diff --git a/CHANGELOG.md b/CHANGELOG.md
index 46d6166f..3eacb45f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -43,14 +43,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#342](https://github.com/nf-core/taxprofiler/pull/342) Fixed docs/usage to correctly list the required database files for Bracken and tips to obtain Kraken2 databases (fix by @husensofteng)
 - [#350](https://github.com/nf-core/taxprofiler/pull/350) Reorganize the CI tests into separate profiles in preparation for implementation of nf-test (fix by @LilyAnderssonLee)
 - [#364](https://github.com/nf-core/taxprofiler/pull/364) Add autoMounts to apptainer profile in nextflow.config (♥ to @hkaspersento for reporting, fix by @LilyAnderssonLee)
+- [#372](https://github.com/nf-core/taxprofiler/pull/372) Update modules to use quay.io nf-core mirrored containers (♥ to @maxulysse for pointing out, fix by @LilyAnderssonLee and @jfy133)
 
 ### `Dependencies`
 
 | Tool      | Previous version | New version |
 | --------- | ---------------- | ----------- |
-| MultiQC   | 1.13             | 1.14        |
+| MultiQC   | 1.13             | 1.15        |
 | TAXPASTA  | 0.2.3            | 0.6.0       |
 | MetaPhlAn | 3.0.12           | 4.0.6       |
+| fastp     | 0.23.2           | 0.23.4      |
+| samtools  | 1.16.1           | 1.17        |
 
 ### `Deprecated`
 
diff --git a/modules.json b/modules.json
index 4baffbee..f7d76b4f 100644
--- a/modules.json
+++ b/modules.json
@@ -7,37 +7,37 @@
                 "nf-core": {
                     "adapterremoval": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "bbmap/bbduk": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "bowtie2/align": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "fe54581f8bed20e4c4a51c616c93fd3379d89820",
                         "installed_by": ["modules"]
                     },
                     "bowtie2/build": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "6a24fbe314bb2e6fe6306c29a63076ea87e8eb3c",
                         "installed_by": ["modules"]
                     },
                     "bracken/bracken": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "bracken/combinebrackenoutputs": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "cat/fastq": {
                         "branch": "master",
-                        "git_sha": "b9829e1064382745d8dff7f1d74d2138d2864f71",
+                        "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
                         "installed_by": ["modules"]
                     },
                     "centrifuge/centrifuge": {
@@ -47,38 +47,38 @@
                     },
                     "centrifuge/kreport": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "76cc4938c1f6ea5c7d83fed1eeffc146787f9543",
+                        "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4",
                         "installed_by": ["modules"]
                     },
                     "diamond/blastx": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "falco": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/falco/falco.diff"
                     },
                     "fastp": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "d497a4868ace3302016ea8ed4b395072d5e833cd",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "9a4517e720bc812e95b56d23d15a1653b6db4f53",
                         "installed_by": ["modules"]
                     },
                     "filtlong": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "ganon/classify": {
@@ -98,22 +98,22 @@
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "b9829e1064382745d8dff7f1d74d2138d2864f71",
+                        "git_sha": "e06548bfa36ee31869b81041879dd6b3a83b1d57",
                         "installed_by": ["modules"]
                     },
                     "kaiju/kaiju": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "kaiju/kaiju2krona": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "kaiju/kaiju2table": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "kmcp/profile": {
@@ -128,47 +128,47 @@
                     },
                     "kraken2/kraken2": {
                         "branch": "master",
-                        "git_sha": "7c695e0147df1157413e06246d9b0094617d3e6b",
+                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
                         "installed_by": ["modules"]
                     },
                     "krakentools/combinekreports": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "krakentools/kreport2krona": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "krakenuniq/preloadedkrakenuniq": {
                         "branch": "master",
-                        "git_sha": "a6eb17f65b3ee5761c25c075a6166c9f76733cee",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "krona/ktimporttaxonomy": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "krona/ktimporttext": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "malt/run": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "megan/rma2info": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "metaphlan/mergemetaphlantables": {
                         "branch": "master",
-                        "git_sha": "9aa59197c0fb35c29e315bcd10c0fc9e1afc70a8",
+                        "git_sha": "efae1c431e539d6a6d323ee2e9223c4b81a152ce",
                         "installed_by": ["modules"]
                     },
                     "metaphlan/metaphlan": {
@@ -178,58 +178,58 @@
                     },
                     "minimap2/align": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
                         "installed_by": ["modules"]
                     },
                     "minimap2/index": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "motus/merge": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "motus/profile": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "f2d63bd5b68925f98f572eed70993d205cc694b7",
+                        "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80",
                         "installed_by": ["modules"]
                     },
                     "porechop/porechop": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/porechop/porechop/porechop-porechop.diff"
                     },
                     "prinseqplusplus": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "samtools/fastq": {
                         "branch": "master",
-                        "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "samtools/stats": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
                         "installed_by": ["modules"]
                     },
                     "samtools/view": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "3ffae3598260a99e8db3207dead9f73f87f90d1f",
                         "installed_by": ["modules"]
                     },
                     "taxpasta/merge": {
@@ -244,7 +244,7 @@
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "b9829e1064382745d8dff7f1d74d2138d2864f71",
+                        "git_sha": "d0b4fc03af52a1cc8c6fb4493b921b57352b1dd8",
                         "installed_by": ["modules"]
                     }
                 }
diff --git a/modules/local/kraken2_standard_report.nf b/modules/local/kraken2_standard_report.nf
index 8fa25215..109503ab 100644
--- a/modules/local/kraken2_standard_report.nf
+++ b/modules/local/kraken2_standard_report.nf
@@ -5,7 +5,7 @@ process KRAKEN2_STANDARD_REPORT {
     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(report)
diff --git a/modules/local/krona_cleanup.nf b/modules/local/krona_cleanup.nf
index 4b33b736..d5da8e5e 100644
--- a/modules/local/krona_cleanup.nf
+++ b/modules/local/krona_cleanup.nf
@@ -5,7 +5,7 @@ process KRONA_CLEANUP {
     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(krona, stageAs: 'uncleaned.krona.txt')
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/bbduk/main.nf b/modules/nf-core/bbmap/bbduk/main.nf
index f33d9379..001e27d4 100644
--- a/modules/nf-core/bbmap/bbduk/main.nf
+++ b/modules/nf-core/bbmap/bbduk/main.nf
@@ -5,7 +5,7 @@ process BBMAP_BBDUK {
     conda "bioconda::bbmap=39.01"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bbmap:39.01--h5c4e2a8_0':
-        'quay.io/biocontainers/bbmap:39.01--h5c4e2a8_0' }"
+        'biocontainers/bbmap:39.01--h5c4e2a8_0' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/nf-core/bbmap/bbduk/meta.yml b/modules/nf-core/bbmap/bbduk/meta.yml
index d79b9d0b..c1719918 100644
--- a/modules/nf-core/bbmap/bbduk/meta.yml
+++ b/modules/nf-core/bbmap/bbduk/meta.yml
@@ -10,8 +10,7 @@ tools:
       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: None
-      doi: ""
+
       licence: ["UC-LBL license (see package)"]
 
