diff --git a/modules.json b/modules.json
index 9c3aac66..73a43c4d 100644
--- a/modules.json
+++ b/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "adapterremoval": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "aria2": {
@@ -18,22 +18,22 @@
                     },
                     "bbmap/bbnorm": {
                         "branch": "master",
-                        "git_sha": "c7f047d51b29a49aff34b86d059291ae43d1f296",
+                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
                         "installed_by": ["modules"]
                     },
                     "bcftools/consensus": {
                         "branch": "master",
-                        "git_sha": "fa12afdf5874c1d11e4a20efe81c97935e8eea24",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "bcftools/index": {
                         "branch": "master",
-                        "git_sha": "fa12afdf5874c1d11e4a20efe81c97935e8eea24",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "bcftools/view": {
                         "branch": "master",
-                        "git_sha": "fa12afdf5874c1d11e4a20efe81c97935e8eea24",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "cat/fastq": {
@@ -43,12 +43,12 @@
                     },
                     "checkm/lineagewf": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "checkm/qa": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "concoct/concoct": {
@@ -78,45 +78,43 @@
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "76cc4938c1f6ea5c7d83fed1eeffc146787f9543",
+                        "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4",
                         "installed_by": ["modules"]
                     },
                     "dastool/dastool": {
                         "branch": "master",
-                        "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "dastool/fastatocontig2bin": {
                         "branch": "master",
-                        "git_sha": "8ffb8ec8e49aafe43240b652147d70d56f150b3c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "fastp": {
                         "branch": "master",
-                        "git_sha": "20a508676f40d0fd3f911ac595af91ec845704c4",
+                        "git_sha": "d497a4868ace3302016ea8ed4b395072d5e833cd",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "9a4517e720bc812e95b56d23d15a1653b6db4f53",
                         "installed_by": ["modules"]
                     },
                     "freebayes": {
                         "branch": "master",
-                        "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "genomad/download": {
                         "branch": "master",
                         "git_sha": "ca813f3f73adedf3547a5a677e992d9d43a71870",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/genomad/download/genomad-download.diff"
+                        "installed_by": ["modules"]
                     },
                     "genomad/endtoend": {
                         "branch": "master",
                         "git_sha": "ca813f3f73adedf3547a5a677e992d9d43a71870",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/genomad/endtoend/genomad-endtoend.diff"
+                        "installed_by": ["modules"]
                     },
                     "gtdbtk/classifywf": {
                         "branch": "master",
@@ -125,32 +123,32 @@
                     },
                     "gunc/downloaddb": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "gunc/mergecheckm": {
                         "branch": "master",
-                        "git_sha": "93f8308f6c1ef35b6b8cd264cefd22853fc51526",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "gunc/run": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "38b16706fa3a9d4ee2bf46fa5805e7397e275cdd",
+                        "git_sha": "e06548bfa36ee31869b81041879dd6b3a83b1d57",
                         "installed_by": ["modules"]
                     },
                     "maxbin2": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "metabat2/jgisummarizebamcontigdepths": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "metabat2/metabat2": {
@@ -170,42 +168,42 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "f2d63bd5b68925f98f572eed70993d205cc694b7",
+                        "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80",
                         "installed_by": ["modules"]
                     },
                     "prodigal": {
                         "branch": "master",
-                        "git_sha": "8c4f2d2ceeb5e9cc4a49a91c0e9a675b6724c043",
+                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
                         "installed_by": ["modules"]
                     },
                     "prokka": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "pydamage/analyze": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "pydamage/filter": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "samtools/faidx": {
                         "branch": "master",
-                        "git_sha": "371eff7748d769c2ddc8bd593773523a364a52fe",
+                        "git_sha": "fd742419940e01ba1c5ecb172c3e32ec840662fe",
                         "installed_by": ["modules"]
                     },
                     "seqtk/mergepe": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "tiara/tiara": {
                         "branch": "master",
-                        "git_sha": "d91e3d3d4806179065b087b91ff36c11976bf233",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     }
                 }
diff --git a/modules/local/adjust_maxbin2_ext.nf b/modules/local/adjust_maxbin2_ext.nf
index 99a7555c..4d7fecd0 100644
--- a/modules/local/adjust_maxbin2_ext.nf
+++ b/modules/local/adjust_maxbin2_ext.nf
@@ -6,7 +6,7 @@ process ADJUST_MAXBIN2_EXT {
     conda "bioconda::multiqc=1.12"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' :
-        'quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0' }"
+        'biocontainers/multiqc:1.12--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(bins)
diff --git a/modules/local/bin_summary.nf b/modules/local/bin_summary.nf
index 8d5e5c25..4503502f 100644
--- a/modules/local/bin_summary.nf
+++ b/modules/local/bin_summary.nf
@@ -3,7 +3,7 @@ process BIN_SUMMARY {
     conda "conda-forge::pandas=1.4.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/pandas:1.4.3' :
-        'quay.io/biocontainers/pandas:1.4.3' }"
+        'biocontainers/pandas:1.4.3' }"
 
     input:
     path(bin_depths)
diff --git a/modules/local/bowtie2_assembly_align.nf b/modules/local/bowtie2_assembly_align.nf
index 17f71ad2..951dfb8d 100644
--- a/modules/local/bowtie2_assembly_align.nf
+++ b/modules/local/bowtie2_assembly_align.nf
@@ -4,7 +4,7 @@ process BOWTIE2_ASSEMBLY_ALIGN {
     conda "bioconda::bowtie2=2.4.2 bioconda::samtools=1.11 conda-forge::pigz=2.3.4"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:577a697be67b5ae9b16f637fd723b8263a3898b3-0' :
-        'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:577a697be67b5ae9b16f637fd723b8263a3898b3-0' }"
+        'biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:577a697be67b5ae9b16f637fd723b8263a3898b3-0' }"
 
     input:
     tuple val(assembly_meta), path(assembly), path(index), val(reads_meta), path(reads)
diff --git a/modules/local/bowtie2_assembly_build.nf b/modules/local/bowtie2_assembly_build.nf
index b3e3332c..1f305f70 100644
--- a/modules/local/bowtie2_assembly_build.nf
+++ b/modules/local/bowtie2_assembly_build.nf
@@ -4,7 +4,7 @@ process BOWTIE2_ASSEMBLY_BUILD {
     conda "bioconda::bowtie2=2.4.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bowtie2:2.4.2--py38h1c8e9b9_1' :
-        'quay.io/biocontainers/bowtie2:2.4.2--py38h1c8e9b9_1' }"
+        'biocontainers/bowtie2:2.4.2--py38h1c8e9b9_1' }"
 
