+process { withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { container = 'docker://community.wave.seqera.io/library/bioconductor-summarizedexperiment:1.32.0--13051b66560c2065' } }
+process { withName: 'TRIMGALORE' { container = 'docker://community.wave.seqera.io/library/cutadapt_trim-galore_pigz:a98edd405b34582d' } }
+process { withName: 'TXIMETA_TXIMPORT' { container = 'docker://community.wave.seqera.io/library/bioconductor-tximeta:1.20.1--cd025af46d4ef23a' } }
+process { withName: 'UCSC_BEDCLIP' { container = 'docker://community.wave.seqera.io/library/ucsc-bedclip:377--41de764ea1c26af4' } }
+process { withName: 'UCSC_BEDGRAPHTOBIGWIG' { container = 'docker://community.wave.seqera.io/library/ucsc-bedgraphtobigwig:469--f66c00635e28f216' } }
+process { withName: 'UMICOLLAPSE' { container = 'docker://community.wave.seqera.io/library/umicollapse:1.1.0--74864b350c72f3a0' } }
+process { withName: 'UMITOOLS_DEDUP' { container = 'docker://community.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60' } }
+process { withName: 'UMITOOLS_EXTRACT' { container = 'docker://community.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60' } }
+process { withName: 'UMITOOLS_PREPAREFORRSEM' { container = 'docker://community.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60' } }
+process { withName: 'UNTAR' { container = 'docker://community.wave.seqera.io/library/grep_sed_tar:4f61255d5eff93dc' } }
diff --git a/conf/containers/containers_singularity_arm64.config b/conf/containers/containers_singularity_arm64.config
new file mode 100644
index 000000000..5fc385fc5
--- /dev/null
+++ b/conf/containers/containers_singularity_arm64.config
@@ -0,0 +1,64 @@
+process { withName: 'BBMAP_BBSPLIT' { container = 'docker://community.wave.seqera.io/library/bbmap:39.10--908996c2fb304bec' } }
+process { withName: 'BEDTOOLS_GENOMECOV' { container = 'docker://community.wave.seqera.io/library/bedtools:2.31.1--efd79503b8c63422' } }
+process { withName: 'BRACKEN_BRACKEN' { container = 'docker://community.wave.seqera.io/library/bracken:2.9--e06b532ae215c74d' } }
+process { withName: 'CAT_FASTQ' { container = 'docker://community.wave.seqera.io/library/coreutils:9.5--3931e2d27d9884e5' } }
+process { withName: 'CUSTOM_CATADDITIONALFASTA' { container = 'docker://community.wave.seqera.io/library/python:3.12.2--0d47e6fe32e00784' } }
+process { withName: 'CUSTOM_GETCHROMSIZES' { container = 'docker://community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } }
+process { withName: 'CUSTOM_TX2GENE' { container = 'docker://community.wave.seqera.io/library/python:3.10.4--d0dc5eb8ea72fa82' } }
+process { withName: 'DESEQ2_QC' { container = 'docker://community.wave.seqera.io/library/r-base_r-optparse_r-ggplot2_r-rcolorbrewer_pruned:8bd3e9db55b129d7' } }
+process { withName: 'DUPRADAR' { container = 'docker://community.wave.seqera.io/library/bioconductor-dupradar:1.32.0--f75495d6abf45328' } }
+process { withName: 'FASTP' { container = 'docker://community.wave.seqera.io/library/fastp:0.23.4--c1051f83dcae53f5' } }
+process { withName: 'FASTQC' { container = 'docker://community.wave.seqera.io/library/fastqc:0.12.1--df99cb252670875a' } }
+process { withName: 'FQ_LINT' { container = 'docker://community.wave.seqera.io/library/fq:0.12.0--ad6857b304869ce9' } }
+process { withName: 'FQ_SUBSAMPLE' { container = 'docker://community.wave.seqera.io/library/fq:0.12.0--ad6857b304869ce9' } }
+process { withName: 'GFFREAD' { container = 'docker://community.wave.seqera.io/library/gffread:0.12.7--1577aa7c95340d9f' } }
+process { withName: 'GTF2BED' { container = 'docker://community.wave.seqera.io/library/perl:5.26.2--2a6adf51d600e047' } }