 input:
diff --git a/modules/nf-core/bowtie2/align/main.nf b/modules/nf-core/bowtie2/align/main.nf
index 3d851866..a77114d2 100644
--- a/modules/nf-core/bowtie2/align/main.nf
+++ b/modules/nf-core/bowtie2/align/main.nf
@@ -5,7 +5,7 @@ process BOWTIE2_ALIGN {
     conda "bioconda::bowtie2=2.4.4 bioconda::samtools=1.16.1 conda-forge::pigz=2.6"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' :
-        'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' }"
+        'biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' }"
 
     input:
     tuple val(meta) , path(reads)
@@ -14,10 +14,10 @@ process BOWTIE2_ALIGN {
     val   sort_bam
 
     output:
-    tuple val(meta), path("*.bam")    , emit: bam
-    tuple val(meta), path("*.log")    , emit: log
-    tuple val(meta), path("*fastq.gz"), emit: fastq, optional:true
-    path  "versions.yml"              , emit: versions
+    tuple val(meta), path("*.{bam,sam}"), emit: aligned
+    tuple val(meta), path("*.log")      , emit: log
+    tuple val(meta), path("*fastq.gz")  , emit: fastq, optional:true
+    path  "versions.yml"                , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -38,6 +38,8 @@ process BOWTIE2_ALIGN {
     }
 
     def samtools_command = sort_bam ? 'sort' : 'view'
+    def extension_pattern = /(--output-fmt|-O)+\s+(\S+)/
+    def extension = (args2 ==~ extension_pattern) ? (args2 =~ extension_pattern)[0][2].toLowerCase() : "bam"
 
     """
     INDEX=`find -L ./ -name "*.rev.1.bt2" | sed "s/\\.rev.1.bt2\$//"`
@@ -51,7 +53,7 @@ process BOWTIE2_ALIGN {
         $unaligned \\
         $args \\
         2> ${prefix}.bowtie2.log \\
-        | samtools $samtools_command $args2 --threads $task.cpus -o ${prefix}.bam -
+        | samtools $samtools_command $args2 --threads $task.cpus -o ${prefix}.${extension} -
 
     if [ -f ${prefix}.unmapped.fastq.1.gz ]; then
         mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz
@@ -68,4 +70,25 @@ process BOWTIE2_ALIGN {
         pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
     END_VERSIONS
     """
+
+    stub:
+    def args2 = task.ext.args2 ?: ""
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def extension_pattern = /(--output-fmt|-O)+\s+(\S+)/
+    def extension = (args2 ==~ extension_pattern) ? (args2 =~ extension_pattern)[0][2].toLowerCase() : "bam"
+
+    """
+    touch ${prefix}.${extension}
+    touch ${prefix}.bowtie2.log
+    touch ${prefix}.unmapped_1.fastq.gz
+    touch ${prefix}.unmapped_2.fastq.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+        pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
+    END_VERSIONS
+    """
+
 }
diff --git a/modules/nf-core/bowtie2/align/meta.yml b/modules/nf-core/bowtie2/align/meta.yml
index c8e9a001..60d04c12 100644
--- a/modules/nf-core/bowtie2/align/meta.yml
+++ b/modules/nf-core/bowtie2/align/meta.yml
@@ -46,10 +46,10 @@ input:
       description: use samtools sort (true) or samtools view (false)
       pattern: "true or false"
 output:
-  - bam:
+  - aligned:
       type: file
-      description: Output BAM file containing read alignments
-      pattern: "*.{bam}"
+      description: Output BAM/SAM file containing read alignments
+      pattern: "*.{bam,sam}"
   - versions:
       type: file
       description: File containing software versions
diff --git a/modules/nf-core/bowtie2/build/main.nf b/modules/nf-core/bowtie2/build/main.nf
index 551893af..069d9c12 100644
--- a/modules/nf-core/bowtie2/build/main.nf
+++ b/modules/nf-core/bowtie2/build/main.nf
@@ -5,7 +5,7 @@ process BOWTIE2_BUILD {
     conda "bioconda::bowtie2=2.4.4"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bowtie2:2.4.4--py39hbb4e92a_0' :
-        'quay.io/biocontainers/bowtie2:2.4.4--py39hbb4e92a_0' }"
+        'biocontainers/bowtie2:2.4.4--py39hbb4e92a_0' }"
 