     input:
     tuple val(meta), path(assembly)
diff --git a/modules/local/bowtie2_removal_align.nf b/modules/local/bowtie2_removal_align.nf
index 924dc343..03cb9b25 100644
--- a/modules/local/bowtie2_removal_align.nf
+++ b/modules/local/bowtie2_removal_align.nf
@@ -7,7 +7,7 @@ process BOWTIE2_REMOVAL_ALIGN {
     conda "bioconda::bowtie2=2.4.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bowtie2:2.4.2--py38h1c8e9b9_1' :
-        'quay.io/biocontainers/bowtie2:2.4.2--py38h1c8e9b9_1' }"
+        'biocontainers/bowtie2:2.4.2--py38h1c8e9b9_1' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/local/bowtie2_removal_build.nf b/modules/local/bowtie2_removal_build.nf
index 70b2c4e7..ba152611 100644
--- a/modules/local/bowtie2_removal_build.nf
+++ b/modules/local/bowtie2_removal_build.nf
@@ -4,7 +4,7 @@ process BOWTIE2_REMOVAL_BUILD {
     conda "bioconda::bowtie2=2.4.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bowtie2:2.4.2--py38h1c8e9b9_1' :
-        'quay.io/biocontainers/bowtie2:2.4.2--py38h1c8e9b9_1' }"
+        'biocontainers/bowtie2:2.4.2--py38h1c8e9b9_1' }"
 
     input:
     path fasta
diff --git a/modules/local/busco.nf b/modules/local/busco.nf
index 9cf4b4ce..58e79efc 100644
--- a/modules/local/busco.nf
+++ b/modules/local/busco.nf
@@ -4,7 +4,7 @@ process BUSCO {
     conda "bioconda::busco=5.4.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/busco:5.4.3--pyhdfd78af_0':
-        'quay.io/biocontainers/busco:5.4.3--pyhdfd78af_0' }"
+        'biocontainers/busco:5.4.3--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(bin)
diff --git a/modules/local/busco_db_preparation.nf b/modules/local/busco_db_preparation.nf
index b78133a5..cddc130d 100644
--- a/modules/local/busco_db_preparation.nf
+++ b/modules/local/busco_db_preparation.nf
@@ -4,7 +4,7 @@ process BUSCO_DB_PREPARATION {
     conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'docker.io/ubuntu:20.04' }"
+        'nf-core/ubuntu:20.04' }"
 
     input:
     path database
diff --git a/modules/local/busco_save_download.nf b/modules/local/busco_save_download.nf
index 89c26e50..74bcffbf 100644
--- a/modules/local/busco_save_download.nf
+++ b/modules/local/busco_save_download.nf
@@ -5,7 +5,7 @@ process BUSCO_SAVE_DOWNLOAD {
     conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'docker.io/ubuntu:20.04' }"
+        'nf-core/ubuntu:20.04' }"
 
     input:
     path(busco_downloads)
diff --git a/modules/local/busco_summary.nf b/modules/local/busco_summary.nf
index c4023276..799196d7 100644
--- a/modules/local/busco_summary.nf
+++ b/modules/local/busco_summary.nf
@@ -3,7 +3,7 @@ process BUSCO_SUMMARY {
     conda "conda-forge::pandas=1.4.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/pandas:1.4.3' :
-        'quay.io/biocontainers/pandas:1.4.3' }"
+        'biocontainers/pandas:1.4.3' }"
 
     input:
     path(summaries_domain)
diff --git a/modules/local/cat.nf b/modules/local/cat.nf
index 8bf77cb0..48af75c0 100644
--- a/modules/local/cat.nf
+++ b/modules/local/cat.nf
@@ -4,7 +4,7 @@ process CAT {
     conda "bioconda::cat=4.6 bioconda::diamond=2.0.6"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-75e2a26f10cbf3629edf2d1600db3fed5ebe6e04:eae321284604f7dabbdf121e3070bda907b91266-0' :
-        'quay.io/biocontainers/mulled-v2-75e2a26f10cbf3629edf2d1600db3fed5ebe6e04:eae321284604f7dabbdf121e3070bda907b91266-0' }"
+        'biocontainers/mulled-v2-75e2a26f10cbf3629edf2d1600db3fed5ebe6e04:eae321284604f7dabbdf121e3070bda907b91266-0' }"
 
     input:
     tuple val(meta), path("bins/*")
diff --git a/modules/local/cat_db.nf b/modules/local/cat_db.nf
index b951a1b6..dac96bb0 100644
--- a/modules/local/cat_db.nf
+++ b/modules/local/cat_db.nf
@@ -4,7 +4,7 @@ process CAT_DB {
     conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'docker.io/ubuntu:20.04' }"
+        'nf-core/ubuntu:20.04' }"
 
     input:
     path(database)
diff --git a/modules/local/cat_db_generate.nf b/modules/local/cat_db_generate.nf
index 7f389aad..eaf6c1b4 100644
--- a/modules/local/cat_db_generate.nf
+++ b/modules/local/cat_db_generate.nf
@@ -3,7 +3,7 @@ process CAT_DB_GENERATE {
     conda "bioconda::cat=4.6 bioconda::diamond=2.0.6"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-75e2a26f10cbf3629edf2d1600db3fed5ebe6e04:eae321284604f7dabbdf121e3070bda907b91266-0' :
-        'quay.io/biocontainers/mulled-v2-75e2a26f10cbf3629edf2d1600db3fed5ebe6e04:eae321284604f7dabbdf121e3070bda907b91266-0' }"
+        'biocontainers/mulled-v2-75e2a26f10cbf3629edf2d1600db3fed5ebe6e04:eae321284604f7dabbdf121e3070bda907b91266-0' }"
 
     output:
     tuple env(DB_NAME), path("database/*"), path("taxonomy/*"), emit: db
diff --git a/modules/local/cat_summary.nf b/modules/local/cat_summary.nf
index f0c6174d..8bd2d815 100644
--- a/modules/local/cat_summary.nf
+++ b/modules/local/cat_summary.nf
@@ -4,7 +4,7 @@ process CAT_SUMMARY {
     conda "bioconda::bioawk=1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioawk:1.0--hed695b0_5' :
-        'quay.io/biocontainers/bioawk:1.0--hed695b0_5' }"
+        'biocontainers/bioawk:1.0--hed695b0_5' }"
 
     input:
     path(cat_summaries)
diff --git a/modules/local/centrifuge.nf b/modules/local/centrifuge.nf
index 1e70896a..c6618417 100644
--- a/modules/local/centrifuge.nf
+++ b/modules/local/centrifuge.nf
@@ -4,7 +4,7 @@ process CENTRIFUGE {
     conda "bioconda::centrifuge=1.0.4_beta"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4_beta--he513fc3_5' :
-        'quay.io/biocontainers/centrifuge:1.0.4_beta--he513fc3_5' }"
+        'biocontainers/centrifuge:1.0.4_beta--he513fc3_5' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/local/centrifuge_db_preparation.nf b/modules/local/centrifuge_db_preparation.nf
index ecfbdb7b..5bd76c69 100644
--- a/modules/local/centrifuge_db_preparation.nf
+++ b/modules/local/centrifuge_db_preparation.nf
@@ -3,7 +3,7 @@ process CENTRIFUGE_DB_PREPARATION {
     conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'docker.io/ubuntu:20.04' }"
+        'nf-core/ubuntu:20.04' }"
 
     input:
     path db
diff --git a/modules/local/combine_tsv.nf b/modules/local/combine_tsv.nf
index 782915d9..5e62be27 100644
--- a/modules/local/combine_tsv.nf
+++ b/modules/local/combine_tsv.nf
@@ -4,7 +4,7 @@ process COMBINE_TSV {
     conda "bioconda::bioawk=1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioawk:1.0--hed695b0_5' :
-        'quay.io/biocontainers/bioawk:1.0--hed695b0_5' }"
+        'biocontainers/bioawk:1.0--hed695b0_5' }"
 