+process { withName: 'GTF_FILTER' { container = 'docker://community.wave.seqera.io/library/python:3.9.5--d54415978b031ba5' } }
+process { withName: 'GUNZIP' { container = 'docker://community.wave.seqera.io/library/grep_sed_tar:4b2523b1c76a5494' } }
+process { withName: 'HISAT2_ALIGN' { container = 'docker://community.wave.seqera.io/library/hisat2_samtools:16f4ce5d5c83f6ec' } }
+process { withName: 'HISAT2_BUILD' { container = 'docker://community.wave.seqera.io/library/hisat2:2.2.1--722945b3f185af3d' } }
+process { withName: 'HISAT2_EXTRACTSPLICESITES' { container = 'docker://community.wave.seqera.io/library/hisat2:2.2.1--722945b3f185af3d' } }
+process { withName: 'KALLISTO_INDEX' { container = 'docker://community.wave.seqera.io/library/kallisto:0.51.1--58dde61fc91c371b' } }
+process { withName: 'KALLISTO_QUANT' { container = 'docker://community.wave.seqera.io/library/kallisto:0.51.1--58dde61fc91c371b' } }
+process { withName: 'KRAKEN2_KRAKEN2' { container = 'docker://community.wave.seqera.io/library/kraken2_coreutils_pigz:efede2ece83f7a32' } }
+process { withName: 'MULTIQC' { container = 'docker://community.wave.seqera.io/library/multiqc:1.27--7cf5785022026d98' } }
+process { withName: 'MULTIQC_CUSTOM_BIOTYPE' { container = 'docker://community.wave.seqera.io/library/python:3.9.5--d54415978b031ba5' } }
+process { withName: 'PICARD_MARKDUPLICATES' { container = 'docker://community.wave.seqera.io/library/picard:3.1.1--c28da730a329ab3c' } }
+process { withName: 'PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' { container = 'docker://community.wave.seqera.io/library/sed:4.7--978821297d2b6677' } }
+process { withName: 'PRESEQ_LCEXTRAP' { container = 'docker://community.wave.seqera.io/library/preseq:3.2.0--80c9d2ffee38d3ac' } }
+process { withName: 'QUALIMAP_RNASEQ' { container = 'docker://community.wave.seqera.io/library/qualimap:2.3--8375b60bba97a2a6' } }
+process { withName: 'RSEM_CALCULATEEXPRESSION' { container = 'docker://community.wave.seqera.io/library/rsem_star:871666abaeb8fb01' } }
+process { withName: 'RSEM_MERGE_COUNTS' { container = 'docker://community.wave.seqera.io/library/sed:4.7--978821297d2b6677' } }
+process { withName: 'RSEM_PREPAREREFERENCE' { container = 'docker://community.wave.seqera.io/library/rsem_star:871666abaeb8fb01' } }
+process { withName: 'RSEQC_BAMSTAT' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } }
+process { withName: 'RSEQC_INFEREXPERIMENT' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } }
+process { withName: 'RSEQC_INNERDISTANCE' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } }
+process { withName: 'RSEQC_JUNCTIONANNOTATION' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } }
+process { withName: 'RSEQC_JUNCTIONSATURATION' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } }
+process { withName: 'RSEQC_READDISTRIBUTION' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } }
+process { withName: 'RSEQC_READDUPLICATION' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } }
+process { withName: 'RSEQC_TIN' { container = 'docker://community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } }
+process { withName: 'SALMON_INDEX' { container = 'docker://community.wave.seqera.io/library/salmon:1.10.3--dc33937abc5bffd1' } }
+process { withName: 'SALMON_QUANT' { container = 'docker://community.wave.seqera.io/library/salmon:1.10.3--dc33937abc5bffd1' } }
+process { withName: 'SAMTOOLS_FLAGSTAT' { container = 'docker://community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } }
+process { withName: 'SAMTOOLS_IDXSTATS' { container = 'docker://community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } }
+process { withName: 'SAMTOOLS_INDEX' { container = 'docker://community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } }
+process { withName: 'SAMTOOLS_SORT' { container = 'docker://community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } }
+process { withName: 'SAMTOOLS_STATS' { container = 'docker://community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } }
+process { withName: 'SORTMERNA' { container = 'docker://community.wave.seqera.io/library/sortmerna:4.3.7--4cc83a7bffbaaa61' } }
+process { withName: 'STAR_ALIGN' { container = 'docker://community.wave.seqera.io/library/htslib_samtools_star_gawk:de8c848656c2c4c5' } }
+process { withName: 'STAR_ALIGN_IGENOMES' { container = 'docker://community.wave.seqera.io/library/star_samtools_gawk:6ae64d775f2cb855' } }
+process { withName: 'STAR_GENOMEGENERATE' { container = 'docker://community.wave.seqera.io/library/htslib_samtools_star_gawk:de8c848656c2c4c5' } }
+process { withName: 'STAR_GENOMEGENERATE_IGENOMES' { container = 'docker://community.wave.seqera.io/library/star_samtools_gawk:6ae64d775f2cb855' } }
+process { withName: 'STRINGTIE_STRINGTIE' { container = 'docker://community.wave.seqera.io/library/stringtie:2.2.3--77d8df3265c94ba1' } }
+process { withName: 'SUBREAD_FEATURECOUNTS' { container = 'docker://community.wave.seqera.io/library/subread:2.0.6--df9c6b502b57bb9c' } }
+process { withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { container = 'docker://community.wave.seqera.io/library/bioconductor-summarizedexperiment:1.32.0--859858039875a2a5' } }
+process { withName: 'TRIMGALORE' { container = 'docker://community.wave.seqera.io/library/cutadapt_trim-galore_pigz:d0b730b6770575ef' } }
+process { withName: 'TXIMETA_TXIMPORT' { container = 'docker://community.wave.seqera.io/library/bioconductor-tximeta:1.20.1--3b0ca8a1710e2b2b' } }
+process { withName: 'UCSC_BEDCLIP' { container = 'docker://community.wave.seqera.io/library/ucsc-bedclip:377--489576e83f1992e0' } }
+process { withName: 'UCSC_BEDGRAPHTOBIGWIG' { container = 'docker://community.wave.seqera.io/library/ucsc-bedgraphtobigwig:469--1db18e1b19f8e5f1' } }
+process { withName: 'UMICOLLAPSE' { container = 'docker://community.wave.seqera.io/library/umicollapse:1.1.0--d406900dbf84ec60' } }
+process { withName: 'UMITOOLS_DEDUP' { container = 'docker://community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' } }
+process { withName: 'UMITOOLS_EXTRACT' { container = 'docker://community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' } }
+process { withName: 'UMITOOLS_PREPAREFORRSEM' { container = 'docker://community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' } }
+process { withName: 'UNTAR' { container = 'docker://community.wave.seqera.io/library/grep_sed_tar:4b2523b1c76a5494' } }
diff --git a/nextflow.config b/nextflow.config
index 1e1a5ed7f..32101af04 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -182,6 +182,8 @@ profiles {
         apptainer.enabled       = false
     }
     docker {
+        // TODO: https://github.com/nf-core/rnaseq/pull/1515#pullrequestreview-3201429623
+        // includeConfig 'conf/containers/containers_docker_amd64.config'
         docker.enabled          = true
         conda.enabled           = false
         singularity.enabled     = false
@@ -191,9 +193,11 @@ profiles {
         apptainer.enabled       = false
         docker.runOptions       = '-u $(id -u):$(id -g)'
     }
-    arm {
+    apple {
         docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'
-        includeConfig 'conf/arm.config'
+    }
+    arm {
+        process.arch            = 'linux/arm64'
     }
     singularity {
         singularity.enabled     = true