     input:
     tuple val(meta), path(fasta)
@@ -27,4 +27,16 @@ process BOWTIE2_BUILD {
         bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    """
+    mkdir bowtie2
+    touch bowtie2/${fasta.baseName}.{1..4}.bt2
+    touch bowtie2/${fasta.baseName}.rev.{1,2}.bt2
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/bracken/bracken/main.nf b/modules/nf-core/bracken/bracken/main.nf
index ddb2d6f8..453b415b 100644
--- a/modules/nf-core/bracken/bracken/main.nf
+++ b/modules/nf-core/bracken/bracken/main.nf
@@ -7,7 +7,7 @@ process BRACKEN_BRACKEN {
     conda "bioconda::bracken=2.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bracken:2.7--py39hc16433a_0':
-        'quay.io/biocontainers/bracken:2.7--py39hc16433a_0' }"
+        'biocontainers/bracken:2.7--py39hc16433a_0' }"
 
     input:
     tuple val(meta), path(kraken_report)
diff --git a/modules/nf-core/bracken/combinebrackenoutputs/main.nf b/modules/nf-core/bracken/combinebrackenoutputs/main.nf
index c57e6a8b..6a3a22e2 100644
--- a/modules/nf-core/bracken/combinebrackenoutputs/main.nf
+++ b/modules/nf-core/bracken/combinebrackenoutputs/main.nf
@@ -5,7 +5,7 @@ process BRACKEN_COMBINEBRACKENOUTPUTS {
     conda "bioconda::bracken=2.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bracken:2.7--py39hc16433a_0':
-        'quay.io/biocontainers/bracken:2.7--py39hc16433a_0' }"
+        'biocontainers/bracken:2.7--py39hc16433a_0' }"
 
     input:
     tuple val(meta), path(input)
diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf
index 4bdec890..5021e6fc 100644
--- a/modules/nf-core/cat/fastq/main.nf
+++ b/modules/nf-core/cat/fastq/main.nf
@@ -5,7 +5,7 @@ process CAT_FASTQ {
     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, stageAs: "input*/*")
diff --git a/modules/nf-core/centrifuge/kreport/main.nf b/modules/nf-core/centrifuge/kreport/main.nf
index 6fcee557..da746ca2 100644
--- a/modules/nf-core/centrifuge/kreport/main.nf
+++ b/modules/nf-core/centrifuge/kreport/main.nf
@@ -5,7 +5,7 @@ process CENTRIFUGE_KREPORT {
     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--h9a82719_6':
-        'quay.io/biocontainers/centrifuge:1.0.4_beta--h9a82719_6' }"
+        'biocontainers/centrifuge:1.0.4_beta--h9a82719_6' }"
 
     input:
     tuple val(meta), path(report)
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/diamond/blastx/main.nf b/modules/nf-core/diamond/blastx/main.nf
index e305b574..e08fb0d9 100644
--- a/modules/nf-core/diamond/blastx/main.nf
+++ b/modules/nf-core/diamond/blastx/main.nf
@@ -5,7 +5,7 @@ process DIAMOND_BLASTX {
     conda "bioconda::diamond=2.0.15"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' :
-        'quay.io/biocontainers/diamond:2.0.15--hb97b32f_0' }"
+        'biocontainers/diamond:2.0.15--hb97b32f_0' }"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/nf-core/diamond/blastx/meta.yml b/modules/nf-core/diamond/blastx/meta.yml
index 327b8937..a2a6013d 100644
--- a/modules/nf-core/diamond/blastx/meta.yml
+++ b/modules/nf-core/diamond/blastx/meta.yml
@@ -11,7 +11,7 @@ tools:
       homepage: https://github.com/bbuchfink/diamond
       documentation: https://github.com/bbuchfink/diamond/wiki
       tool_dev_url: https://github.com/bbuchfink/diamond
-      doi: "doi:10.1038/s41592-021-01101-x"
+      doi: "10.1038/s41592-021-01101-x"
       licence: ["GPL v3.0"]
 
 input:
diff --git a/modules/nf-core/falco/main.nf b/modules/nf-core/falco/main.nf
index f0f131e3..29ccc4bc 100644
--- a/modules/nf-core/falco/main.nf
+++ b/modules/nf-core/falco/main.nf
@@ -6,7 +6,7 @@ process FALCO {
     conda "bioconda::falco=1.2.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/falco:1.2.1--h867801b_3':
-        'quay.io/biocontainers/falco:1.2.1--h867801b_3' }"
+        'biocontainers/falco:1.2.1--h867801b_3' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/nf-core/falco/meta.yml b/modules/nf-core/falco/meta.yml
index 6f77fb1c..63846491 100644
--- a/modules/nf-core/falco/meta.yml
+++ b/modules/nf-core/falco/meta.yml
@@ -11,8 +11,7 @@ tools:
 
       homepage: "https://falco.readthedocs.io/"
       documentation: "https://falco.readthedocs.io/"
-      tool_dev_url: "None"
-      doi: ""
+
       licence: "['GPL v3']"
 
 input:
diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf
index e1ed9288..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)
@@ -58,7 +58,6 @@ process FASTP {
         [ ! -f  ${prefix}.fastq.gz ] && ln -sf $reads ${prefix}.fastq.gz
 