     input:
     path(bin_summaries)
diff --git a/modules/local/convert_depths.nf b/modules/local/convert_depths.nf
index 240da1b6..f61e0c29 100644
--- a/modules/local/convert_depths.nf
+++ b/modules/local/convert_depths.nf
@@ -4,7 +4,7 @@ process CONVERT_DEPTHS {
     conda "bioconda::bioawk=1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioawk:1.0--hed695b0_5' :
-        'quay.io/biocontainers/bioawk:1.0--hed695b0_5' }"
+        'biocontainers/bioawk:1.0--hed695b0_5' }"
 
     input:
     tuple val(meta), path(fasta), path(depth)
diff --git a/modules/local/filtlong.nf b/modules/local/filtlong.nf
index 6024b561..5410c1cb 100644
--- a/modules/local/filtlong.nf
+++ b/modules/local/filtlong.nf
@@ -4,7 +4,7 @@ process FILTLONG {
     conda "bioconda::filtlong=0.2.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/filtlong:0.2.0--he513fc3_3' :
-        'quay.io/biocontainers/filtlong:0.2.0--he513fc3_3' }"
+        'biocontainers/filtlong:0.2.0--he513fc3_3' }"
 
     input:
     tuple val(meta), path(long_reads), path(short_reads_1), path(short_reads_2)
diff --git a/modules/local/gtdbtk_db_preparation.nf b/modules/local/gtdbtk_db_preparation.nf
index 6c987a32..3be79c96 100644
--- a/modules/local/gtdbtk_db_preparation.nf
+++ b/modules/local/gtdbtk_db_preparation.nf
@@ -4,7 +4,7 @@ process GTDBTK_DB_PREPARATION {
     conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'docker.io/ubuntu:20.04' }"
+        'nf-core/ubuntu:20.04' }"
 
     input:
     path(database)
diff --git a/modules/local/gtdbtk_summary.nf b/modules/local/gtdbtk_summary.nf
index cb79bbec..52c0a40d 100644
--- a/modules/local/gtdbtk_summary.nf
+++ b/modules/local/gtdbtk_summary.nf
@@ -4,7 +4,7 @@ process GTDBTK_SUMMARY {
     conda "conda-forge::pandas=1.4.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/pandas:1.4.3' :
-        'quay.io/biocontainers/pandas:1.4.3' }"
+        'biocontainers/pandas:1.4.3' }"
 
     input:
     path(qc_discarded_bins)
diff --git a/modules/local/kraken2.nf b/modules/local/kraken2.nf
index f2f7f560..b67118a9 100644
--- a/modules/local/kraken2.nf
+++ b/modules/local/kraken2.nf
@@ -4,7 +4,7 @@ process KRAKEN2 {
     conda "bioconda::kraken2=2.0.8_beta"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/kraken2:2.0.8_beta--pl526hc9558a2_2' :
-        'quay.io/biocontainers/kraken2:2.0.8_beta--pl526hc9558a2_2' }"
+        'biocontainers/kraken2:2.0.8_beta--pl526hc9558a2_2' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/local/kraken2_db_preparation.nf b/modules/local/kraken2_db_preparation.nf
index ebc9f912..5ae68b7f 100644
--- a/modules/local/kraken2_db_preparation.nf
+++ b/modules/local/kraken2_db_preparation.nf
@@ -3,7 +3,7 @@ process KRAKEN2_DB_PREPARATION {
     conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'docker.io/ubuntu:20.04' }"
+        'nf-core/ubuntu:20.04' }"
 
     input:
     path db
diff --git a/modules/local/krona.nf b/modules/local/krona.nf
index 95f482f3..827cbc4a 100644
--- a/modules/local/krona.nf
+++ b/modules/local/krona.nf
@@ -4,7 +4,7 @@ process KRONA {
     conda "bioconda::krona=2.7.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/krona:2.7.1--pl526_5' :
-        'quay.io/biocontainers/krona:2.7.1--pl526_5' }"
+        'biocontainers/krona:2.7.1--pl526_5' }"
 
     input:
     tuple val(meta), path(report)
diff --git a/modules/local/krona_db.nf b/modules/local/krona_db.nf
index 1f0539b1..0b1f4125 100644
--- a/modules/local/krona_db.nf
+++ b/modules/local/krona_db.nf
@@ -3,7 +3,7 @@ process KRONA_DB {
     conda "bioconda::krona=2.7.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/krona:2.7.1--pl526_5' :
-        'quay.io/biocontainers/krona:2.7.1--pl526_5' }"
+        'biocontainers/krona:2.7.1--pl526_5' }"
 
     output:
     path("taxonomy/taxonomy.tab"), emit: db
diff --git a/modules/local/mag_depths.nf b/modules/local/mag_depths.nf
index f55941f5..2ee63523 100644
--- a/modules/local/mag_depths.nf
+++ b/modules/local/mag_depths.nf
@@ -5,7 +5,7 @@ process MAG_DEPTHS {
     conda "bioconda::metabat2=2.15 conda-forge::python=3.6.7 conda-forge::biopython=1.74 conda-forge::pandas=1.1.5"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-e25d1fa2bb6cbacd47a4f8b2308bd01ba38c5dd7:75310f02364a762e6ba5206fcd11d7529534ed6e-0' :
-        'quay.io/biocontainers/mulled-v2-e25d1fa2bb6cbacd47a4f8b2308bd01ba38c5dd7:75310f02364a762e6ba5206fcd11d7529534ed6e-0' }"
+        'biocontainers/mulled-v2-e25d1fa2bb6cbacd47a4f8b2308bd01ba38c5dd7:75310f02364a762e6ba5206fcd11d7529534ed6e-0' }"
 
     input:
     tuple val(meta), path(bins), path(contig_depths)
diff --git a/modules/local/mag_depths_plot.nf b/modules/local/mag_depths_plot.nf
index b25cdc47..150d96fa 100644
--- a/modules/local/mag_depths_plot.nf
+++ b/modules/local/mag_depths_plot.nf
@@ -4,7 +4,7 @@ process MAG_DEPTHS_PLOT {
     conda "conda-forge::python=3.9 conda-forge::pandas=1.3.0 anaconda::seaborn=0.11.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-d14219255233ee6cacc427e28a7caf8ee42e8c91:0a22c7568e4a509925048454dad9ab37fa8fe776-0' :
-        'quay.io/biocontainers/mulled-v2-d14219255233ee6cacc427e28a7caf8ee42e8c91:0a22c7568e4a509925048454dad9ab37fa8fe776-0' }"
+        'biocontainers/mulled-v2-d14219255233ee6cacc427e28a7caf8ee42e8c91:0a22c7568e4a509925048454dad9ab37fa8fe776-0' }"
 
     input:
     tuple val(meta), path(depths)
diff --git a/modules/local/mag_depths_summary.nf b/modules/local/mag_depths_summary.nf
index 62c476b8..1be7becc 100644
--- a/modules/local/mag_depths_summary.nf
+++ b/modules/local/mag_depths_summary.nf
@@ -3,7 +3,7 @@ process MAG_DEPTHS_SUMMARY {
     conda "conda-forge::pandas=1.4.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/pandas:1.4.3' :
-        'quay.io/biocontainers/pandas:1.4.3' }"
+        'biocontainers/pandas:1.4.3' }"
 