         fastp \\
-            --stdout \\
             --in1 ${prefix}.fastq.gz \\
             --out1  ${prefix}.fastp.fastq.gz \\
             --thread $task.cpus \\
diff --git a/modules/nf-core/fastp/meta.yml b/modules/nf-core/fastp/meta.yml
index 6f6fad74..197ea7ca 100644
--- a/modules/nf-core/fastp/meta.yml
+++ b/modules/nf-core/fastp/meta.yml
@@ -9,7 +9,7 @@ tools:
       description: |
         A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.
       documentation: https://github.com/OpenGene/fastp
-      doi: https://doi.org/10.1093/bioinformatics/bty560
+      doi: 10.1093/bioinformatics/bty560
       licence: ["MIT"]
 input:
   - meta:
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index 9ae58381..249f9064 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -5,7 +5,7 @@ process FASTQC {
     conda "bioconda::fastqc=0.11.9"
     container "${ 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
     "${task.process}":
diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test
new file mode 100644
index 00000000..3961de60
--- /dev/null
+++ b/modules/nf-core/fastqc/tests/main.nf.test
@@ -0,0 +1,32 @@
+nextflow_process {
+
+    name "Test Process FASTQC"
+    script "modules/nf-core/fastqc/main.nf"
+    process "FASTQC"
+    tag "fastqc"
+
+    test("Single-Read") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id: 'test', single_end:true ],
+                    [
+                        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+                    ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert process.out.html.get(0).get(1) ==~ ".*/test_fastqc.html"
+            assert path(process.out.html.get(0).get(1)).getText().contains("<tr><td>File type</td><td>Conventional base calls</td></tr>")
+            assert process.out.zip.get(0).get(1) ==~ ".*/test_fastqc.zip"
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/filtlong/main.nf b/modules/nf-core/filtlong/main.nf
index e920fefa..a377095c 100644
--- a/modules/nf-core/filtlong/main.nf
+++ b/modules/nf-core/filtlong/main.nf
@@ -5,7 +5,7 @@ process FILTLONG {
     conda "bioconda::filtlong=0.2.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/filtlong:0.2.1--h9a82719_0' :
-        'quay.io/biocontainers/filtlong:0.2.1--h9a82719_0' }"
+        'biocontainers/filtlong:0.2.1--h9a82719_0' }"
 
     input:
     tuple val(meta), path(shortreads), path(longreads)
diff --git a/modules/nf-core/filtlong/meta.yml b/modules/nf-core/filtlong/meta.yml
index a50b452c..9be850b0 100644
--- a/modules/nf-core/filtlong/meta.yml
+++ b/modules/nf-core/filtlong/meta.yml
@@ -11,9 +11,9 @@ tools:
   - filtlong:
       description: Filtlong is a tool for filtering long reads. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.
       homepage: https://anaconda.org/bioconda/filtlong
-      documentation: None
+
       tool_dev_url: https://github.com/rrwick/Filtlong
-      doi: ""
+
       licence: ["GPL v3"]
 
 input:
diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf
index 194dfc32..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/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
     "${task.process}":
diff --git a/modules/nf-core/kaiju/kaiju/main.nf b/modules/nf-core/kaiju/kaiju/main.nf
index 1d24e64d..12f51f2c 100644
--- a/modules/nf-core/kaiju/kaiju/main.nf
+++ b/modules/nf-core/kaiju/kaiju/main.nf
@@ -5,7 +5,7 @@ process KAIJU_KAIJU {
     conda "bioconda::kaiju=1.8.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1':
-        'quay.io/biocontainers/kaiju:1.8.2--h5b5514e_1' }"
+        'biocontainers/kaiju:1.8.2--h5b5514e_1' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/nf-core/kaiju/kaiju2krona/main.nf b/modules/nf-core/kaiju/kaiju2krona/main.nf
index fb8da1ea..efa05d4d 100644
--- a/modules/nf-core/kaiju/kaiju2krona/main.nf
+++ b/modules/nf-core/kaiju/kaiju2krona/main.nf
@@ -5,7 +5,7 @@ process KAIJU_KAIJU2KRONA {
     conda "bioconda::kaiju=1.8.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1':
-        'quay.io/biocontainers/kaiju:1.8.2--h5b5514e_1' }"
+        'biocontainers/kaiju:1.8.2--h5b5514e_1' }"
 
     input:
     tuple val(meta), path(tsv)
diff --git a/modules/nf-core/kaiju/kaiju2table/main.nf b/modules/nf-core/kaiju/kaiju2table/main.nf
index 52bd6437..e426a062 100644
--- a/modules/nf-core/kaiju/kaiju2table/main.nf
+++ b/modules/nf-core/kaiju/kaiju2table/main.nf
@@ -5,7 +5,7 @@ process KAIJU_KAIJU2TABLE {
     conda "bioconda::kaiju=1.8.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1':
-        'quay.io/biocontainers/kaiju:1.8.2--h2e03b76_0' }"
+        'biocontainers/kaiju:1.8.2--h2e03b76_0' }"
 
     input:
     tuple val(meta), path(results)
diff --git a/modules/nf-core/kraken2/kraken2/main.nf b/modules/nf-core/kraken2/kraken2/main.nf
index 5901064e..da8d8c6d 100644
--- a/modules/nf-core/kraken2/kraken2/main.nf
+++ b/modules/nf-core/kraken2/kraken2/main.nf
@@ -5,7 +5,7 @@ process KRAKEN2_KRAKEN2 {
     conda "bioconda::kraken2=2.1.2 conda-forge::pigz=2.6"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0' :
-        'quay.io/biocontainers/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0' }"
+        'biocontainers/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/nf-core/kraken2/kraken2/meta.yml b/modules/nf-core/kraken2/kraken2/meta.yml
index 7129fe3a..4721f45b 100644
--- a/modules/nf-core/kraken2/kraken2/meta.yml
+++ b/modules/nf-core/kraken2/kraken2/meta.yml
@@ -28,12 +28,12 @@ input:
       type: directory
       description: Kraken2 database
   - save_output_fastqs:
-      type: boolean
+      type: string
       description: |
         If true, optional commands are added to save classified and unclassified reads
         as fastq files
   - save_reads_assignment:
-      type: boolean
+      type: string
       description: |
         If true, an optional command is added to save a file reporting the taxonomic
         classification of each input read
diff --git a/modules/nf-core/krakentools/combinekreports/main.nf b/modules/nf-core/krakentools/combinekreports/main.nf
index b4ea504e..43cc3793 100644
--- a/modules/nf-core/krakentools/combinekreports/main.nf
+++ b/modules/nf-core/krakentools/combinekreports/main.nf
@@ -4,7 +4,7 @@ process KRAKENTOOLS_COMBINEKREPORTS {
     conda "bioconda::krakentools=1.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/krakentools:1.2--pyh5e36f6f_0':
-        'quay.io/biocontainers/krakentools:1.2--pyh5e36f6f_0' }"
+        'biocontainers/krakentools:1.2--pyh5e36f6f_0' }"
 
     input:
     tuple val(meta), path(kreports)
diff --git a/modules/nf-core/krakentools/kreport2krona/main.nf b/modules/nf-core/krakentools/kreport2krona/main.nf
index df439acd..a3923afe 100644
--- a/modules/nf-core/krakentools/kreport2krona/main.nf
+++ b/modules/nf-core/krakentools/kreport2krona/main.nf
@@ -6,7 +6,7 @@ process KRAKENTOOLS_KREPORT2KRONA {
     conda "bioconda::krakentools=1.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/krakentools:1.2--pyh5e36f6f_0':
-        'quay.io/biocontainers/krakentools:1.2--pyh5e36f6f_0' }"
+        'biocontainers/krakentools:1.2--pyh5e36f6f_0' }"
 
     input:
     tuple val(meta), path(kreport)
diff --git a/modules/nf-core/krakenuniq/preloadedkrakenuniq/main.nf b/modules/nf-core/krakenuniq/preloadedkrakenuniq/main.nf
index 0cb402f7..69f06581 100644
--- a/modules/nf-core/krakenuniq/preloadedkrakenuniq/main.nf
+++ b/modules/nf-core/krakenuniq/preloadedkrakenuniq/main.nf
@@ -5,7 +5,7 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
     conda "bioconda::krakenuniq=1.0.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/krakenuniq:1.0.2--pl5321h19e8d03_0':
-        'quay.io/biocontainers/krakenuniq:1.0.2--pl5321h19e8d03_0' }"
+        'biocontainers/krakenuniq:1.0.2--pl5321h19e8d03_0' }"
 
     input:
     tuple val(meta), path(fastqs)
diff --git a/modules/nf-core/krona/ktimporttaxonomy/main.nf b/modules/nf-core/krona/ktimporttaxonomy/main.nf
index 3a76f66f..0758a382 100644
--- a/modules/nf-core/krona/ktimporttaxonomy/main.nf
+++ b/modules/nf-core/krona/ktimporttaxonomy/main.nf
@@ -6,7 +6,7 @@ process KRONA_KTIMPORTTAXONOMY {
     conda "bioconda::krona=2.8"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/krona:2.8--pl5262hdfd78af_2' :
-        'quay.io/biocontainers/krona:2.8--pl5262hdfd78af_2' }"
+        'biocontainers/krona:2.8--pl5262hdfd78af_2' }"
 
     input:
     tuple val(meta), path(report)
diff --git a/modules/nf-core/krona/ktimporttaxonomy/meta.yml b/modules/nf-core/krona/ktimporttaxonomy/meta.yml
index 0fd7d5f4..dfcd2f2b 100644
--- a/modules/nf-core/krona/ktimporttaxonomy/meta.yml
+++ b/modules/nf-core/krona/ktimporttaxonomy/meta.yml
@@ -12,9 +12,7 @@ tools:
       description: Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.
       homepage: https://github.com/marbl/Krona/wiki/KronaTools
       documentation: http://manpages.ubuntu.com/manpages/impish/man1/ktImportTaxonomy.1.html
-      tool_dev_url:
-      doi: https://doi.org/10.1186/1471-2105-12-385
-      licence:
+      doi: 10.1186/1471-2105-12-385
 
 input:
   - meta:
diff --git a/modules/nf-core/krona/ktimporttext/main.nf b/modules/nf-core/krona/ktimporttext/main.nf
index 53f30266..43280191 100644
--- a/modules/nf-core/krona/ktimporttext/main.nf
+++ b/modules/nf-core/krona/ktimporttext/main.nf
@@ -5,7 +5,7 @@ process KRONA_KTIMPORTTEXT {
     conda "bioconda::krona=2.8.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/krona:2.8.1--pl5321hdfd78af_1':
-        'quay.io/biocontainers/krona:2.8.1--pl5321hdfd78af_1' }"
+        'biocontainers/krona:2.8.1--pl5321hdfd78af_1' }"
 
     input:
     tuple val(meta), path(report)
diff --git a/modules/nf-core/malt/run/main.nf b/modules/nf-core/malt/run/main.nf
index 83987d99..3ece2a45 100644
--- a/modules/nf-core/malt/run/main.nf
+++ b/modules/nf-core/malt/run/main.nf
@@ -5,7 +5,7 @@ process MALT_RUN {
     conda "bioconda::malt=0.61"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/malt:0.61--hdfd78af_0' :
-        'quay.io/biocontainers/malt:0.61--hdfd78af_0' }"
+        'biocontainers/malt:0.61--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(fastqs)
@@ -23,12 +23,6 @@ process MALT_RUN {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def avail_mem = 6
-    if (!task.memory) {
-        log.info '[MALT_RUN] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.'
-    } else {
-        avail_mem = task.memory.giga
-    }
 