     input:
     path(mag_depths)
diff --git a/modules/local/megahit.nf b/modules/local/megahit.nf
index 6aa3d64b..5be5d01a 100644
--- a/modules/local/megahit.nf
+++ b/modules/local/megahit.nf
@@ -4,7 +4,7 @@ process MEGAHIT {
     conda "bioconda::megahit=1.2.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/megahit:1.2.9--h2e03b76_1' :
-        'quay.io/biocontainers/megahit:1.2.9--h2e03b76_1' }"
+        'biocontainers/megahit:1.2.9--h2e03b76_1' }"
 
     input:
     tuple val(meta), path(reads1), path(reads2)
diff --git a/modules/local/nanolyse.nf b/modules/local/nanolyse.nf
index de4c1e69..4cd46d4f 100644
--- a/modules/local/nanolyse.nf
+++ b/modules/local/nanolyse.nf
@@ -4,7 +4,7 @@ process NANOLYSE {
     conda "bioconda::nanolyse=1.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/nanolyse:1.1.0--py36_1' :
-        'quay.io/biocontainers/nanolyse:1.1.0--py36_1' }"
+        'biocontainers/nanolyse:1.1.0--py36_1' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/local/nanoplot.nf b/modules/local/nanoplot.nf
index 16e95868..d3c347aa 100644
--- a/modules/local/nanoplot.nf
+++ b/modules/local/nanoplot.nf
@@ -4,7 +4,7 @@ process NANOPLOT {
     conda "bioconda::nanoplot=1.26.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/nanoplot:1.26.3--py_0' :
-        'quay.io/biocontainers/nanoplot:1.26.3--py_0' }"
+        'biocontainers/nanoplot:1.26.3--py_0' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/local/pool_paired_reads.nf b/modules/local/pool_paired_reads.nf
index f0685793..9e73028e 100644
--- a/modules/local/pool_paired_reads.nf
+++ b/modules/local/pool_paired_reads.nf
@@ -4,7 +4,7 @@ process POOL_PAIRED_READS {
     conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'docker.io/ubuntu:20.04' }"
+        'nf-core/ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(reads1), path(reads2)
diff --git a/modules/local/pool_single_reads.nf b/modules/local/pool_single_reads.nf
index e5450f9a..3ab6cc7c 100644
--- a/modules/local/pool_single_reads.nf
+++ b/modules/local/pool_single_reads.nf
@@ -4,7 +4,7 @@ process POOL_SINGLE_READS {
     conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'docker.io/ubuntu:20.04' }"
+        'nf-core/ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/local/porechop.nf b/modules/local/porechop.nf
index d397284d..91576887 100644
--- a/modules/local/porechop.nf
+++ b/modules/local/porechop.nf
@@ -4,7 +4,7 @@ process PORECHOP {
     conda "bioconda::porechop=0.2.3_seqan2.1.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/porechop:0.2.3_seqan2.1.1--py36h2d50403_3' :
-        'quay.io/biocontainers/porechop:0.2.3_seqan2.1.1--py36h2d50403_3' }"
+        'biocontainers/porechop:0.2.3_seqan2.1.1--py36h2d50403_3' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/local/quast.nf b/modules/local/quast.nf
index 5cf0a13e..4b68f412 100644
--- a/modules/local/quast.nf
+++ b/modules/local/quast.nf
@@ -4,7 +4,7 @@ process QUAST {
     conda "bioconda::quast=5.0.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/quast:5.0.2--py37pl526hb5aa323_2' :
-        'quay.io/biocontainers/quast:5.0.2--py37pl526hb5aa323_2' }"
+        'biocontainers/quast:5.0.2--py37pl526hb5aa323_2' }"
 
     input:
     tuple val(meta), path(assembly)
diff --git a/modules/local/quast_bins.nf b/modules/local/quast_bins.nf
index 5d43815a..b8015ad5 100644
--- a/modules/local/quast_bins.nf
+++ b/modules/local/quast_bins.nf
@@ -4,7 +4,7 @@ process QUAST_BINS {
     conda "bioconda::quast=5.0.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/quast:5.0.2--py37pl526hb5aa323_2' :
-        'quay.io/biocontainers/quast:5.0.2--py37pl526hb5aa323_2' }"
+        'biocontainers/quast:5.0.2--py37pl526hb5aa323_2' }"
 
     input:
     tuple val(meta), path(bins)
diff --git a/modules/local/quast_bins_summary.nf b/modules/local/quast_bins_summary.nf
index 857b7cc1..8b1734df 100644
--- a/modules/local/quast_bins_summary.nf
+++ b/modules/local/quast_bins_summary.nf
@@ -3,7 +3,7 @@ process QUAST_BINS_SUMMARY {
     conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'docker.io/ubuntu:20.04' }"
+        'nf-core/ubuntu:20.04' }"
 
     input:
     path(summaries)
diff --git a/modules/local/rename_postdastool.nf b/modules/local/rename_postdastool.nf
index 99cd9ad2..7d5a325e 100644
--- a/modules/local/rename_postdastool.nf
+++ b/modules/local/rename_postdastool.nf
@@ -6,7 +6,7 @@ process RENAME_POSTDASTOOL {
     conda "bioconda::multiqc=1.12"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' :
-        'quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0' }"
+        'biocontainers/multiqc:1.12--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(bins)
diff --git a/modules/local/rename_predastool.nf b/modules/local/rename_predastool.nf
index 9c73abfd..cc3bab18 100644
--- a/modules/local/rename_predastool.nf
+++ b/modules/local/rename_predastool.nf
@@ -6,7 +6,7 @@ process RENAME_PREDASTOOL {
     conda "bioconda::multiqc=1.12"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' :
-        'quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0' }"
+        'biocontainers/multiqc:1.12--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(bins)
diff --git a/modules/local/spades.nf b/modules/local/spades.nf
index ead45480..9ef7ec77 100644
--- a/modules/local/spades.nf
+++ b/modules/local/spades.nf
@@ -4,7 +4,7 @@ process SPADES {
     conda "bioconda::spades=3.15.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/spades:3.15.3--h95f258a_0' :
-        'quay.io/biocontainers/spades:3.15.3--h95f258a_0' }"
+        'biocontainers/spades:3.15.3--h95f258a_0' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/local/spadeshybrid.nf b/modules/local/spadeshybrid.nf
index b0957bb1..13578a69 100644
--- a/modules/local/spadeshybrid.nf
+++ b/modules/local/spadeshybrid.nf
@@ -4,7 +4,7 @@ process SPADESHYBRID {
     conda "bioconda::spades=3.15.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/spades:3.15.3--h95f258a_0' :
-        'quay.io/biocontainers/spades:3.15.3--h95f258a_0' }"
+        'biocontainers/spades:3.15.3--h95f258a_0' }"
 