     """
     malt-run \\
diff --git a/modules/nf-core/malt/run/meta.yml b/modules/nf-core/malt/run/meta.yml
index 8fa19586..f5ee655a 100644
--- a/modules/nf-core/malt/run/meta.yml
+++ b/modules/nf-core/malt/run/meta.yml
@@ -13,8 +13,8 @@ tools:
   - malt:
       description: A tool for mapping metagenomic data
       homepage: https://www.wsi.uni-tuebingen.de/lehrstuehle/algorithms-in-bioinformatics/software/malt/
-      documentation: https://software-ab.informatik.uni-tuebingen.de/download/malt/manual.pdf
-      tool_dev_url: None
+      documentation: https://software-ab.cs.uni-tuebingen.de/download/malt/manual.pdf
+
       doi: "10.1038/s41559-017-0446-6"
       licence: ["GPL v3"]
 
diff --git a/modules/nf-core/megan/rma2info/main.nf b/modules/nf-core/megan/rma2info/main.nf
index a37a4d6d..a1f2045a 100644
--- a/modules/nf-core/megan/rma2info/main.nf
+++ b/modules/nf-core/megan/rma2info/main.nf
@@ -5,7 +5,7 @@ process MEGAN_RMA2INFO {
     conda "bioconda::megan=6.21.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/megan:6.21.7--h9ee0642_0':
-        'quay.io/biocontainers/megan:6.21.7--h9ee0642_0' }"
+        'biocontainers/megan:6.21.7--h9ee0642_0' }"
 
     input:
     tuple val(meta), path(rma6)
diff --git a/modules/nf-core/megan/rma2info/meta.yml b/modules/nf-core/megan/rma2info/meta.yml
index 0f2d5a9b..710d9346 100644
--- a/modules/nf-core/megan/rma2info/meta.yml
+++ b/modules/nf-core/megan/rma2info/meta.yml
@@ -9,7 +9,7 @@ tools:
   - "megan":
       description: "A tool for studying the taxonomic content of a set of DNA reads"
       homepage: "https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/megan6/"
-      documentation: "https://software-ab.informatik.uni-tuebingen.de/download/megan6/welcome.html"
+      documentation: "https://software-ab.cs.uni-tuebingen.de/download/megan6/welcome.html"
       tool_dev_url: "https://github.com/husonlab/megan-ce"
       doi: "10.1371/journal.pcbi.1004957"
       licence: "['GPL >=3']"
diff --git a/modules/nf-core/metaphlan/mergemetaphlantables/main.nf b/modules/nf-core/metaphlan/mergemetaphlantables/main.nf
index 94c70cd6..0403bee9 100644
--- a/modules/nf-core/metaphlan/mergemetaphlantables/main.nf
+++ b/modules/nf-core/metaphlan/mergemetaphlantables/main.nf
@@ -4,7 +4,7 @@ process METAPHLAN_MERGEMETAPHLANTABLES {
     conda "bioconda::metaphlan=4.0.6"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/metaphlan:4.0.6--pyhca03a8a_0' :
-        'quay.io/biocontainers/metaphlan:4.0.6--pyhca03a8a_0' }"
+        'biocontainers/metaphlan:4.0.6--pyhca03a8a_0' }"
 
     input:
     tuple val(meta), path(profiles)
diff --git a/modules/nf-core/minimap2/align/main.nf b/modules/nf-core/minimap2/align/main.nf
index 430dbab9..4da47c18 100644
--- a/modules/nf-core/minimap2/align/main.nf
+++ b/modules/nf-core/minimap2/align/main.nf
@@ -6,7 +6,7 @@ process MINIMAP2_ALIGN {
     conda "bioconda::minimap2=2.24 bioconda::samtools=1.14"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' :
-        'quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' }"
+        'biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/nf-core/minimap2/index/main.nf b/modules/nf-core/minimap2/index/main.nf
index 73dd4eef..7a1bb227 100644
--- a/modules/nf-core/minimap2/index/main.nf
+++ b/modules/nf-core/minimap2/index/main.nf
@@ -5,7 +5,7 @@ process MINIMAP2_INDEX {
     conda "bioconda::minimap2=2.24"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/minimap2:2.24--h7132678_1' :
-        'quay.io/biocontainers/minimap2:2.24--h7132678_1' }"
+        'biocontainers/minimap2:2.24--h7132678_1' }"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/nf-core/motus/merge/main.nf b/modules/nf-core/motus/merge/main.nf
index 23d2a49b..adc60dc8 100644
--- a/modules/nf-core/motus/merge/main.nf
+++ b/modules/nf-core/motus/merge/main.nf
@@ -5,7 +5,7 @@ process MOTUS_MERGE {
     conda "bioconda::motus=3.0.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/motus:3.0.3--pyhdfd78af_0':
-        'quay.io/biocontainers/motus:3.0.3--pyhdfd78af_0' }"
+        'biocontainers/motus:3.0.3--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(input)
diff --git a/modules/nf-core/motus/profile/main.nf b/modules/nf-core/motus/profile/main.nf
index 1491c463..ca61865a 100644
--- a/modules/nf-core/motus/profile/main.nf
+++ b/modules/nf-core/motus/profile/main.nf
@@ -5,7 +5,7 @@ process MOTUS_PROFILE {
     conda "bioconda::motus=3.0.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/motus:3.0.3--pyhdfd78af_0':
-        'quay.io/biocontainers/motus:3.0.3--pyhdfd78af_0' }"
+        'biocontainers/motus:3.0.3--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(reads)
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/porechop/porechop/main.nf b/modules/nf-core/porechop/porechop/main.nf
index 0b00759d..648f2029 100644
--- a/modules/nf-core/porechop/porechop/main.nf
+++ b/modules/nf-core/porechop/porechop/main.nf
@@ -5,7 +5,7 @@ process PORECHOP_PORECHOP {
     conda "bioconda::porechop=0.2.4"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/porechop:0.2.4--py39h7cff6ad_2' :
-        'quay.io/biocontainers/porechop:0.2.4--py39h7cff6ad_2' }"
+        'biocontainers/porechop:0.2.4--py39h7cff6ad_2' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/nf-core/prinseqplusplus/main.nf b/modules/nf-core/prinseqplusplus/main.nf
index f6c1c5b0..63b2c723 100644
--- a/modules/nf-core/prinseqplusplus/main.nf
+++ b/modules/nf-core/prinseqplusplus/main.nf
@@ -5,7 +5,7 @@ process PRINSEQPLUSPLUS {
     conda "bioconda::prinseq-plus-plus=1.2.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/prinseq-plus-plus:1.2.3--hc90279e_1':
-        'quay.io/biocontainers/prinseq-plus-plus:1.2.3--hc90279e_1' }"
+        'biocontainers/prinseq-plus-plus:1.2.3--hc90279e_1' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/nf-core/samtools/fastq/main.nf b/modules/nf-core/samtools/fastq/main.nf
index c0b36f6f..15d89769 100644
--- a/modules/nf-core/samtools/fastq/main.nf
+++ b/modules/nf-core/samtools/fastq/main.nf
@@ -2,10 +2,10 @@ process SAMTOOLS_FASTQ {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::samtools=1.16.1"
+    conda "bioconda::samtools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' :
-        'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' :
+        'biocontainers/samtools:1.17--h00cdaf9_0' }"
 
     input:
     tuple val(meta), path(input)
diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf
index 8b95687a..0b20aa4b 100644
--- a/modules/nf-core/samtools/index/main.nf
+++ b/modules/nf-core/samtools/index/main.nf
@@ -2,10 +2,10 @@ process SAMTOOLS_INDEX {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::samtools=1.16.1"
+    conda "bioconda::samtools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' :
-        'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' :
+        'biocontainers/samtools:1.17--h00cdaf9_0' }"
 
     input:
     tuple val(meta), path(input)
diff --git a/modules/nf-core/samtools/index/meta.yml b/modules/nf-core/samtools/index/meta.yml
index e5cadbc2..8bd2fa6f 100644
--- a/modules/nf-core/samtools/index/meta.yml
+++ b/modules/nf-core/samtools/index/meta.yml
@@ -12,7 +12,7 @@ tools:
         short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
         These files are generated as output by short read aligners like BWA.
       homepage: http://www.htslib.org/
-      documentation: hhttp://www.htslib.org/doc/samtools.html
+      documentation: http://www.htslib.org/doc/samtools.html
       doi: 10.1093/bioinformatics/btp352
       licence: ["MIT"]
 input:
diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf
index 0a2a3640..4a2607de 100644
--- a/modules/nf-core/samtools/stats/main.nf
+++ b/modules/nf-core/samtools/stats/main.nf
@@ -2,14 +2,14 @@ process SAMTOOLS_STATS {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::samtools=1.16.1"
+    conda "bioconda::samtools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' :
-        'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' :
+        'biocontainers/samtools:1.17--h00cdaf9_0' }"
 
     input:
     tuple val(meta), path(input), path(input_index)
-    path fasta
+    tuple val(meta2), path(fasta)
 
     output:
     tuple val(meta), path("*.stats"), emit: stats
diff --git a/modules/nf-core/samtools/stats/meta.yml b/modules/nf-core/samtools/stats/meta.yml
index cac50b1c..90e6345f 100644
--- a/modules/nf-core/samtools/stats/meta.yml
+++ b/modules/nf-core/samtools/stats/meta.yml
@@ -13,7 +13,7 @@ tools:
         short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
         These files are generated as output by short read aligners like BWA.
       homepage: http://www.htslib.org/
-      documentation: hhttp://www.htslib.org/doc/samtools.html
+      documentation: http://www.htslib.org/doc/samtools.html
       doi: 10.1093/bioinformatics/btp352
       licence: ["MIT"]
 input:
@@ -23,16 +23,21 @@ input:
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
   - input:
-    type: file
-    description: BAM/CRAM file from alignment
-    pattern: "*.{bam,cram}"
+      type: file
+      description: BAM/CRAM file from alignment
+      pattern: "*.{bam,cram}"
   - input_index:
-    type: file
-    description: BAI/CRAI file from alignment
-    pattern: "*.{bai,crai}"
+      type: file
+      description: BAI/CRAI file from alignment
+      pattern: "*.{bai,crai}"
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'genome' ]
   - fasta:
-      type: optional file
-      description: Reference file the CRAM was created with
+      type: file
+      description: Reference file the CRAM was created with (optional)
       pattern: "*.{fasta,fa}"
 output:
   - meta:
@@ -51,3 +56,4 @@ output:
 authors:
   - "@drpatelh"
   - "@FriederikeHanssen"
+  - "@ramprasadn"
diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf
index 729c85e5..cb91facf 100644
--- a/modules/nf-core/samtools/view/main.nf
+++ b/modules/nf-core/samtools/view/main.nf
@@ -2,14 +2,14 @@ process SAMTOOLS_VIEW {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::samtools=1.16.1"
+    conda "bioconda::samtools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' :
-        'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' :
+        'biocontainers/samtools:1.17--h00cdaf9_0' }"
 
     input:
     tuple val(meta), path(input), path(index)
-    path fasta
+    tuple val(meta2), path(fasta)
     path qname
 