     input:
     tuple val(meta), path(long_reads), path(short_reads)
diff --git a/modules/local/split_fasta.nf b/modules/local/split_fasta.nf
index 3a42ba78..4ea3b757 100644
--- a/modules/local/split_fasta.nf
+++ b/modules/local/split_fasta.nf
@@ -6,7 +6,7 @@ process SPLIT_FASTA {
     conda "bioconda::metabat2=2.15 conda-forge::python=3.6.7 conda-forge::biopython=1.74 conda-forge::pandas=1.1.5"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-e25d1fa2bb6cbacd47a4f8b2308bd01ba38c5dd7:75310f02364a762e6ba5206fcd11d7529534ed6e-0' :
-        'quay.io/biocontainers/mulled-v2-e25d1fa2bb6cbacd47a4f8b2308bd01ba38c5dd7:75310f02364a762e6ba5206fcd11d7529534ed6e-0' }"
+        'biocontainers/mulled-v2-e25d1fa2bb6cbacd47a4f8b2308bd01ba38c5dd7:75310f02364a762e6ba5206fcd11d7529534ed6e-0' }"
 
     input:
     tuple val(meta), path(unbinned)
diff --git a/modules/local/tiara_classify.nf b/modules/local/tiara_classify.nf
index 48b44df6..8fde5241 100644
--- a/modules/local/tiara_classify.nf
+++ b/modules/local/tiara_classify.nf
@@ -5,7 +5,7 @@ process TIARA_CLASSIFY {
     conda "conda-forge::r-tidyverse=1.3.1 conda-forge::r-optparse=1.7.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-1021c2bc41756fa99bc402f461dad0d1c35358c1:b0c847e4fb89c343b04036e33b2daa19c4152cf5-0' :
-        'quay.io/biocontainers/mulled-v2-1021c2bc41756fa99bc402f461dad0d1c35358c1:b0c847e4fb89c343b04036e33b2daa19c4152cf5-0' }"
+        'biocontainers/mulled-v2-1021c2bc41756fa99bc402f461dad0d1c35358c1:b0c847e4fb89c343b04036e33b2daa19c4152cf5-0' }"
 
     input:
     tuple val(meta), path(classification), path(contig2bin), path(bins)
diff --git a/modules/nf-core/adapterremoval/main.nf b/modules/nf-core/adapterremoval/main.nf
index 324b4b06..29aac1c0 100644
--- a/modules/nf-core/adapterremoval/main.nf
+++ b/modules/nf-core/adapterremoval/main.nf
@@ -5,7 +5,7 @@ process ADAPTERREMOVAL {
     conda "bioconda::adapterremoval=2.3.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/adapterremoval:2.3.2--hb7ba0dd_0' :
-        'quay.io/biocontainers/adapterremoval:2.3.2--hb7ba0dd_0' }"
+        'biocontainers/adapterremoval:2.3.2--hb7ba0dd_0' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/nf-core/bbmap/bbnorm/main.nf b/modules/nf-core/bbmap/bbnorm/main.nf
index a468cc45..9974bfb4 100644
--- a/modules/nf-core/bbmap/bbnorm/main.nf
+++ b/modules/nf-core/bbmap/bbnorm/main.nf
@@ -5,7 +5,7 @@ process BBMAP_BBNORM {
     conda "bioconda::bbmap=39.01 pigz=2.6"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:e8a286b2e789c091bac0a57302cdc78aa0112353-0':
-        'quay.io/biocontainers/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:e8a286b2e789c091bac0a57302cdc78aa0112353-0' }"
+        'biocontainers/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:e8a286b2e789c091bac0a57302cdc78aa0112353-0' }"
 
     input:
     tuple val(meta), path(fastq)
diff --git a/modules/nf-core/bbmap/bbnorm/meta.yml b/modules/nf-core/bbmap/bbnorm/meta.yml
index 8eeb0caf..6c81bb41 100644
--- a/modules/nf-core/bbmap/bbnorm/meta.yml
+++ b/modules/nf-core/bbmap/bbnorm/meta.yml
@@ -1,16 +1,15 @@
-name: "bbmap_bbnorm"
+name: bbmap_bbnorm
 description: BBNorm is designed to normalize coverage by down-sampling reads over high-depth areas of a genome, to result in a flat coverage distribution.
 keywords:
   - normalization
   - assembly
-
+  - coverage
 tools:
-  - "bbmap":
+  - bbmap:
       description: "BBMap is a short read aligner, as well as various other bioinformatic tools."
       homepage: "https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/"
       documentation: "https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/"
       tool_dev_url: "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbnorm-guide/"
-      doi: ""
       licence: "BBMap - Bushnell B. - sourceforge.net/projects/bbmap/"
 
 input:
diff --git a/modules/nf-core/bcftools/consensus/main.nf b/modules/nf-core/bcftools/consensus/main.nf
index db2c758a..2c5e8607 100644
--- a/modules/nf-core/bcftools/consensus/main.nf
+++ b/modules/nf-core/bcftools/consensus/main.nf
@@ -5,7 +5,7 @@ process BCFTOOLS_CONSENSUS {
     conda "bioconda::bcftools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
-        'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }"
+        'biocontainers/bcftools:1.17--haef29d1_0' }"
 
     input:
     tuple val(meta), path(vcf), path(tbi), path(fasta)
diff --git a/modules/nf-core/bcftools/index/main.nf b/modules/nf-core/bcftools/index/main.nf
index c99b981c..43360aab 100644
--- a/modules/nf-core/bcftools/index/main.nf
+++ b/modules/nf-core/bcftools/index/main.nf
@@ -5,7 +5,7 @@ process BCFTOOLS_INDEX {
     conda "bioconda::bcftools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
-        'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }"
+        'biocontainers/bcftools:1.17--haef29d1_0' }"
 
     input:
     tuple val(meta), path(vcf)
diff --git a/modules/nf-core/bcftools/view/main.nf b/modules/nf-core/bcftools/view/main.nf
index 01a58823..86f807d3 100644
--- a/modules/nf-core/bcftools/view/main.nf
+++ b/modules/nf-core/bcftools/view/main.nf
@@ -5,7 +5,7 @@ process BCFTOOLS_VIEW {
     conda "bioconda::bcftools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
-        'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }"
+        'biocontainers/bcftools:1.17--haef29d1_0' }"
 
     input:
     tuple val(meta), path(vcf), path(index)
diff --git a/modules/nf-core/checkm/lineagewf/main.nf b/modules/nf-core/checkm/lineagewf/main.nf
index 85d5f7f9..d8674ddc 100644
--- a/modules/nf-core/checkm/lineagewf/main.nf
+++ b/modules/nf-core/checkm/lineagewf/main.nf
@@ -5,7 +5,7 @@ process CHECKM_LINEAGEWF {
     conda "bioconda::checkm-genome=1.2.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/checkm-genome:1.2.1--pyhdfd78af_0' :
-        'quay.io/biocontainers/checkm-genome:1.2.1--pyhdfd78af_0' }"
+        'biocontainers/checkm-genome:1.2.1--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(fasta, stageAs: "input_bins/*")
diff --git a/modules/nf-core/checkm/qa/main.nf b/modules/nf-core/checkm/qa/main.nf
index e62eb5ef..b0c0e69a 100644
--- a/modules/nf-core/checkm/qa/main.nf
+++ b/modules/nf-core/checkm/qa/main.nf
@@ -5,7 +5,7 @@ process CHECKM_QA {
     conda "bioconda::checkm-genome=1.2.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/checkm-genome:1.2.1--pyhdfd78af_0' :
-        'quay.io/biocontainers/checkm-genome:1.2.1--pyhdfd78af_0' }"
+        'biocontainers/checkm-genome:1.2.1--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(analysis_dir), path(marker_file), path(coverage_file)
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
index 800a6099..c9d014b1 100644
--- a/modules/nf-core/custom/dumpsoftwareversions/main.nf
+++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf
@@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
     label 'process_single'
 
     // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
-    conda "bioconda::multiqc=1.14"
+    conda "bioconda::multiqc=1.15"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
-        'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.15--pyhdfd78af_0' }"
 
     input:
     path versions
diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
index e55b8d43..da033408 100755
--- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
+++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
@@ -4,11 +4,10 @@
 """Provide functions to merge multiple versions.yml files."""
 
 
+import yaml
 import platform
 from textwrap import dedent
 
-import yaml
-
 
 def _make_versions_html(versions):
     """Generate a tabular HTML output of all versions for MultiQC."""
diff --git a/modules/nf-core/dastool/dastool/main.nf b/modules/nf-core/dastool/dastool/main.nf
index cfa36ec8..8440edc7 100644
--- a/modules/nf-core/dastool/dastool/main.nf
+++ b/modules/nf-core/dastool/dastool/main.nf
@@ -5,7 +5,7 @@ process DASTOOL_DASTOOL {
     conda "bioconda::das_tool=1.1.6"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/das_tool:1.1.6--r42hdfd78af_0' :
-        'quay.io/biocontainers/das_tool:1.1.6--r42hdfd78af_0' }"
+        'biocontainers/das_tool:1.1.6--r42hdfd78af_0' }"
 
     input:
     tuple val(meta), path(contigs), path(bins)
diff --git a/modules/nf-core/dastool/fastatocontig2bin/main.nf b/modules/nf-core/dastool/fastatocontig2bin/main.nf
index 5e024d10..f4f77c0f 100644
--- a/modules/nf-core/dastool/fastatocontig2bin/main.nf
+++ b/modules/nf-core/dastool/fastatocontig2bin/main.nf
@@ -5,7 +5,7 @@ process DASTOOL_FASTATOCONTIG2BIN {
     conda "bioconda::das_tool=1.1.6"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/das_tool:1.1.6--r42hdfd78af_0' :
-        'quay.io/biocontainers/das_tool:1.1.6--r42hdfd78af_0' }"
+        'biocontainers/das_tool:1.1.6--r42hdfd78af_0' }"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf
index 5eeb9b09..831b7f12 100644
--- a/modules/nf-core/fastp/main.nf
+++ b/modules/nf-core/fastp/main.nf
@@ -2,10 +2,10 @@ process FASTP {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::fastp=0.23.2"
+    conda "bioconda::fastp=0.23.4"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/fastp:0.23.2--h79da9fb_0' :
-        'quay.io/biocontainers/fastp:0.23.2--h79da9fb_0' }"
+        'https://depot.galaxyproject.org/singularity/fastp:0.23.4--h5f740d0_0' :
+        'biocontainers/fastp:0.23.4--h5f740d0_0' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index 9ae58381..249f9064 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -5,7 +5,7 @@ process FASTQC {
     conda "bioconda::fastqc=0.11.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' :
-        'quay.io/biocontainers/fastqc:0.11.9--0' }"
+        'biocontainers/fastqc:0.11.9--0' }"
 
     input:
     tuple val(meta), path(reads)
@@ -29,7 +29,11 @@ process FASTQC {
     printf "%s %s\\n" $rename_to | while read old_name new_name; do
         [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
     done
-    fastqc $args --threads $task.cpus $renamed_files
+
+    fastqc \\
+        $args \\
+        --threads $task.cpus \\
+        $renamed_files
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test
new file mode 100644
index 00000000..3961de60
--- /dev/null
+++ b/modules/nf-core/fastqc/tests/main.nf.test
@@ -0,0 +1,32 @@
+nextflow_process {
+
+    name "Test Process FASTQC"
+    script "modules/nf-core/fastqc/main.nf"
+    process "FASTQC"
+    tag "fastqc"
+
+    test("Single-Read") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id: 'test', single_end:true ],
+                    [
+                        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+                    ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert process.out.html.get(0).get(1) ==~ ".*/test_fastqc.html"
+            assert path(process.out.html.get(0).get(1)).getText().contains("<tr><td>File type</td><td>Conventional base calls</td></tr>")
+            assert process.out.zip.get(0).get(1) ==~ ".*/test_fastqc.zip"
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/freebayes/main.nf b/modules/nf-core/freebayes/main.nf
index 35ced9f1..1466f085 100644
--- a/modules/nf-core/freebayes/main.nf
+++ b/modules/nf-core/freebayes/main.nf
@@ -5,7 +5,7 @@ process FREEBAYES {
     conda "bioconda::freebayes=1.3.6"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/freebayes:1.3.6--hbfe0e7f_2' :
-        'quay.io/biocontainers/freebayes:1.3.6--hbfe0e7f_2' }"
+        'biocontainers/freebayes:1.3.6--hbfe0e7f_2' }"
 
     input:
     tuple val(meta), path(input_1), path(input_1_index), path(input_2), path(input_2_index), path(target_bed)
diff --git a/modules/nf-core/genomad/download/genomad-download.diff b/modules/nf-core/genomad/download/genomad-download.diff
deleted file mode 100644
index 6fdbf03b..00000000
--- a/modules/nf-core/genomad/download/genomad-download.diff
+++ /dev/null
@@ -1,14 +0,0 @@
-Changes in module 'nf-core/genomad/download'
---- modules/nf-core/genomad/download/main.nf
-+++ modules/nf-core/genomad/download/main.nf
-@@ -4,7 +4,7 @@
-     conda "bioconda::genomad=1.5.2"
-     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-         'https://depot.galaxyproject.org/singularity/genomad:1.5.2--pyhdfd78af_0':
--        'biocontainers/genomad:1.5.2--pyhdfd78af_0' }"
-+        'quay.io/biocontainers/genomad:1.5.2--pyhdfd78af_0' }"
- 
-     output:
-     path "genomad_db/"  , emit: genomad_db
-
-************************************************************
diff --git a/modules/nf-core/genomad/download/main.nf b/modules/nf-core/genomad/download/main.nf
index deece028..a2ac6ecb 100644
--- a/modules/nf-core/genomad/download/main.nf
+++ b/modules/nf-core/genomad/download/main.nf
@@ -4,7 +4,7 @@ process GENOMAD_DOWNLOAD {
     conda "bioconda::genomad=1.5.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/genomad:1.5.2--pyhdfd78af_0':
-        'quay.io/biocontainers/genomad:1.5.2--pyhdfd78af_0' }"
+        'biocontainers/genomad:1.5.2--pyhdfd78af_0' }"
 