     output:
diff --git a/modules/nf-core/samtools/view/meta.yml b/modules/nf-core/samtools/view/meta.yml
index a52e4f8d..3b05450b 100644
--- a/modules/nf-core/samtools/view/meta.yml
+++ b/modules/nf-core/samtools/view/meta.yml
@@ -12,7 +12,7 @@ tools:
         short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
         These files are generated as output by short read aligners like BWA.
       homepage: http://www.htslib.org/
-      documentation: hhttp://www.htslib.org/doc/samtools.html
+      documentation: http://www.htslib.org/doc/samtools.html
       doi: 10.1093/bioinformatics/btp352
       licence: ["MIT"]
 input:
@@ -26,12 +26,17 @@ input:
       description: BAM/CRAM/SAM file
       pattern: "*.{bam,cram,sam}"
   - index:
-      type: optional file
-      description: BAM.BAI/CRAM.CRAI file
-      pattern: "*.{.bai,.crai}"
+      type: file
+      description: BAM.BAI/BAM.CSI/CRAM.CRAI file (optional)
+      pattern: "*.{.bai,.csi,.crai}"
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'test' ]
   - fasta:
-      type: optional file
-      description: Reference file the CRAM was created with
+      type: file
+      description: Reference file the CRAM was created with (optional)
       pattern: "*.{fasta,fa}"
   - qname:
       type: file
diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf
index 67f497ee..61461c39 100644
--- a/modules/nf-core/untar/main.nf
+++ b/modules/nf-core/untar/main.nf
@@ -2,10 +2,10 @@ process UNTAR {
     tag "$archive"
     label 'process_single'
 
-    conda "conda-forge::sed=4.7 bioconda::grep=3.4 conda-forge::tar=1.34"
+    conda "conda-forge::sed=4.7 conda-forge::grep=3.11 conda-forge::tar=1.34"
     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(archive)
diff --git a/subworkflows/local/longread_hostremoval.nf b/subworkflows/local/longread_hostremoval.nf
index f05e6a61..c5a10436 100644
--- a/subworkflows/local/longread_hostremoval.nf
+++ b/subworkflows/local/longread_hostremoval.nf
@@ -35,7 +35,7 @@ workflow LONGREAD_HOSTREMOVAL {
         }
 
     // Generate unmapped reads FASTQ for downstream taxprofiling
-    SAMTOOLS_VIEW ( ch_minimap2_mapped , [], [] )
+    SAMTOOLS_VIEW ( ch_minimap2_mapped , [[],[]], [] )
     ch_versions      = ch_versions.mix( SAMTOOLS_VIEW.out.versions.first() )
 
     SAMTOOLS_FASTQ ( SAMTOOLS_VIEW.out.bam, false )
@@ -48,7 +48,7 @@ workflow LONGREAD_HOSTREMOVAL {
     bam_bai = MINIMAP2_ALIGN.out.bam
         .join(SAMTOOLS_INDEX.out.bai)
 
-    SAMTOOLS_STATS ( bam_bai, reference )
+    SAMTOOLS_STATS ( bam_bai, [[],reference] )
     ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions.first())
     ch_multiqc_files = ch_multiqc_files.mix( SAMTOOLS_STATS.out.stats )
 
diff --git a/subworkflows/local/shortread_fastp.nf b/subworkflows/local/shortread_fastp.nf
index d92208a5..ac421854 100644
--- a/subworkflows/local/shortread_fastp.nf
+++ b/subworkflows/local/shortread_fastp.nf
@@ -29,7 +29,7 @@ workflow SHORTREAD_FASTP {
                                         .map {
                                             meta, reads ->
                                                 def meta_new = meta + [single_end: true]
-                                                [ meta_new, [ reads ].flatten() ]
+                                                [ meta + [single_end:true], [ reads ].flatten() ]
                                         }
 
         ch_fastp_reads_prepped = ch_fastp_reads_prepped_pe.mix( FASTP_SINGLE.out.reads )
diff --git a/subworkflows/local/shortread_hostremoval.nf b/subworkflows/local/shortread_hostremoval.nf
index 50cd0d72..32d64749 100644
--- a/subworkflows/local/shortread_hostremoval.nf
+++ b/subworkflows/local/shortread_hostremoval.nf
@@ -30,13 +30,13 @@ workflow SHORTREAD_HOSTREMOVAL {
     ch_multiqc_files = ch_multiqc_files.mix( BOWTIE2_ALIGN.out.log )
 
     // Indexing whole BAM for host removal statistics
-    SAMTOOLS_INDEX ( BOWTIE2_ALIGN.out.bam )
+    SAMTOOLS_INDEX ( BOWTIE2_ALIGN.out.aligned )
     ch_versions      = ch_versions.mix( SAMTOOLS_INDEX.out.versions.first() )
 
-    bam_bai = BOWTIE2_ALIGN.out.bam
+    bam_bai = BOWTIE2_ALIGN.out.aligned
         .join(SAMTOOLS_INDEX.out.bai, remainder: true)
 
-    SAMTOOLS_STATS ( bam_bai, reference )
+    SAMTOOLS_STATS ( bam_bai, [[],reference] )
     ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions.first())
     ch_multiqc_files = ch_multiqc_files.mix( SAMTOOLS_STATS.out.stats )
 
diff --git a/subworkflows/local/standardisation_profiles.nf b/subworkflows/local/standardisation_profiles.nf
index cd898a56..c4e36009 100644
--- a/subworkflows/local/standardisation_profiles.nf
+++ b/subworkflows/local/standardisation_profiles.nf
@@ -53,7 +53,7 @@ workflow STANDARDISATION_PROFILES {
                                     meta, profile ->
                                         def meta_new = [:]
                                         meta_new.id = meta.db_name
-                                        meta_new.tool = meta.tool == 'metaphlan' ? 'metaphlan' : meta.tool == 'malt' ? 'megan6' : meta.tool
+                                        meta_new.tool = meta.tool == 'malt' ? 'megan6' : meta.tool
                                         [meta_new, profile]
                             }
                             .groupTuple ()