     output:
     path "genomad_db/"  , emit: genomad_db
diff --git a/modules/nf-core/genomad/endtoend/genomad-endtoend.diff b/modules/nf-core/genomad/endtoend/genomad-endtoend.diff
deleted file mode 100644
index bc12a0fc..00000000
--- a/modules/nf-core/genomad/endtoend/genomad-endtoend.diff
+++ /dev/null
@@ -1,14 +0,0 @@
-Changes in module 'nf-core/genomad/endtoend'
---- modules/nf-core/genomad/endtoend/main.nf
-+++ modules/nf-core/genomad/endtoend/main.nf
-@@ -5,7 +5,7 @@
-     conda "bioconda::genomad=1.5.2"
-     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-         'https://depot.galaxyproject.org/singularity/genomad:1.5.2--pyhdfd78af_0':
--        'biocontainers/genomad:1.5.2--pyhdfd78af_0' }"
-+        'quay.io/biocontainers/genomad:1.5.2--pyhdfd78af_0' }"
- 
-     input:
-     tuple val(meta) , path(fasta)
-
-************************************************************
diff --git a/modules/nf-core/genomad/endtoend/main.nf b/modules/nf-core/genomad/endtoend/main.nf
index ad3cc2c7..48276578 100644
--- a/modules/nf-core/genomad/endtoend/main.nf
+++ b/modules/nf-core/genomad/endtoend/main.nf
@@ -5,7 +5,7 @@ process GENOMAD_ENDTOEND {
     conda "bioconda::genomad=1.5.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/genomad:1.5.2--pyhdfd78af_0':
-        'quay.io/biocontainers/genomad:1.5.2--pyhdfd78af_0' }"
+        'biocontainers/genomad:1.5.2--pyhdfd78af_0' }"
 
     input:
     tuple val(meta) , path(fasta)
diff --git a/modules/nf-core/gunc/downloaddb/main.nf b/modules/nf-core/gunc/downloaddb/main.nf
index 1e77a4c6..a080d8f2 100644
--- a/modules/nf-core/gunc/downloaddb/main.nf
+++ b/modules/nf-core/gunc/downloaddb/main.nf
@@ -5,7 +5,7 @@ process GUNC_DOWNLOADDB {
     conda "bioconda::gunc=1.0.5"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/gunc:1.0.5--pyhdfd78af_0' :
-        'quay.io/biocontainers/gunc:1.0.5--pyhdfd78af_0' }"
+        'biocontainers/gunc:1.0.5--pyhdfd78af_0' }"
 
     input:
     val db_name
diff --git a/modules/nf-core/gunc/mergecheckm/main.nf b/modules/nf-core/gunc/mergecheckm/main.nf
index a5c46aca..b6399f22 100644
--- a/modules/nf-core/gunc/mergecheckm/main.nf
+++ b/modules/nf-core/gunc/mergecheckm/main.nf
@@ -5,7 +5,7 @@ process GUNC_MERGECHECKM {
     conda "bioconda::gunc=1.0.5"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/gunc:1.0.5--pyhdfd78af_0' :
-        'quay.io/biocontainers/gunc:1.0.5--pyhdfd78af_0' }"
+        'biocontainers/gunc:1.0.5--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(gunc_file), path(checkm_file)
diff --git a/modules/nf-core/gunc/run/main.nf b/modules/nf-core/gunc/run/main.nf
index 07511c51..2f1167fa 100644
--- a/modules/nf-core/gunc/run/main.nf
+++ b/modules/nf-core/gunc/run/main.nf
@@ -5,7 +5,7 @@ process GUNC_RUN {
     conda "bioconda::gunc=1.0.5"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/gunc:1.0.5--pyhdfd78af_0' :
-        'quay.io/biocontainers/gunc:1.0.5--pyhdfd78af_0' }"
+        'biocontainers/gunc:1.0.5--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf
index 16e2b83d..73bf08cd 100644
--- a/modules/nf-core/gunzip/main.nf
+++ b/modules/nf-core/gunzip/main.nf
@@ -5,7 +5,7 @@ process GUNZIP {
     conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'docker.io/library/ubuntu:20.04' }"
+        'nf-core/ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(archive)
@@ -21,10 +21,14 @@ process GUNZIP {
     def args = task.ext.args ?: ''
     gunzip = archive.toString() - '.gz'
     """
-    gunzip \\
-        -f \\
+    # Not calling gunzip itself because it creates files
+    # with the original group ownership rather than the
+    # default one for that user / the work directory
+    gzip \\
+        -cd \\
         $args \\
-        $archive
+        $archive \\
+        > $gunzip
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/maxbin2/main.nf b/modules/nf-core/maxbin2/main.nf
index 3df1bc5f..d5f49344 100644
--- a/modules/nf-core/maxbin2/main.nf
+++ b/modules/nf-core/maxbin2/main.nf
@@ -5,7 +5,7 @@ process MAXBIN2 {
     conda "bioconda::maxbin2=2.2.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/maxbin2:2.2.7--he1b5a44_2' :
-        'quay.io/biocontainers/maxbin2:2.2.7--he1b5a44_2' }"
+        'biocontainers/maxbin2:2.2.7--he1b5a44_2' }"
 
     input:
     tuple val(meta), path(contigs), path(reads), path(abund)
diff --git a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf
index 7b161a89..7804ea01 100644
--- a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf
+++ b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf
@@ -5,7 +5,7 @@ process METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS {
     conda "bioconda::metabat2=2.15"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/metabat2:2.15--h986a166_1' :
-        'quay.io/biocontainers/metabat2:2.15--h986a166_1' }"
+        'biocontainers/metabat2:2.15--h986a166_1' }"
 
     input:
     tuple val(meta), path(bam), path(bai)
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 4b604749..65d7dd0d 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -1,10 +1,10 @@
 process MULTIQC {
     label 'process_single'
 
-    conda "bioconda::multiqc=1.14"
+    conda "bioconda::multiqc=1.15"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
-        'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.15--pyhdfd78af_0' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
diff --git a/modules/nf-core/prodigal/main.nf b/modules/nf-core/prodigal/main.nf
index 4206166d..8cf87a6d 100644
--- a/modules/nf-core/prodigal/main.nf
+++ b/modules/nf-core/prodigal/main.nf
@@ -5,7 +5,7 @@ process PRODIGAL {
     conda "bioconda::prodigal=2.6.3 conda-forge::pigz=2.6"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0' :
-        'quay.io/biocontainers/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0' }"
+        'biocontainers/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0' }"
 
     input:
     tuple val(meta), path(genome)
diff --git a/modules/nf-core/prodigal/meta.yml b/modules/nf-core/prodigal/meta.yml
index 8cb3d12e..30747a90 100644
--- a/modules/nf-core/prodigal/meta.yml
+++ b/modules/nf-core/prodigal/meta.yml
@@ -1,7 +1,9 @@
 name: prodigal
 description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program
 keywords:
-  - sort
+  - prokaryotes
+  - gene finding
+  - microbial
 tools:
   - prodigal:
       description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program
diff --git a/modules/nf-core/prokka/main.nf b/modules/nf-core/prokka/main.nf
index 048d373f..60fbe232 100644
--- a/modules/nf-core/prokka/main.nf
+++ b/modules/nf-core/prokka/main.nf
@@ -5,7 +5,7 @@ process PROKKA {
     conda "bioconda::prokka=1.14.6"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/prokka%3A1.14.6--pl5321hdfd78af_4' :
-        'quay.io/biocontainers/prokka:1.14.6--pl5321hdfd78af_4' }"
+        'biocontainers/prokka:1.14.6--pl5321hdfd78af_4' }"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/nf-core/pydamage/analyze/main.nf b/modules/nf-core/pydamage/analyze/main.nf
index 5d6fc817..03cbe62a 100644
--- a/modules/nf-core/pydamage/analyze/main.nf
+++ b/modules/nf-core/pydamage/analyze/main.nf
@@ -5,7 +5,7 @@ process PYDAMAGE_ANALYZE {
     conda "bioconda::pydamage=0.70"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/pydamage:0.70--pyhdfd78af_0' :
-        'quay.io/biocontainers/pydamage:0.70--pyhdfd78af_0' }"
+        'biocontainers/pydamage:0.70--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai)
diff --git a/modules/nf-core/pydamage/filter/main.nf b/modules/nf-core/pydamage/filter/main.nf
index 71f11d8f..59d6e4b9 100644
--- a/modules/nf-core/pydamage/filter/main.nf
+++ b/modules/nf-core/pydamage/filter/main.nf
@@ -5,7 +5,7 @@ process PYDAMAGE_FILTER {
     conda "bioconda::pydamage=0.70"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/pydamage:0.70--pyhdfd78af_0' :
-        'quay.io/biocontainers/pydamage:0.70--pyhdfd78af_0' }"
+        'biocontainers/pydamage:0.70--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(csv)
diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf
index 21be8bad..59ed3088 100644
--- a/modules/nf-core/samtools/faidx/main.nf
+++ b/modules/nf-core/samtools/faidx/main.nf
@@ -5,15 +5,17 @@ process SAMTOOLS_FAIDX {
     conda "bioconda::samtools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' :
-        'quay.io/biocontainers/samtools:1.17--h00cdaf9_0' }"
+        'biocontainers/samtools:1.17--h00cdaf9_0' }"
 
     input:
     tuple val(meta), path(fasta)
+    tuple val(meta2), path(fai)
 
     output:
-    tuple val(meta), path ("*.fai"), emit: fai
-    tuple val(meta), path ("*.gzi"), emit: gzi, optional: true
-    path "versions.yml"            , emit: versions
+    tuple val(meta), path ("*.{fa,fasta}") , emit: fa , optional: true
+    tuple val(meta), path ("*.fai")        , emit: fai, optional: true
+    tuple val(meta), path ("*.gzi")        , emit: gzi, optional: true
+    path "versions.yml"                    , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -23,8 +25,8 @@ process SAMTOOLS_FAIDX {
     """
     samtools \\
         faidx \\
-        $args \\
-        $fasta
+        $fasta \\
+        $args
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -33,8 +35,12 @@ process SAMTOOLS_FAIDX {
     """
 
     stub:
+    def match = (task.ext.args =~ /-o(?:utput)?\s(.*)\s?/).findAll()
+    def fastacmd = match[0] ? "touch ${match[0][1]}" : ''
     """
+    ${fastacmd}
     touch ${fasta}.fai
+
     cat <<-END_VERSIONS > versions.yml
 
     "${task.process}":
diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml
index fe2fe9a1..957b25e5 100644
--- a/modules/nf-core/samtools/faidx/meta.yml
+++ b/modules/nf-core/samtools/faidx/meta.yml
@@ -3,6 +3,7 @@ description: Index FASTA file
 keywords:
   - index
   - fasta
+  - faidx
 tools:
   - samtools:
       description: |
@@ -17,12 +18,21 @@ input:
   - meta:
       type: map
       description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
+        Groovy Map containing reference information
+        e.g. [ id:'test' ]
   - fasta:
       type: file
       description: FASTA file
       pattern: "*.{fa,fasta}"
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'test' ]
+  - fai:
+      type: file
+      description: FASTA index file
+      pattern: "*.{fai}"
 output:
   - meta:
       type: map
diff --git a/modules/nf-core/seqtk/mergepe/main.nf b/modules/nf-core/seqtk/mergepe/main.nf
index 6ea17783..6a4362e5 100644
--- a/modules/nf-core/seqtk/mergepe/main.nf
+++ b/modules/nf-core/seqtk/mergepe/main.nf
@@ -5,7 +5,7 @@ process SEQTK_MERGEPE {
     conda "bioconda::seqtk=1.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' :
-        'quay.io/biocontainers/seqtk:1.3--h5bf99c6_3' }"
+        'biocontainers/seqtk:1.3--h5bf99c6_3' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/nf-core/tiara/tiara/main.nf b/modules/nf-core/tiara/tiara/main.nf
index c2f34c20..ec28032d 100644
--- a/modules/nf-core/tiara/tiara/main.nf
+++ b/modules/nf-core/tiara/tiara/main.nf
@@ -6,7 +6,7 @@ process TIARA_TIARA {
     conda "conda-forge::tiara=1.0.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/tiara:1.0.3' :
-        'quay.io/biocontainers/tiara:1.0.3' }"
+        'biocontainers/tiara:1.0.3' }"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/nf-core/tiara/tiara/meta.yml b/modules/nf-core/tiara/tiara/meta.yml
index 84cc047f..687bb63e 100644
--- a/modules/nf-core/tiara/tiara/meta.yml
+++ b/modules/nf-core/tiara/tiara/meta.yml
@@ -10,7 +10,7 @@ tools:
       homepage: "https://ibe-uw.github.io/tiara/"
       documentation: https://ibe-uw.github.io/tiara/"
       tool_dev_url: "https://github.com/ibe-uw/tiara"
-      doi: "https://doi.org/10.1093/bioinformatics/btab672"
+      doi: "10.1093/bioinformatics/btab672"
       licence: "MIT"
 
 input:
diff --git a/subworkflows/local/ancient_dna.nf b/subworkflows/local/ancient_dna.nf
index de47e49b..a8188a69 100644
--- a/subworkflows/local/ancient_dna.nf
+++ b/subworkflows/local/ancient_dna.nf
@@ -21,11 +21,17 @@ workflow ANCIENT_DNA_ASSEMBLY_VALIDATION {
         }
 
         if ( !params.skip_ancient_damagecorrection ) {
-            FAIDX(input.map { item -> [ item[0], item[1] ] })
-            freebayes_input = input.join(FAIDX.out.fai) // [val(meta), path(contigs), path(bam), path(bam_index), path(fai)]
-            FREEBAYES (freebayes_input.map { item -> [item[0], item[2], item[3], [], [], []] },
-                        freebayes_input.map { item -> item[1] },
-                        freebayes_input.map { item -> item[4] },
+            FAIDX(input.map { item -> [ item[0], item[1] ] }, [[],[]] )
+            freebayes_input = input.join(FAIDX.out.fai)  // [val(meta), path(contigs), path(bam), path(bam_index), path(fai)]
+                                .multiMap{
+                                    meta, contigs, bam, bai, fai ->
+                                        reads: [ meta, bam, bai, [], [], [] ]
+                                        fasta: [ contigs ]
+                                        fai: [ fai ]
+                                }
+            FREEBAYES ( freebayes_input.reads.dump(tag: 'reads'),
+                        freebayes_input.fasta.dump(tag: 'fasta'),
+                        freebayes_input.fai.dump(tag: 'fai'),
                         [],
                         [],
                         [] )