diff --git a/modules.json b/modules.json
index 5e1789a2..527289bd 100644
--- a/modules.json
+++ b/modules.json
@@ -7,137 +7,137 @@
                 "nf-core": {
                     "bowtie/align": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
                         "installed_by": ["modules"]
                     },
                     "bowtie/build": {
                         "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"]
                     },
                     "bwa/index": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "bfed129da5134b4439b1821c917972570d44d39c",
                         "installed_by": ["modules"]
                     },
                     "cat/fastq": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
                         "installed_by": ["modules"]
                     },
                     "circexplorer2/annotate": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "circexplorer2/parse": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "bd8092b67b5103bdd52e300f75889442275c3117",
+                        "git_sha": "9a4517e720bc812e95b56d23d15a1653b6db4f53",
                         "installed_by": ["modules"]
                     },
                     "hisat2/align": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "a1881f6374506f9e031b7af814768cdb44a6a7d3",
                         "installed_by": ["modules"]
                     },
                     "hisat2/build": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "f2f48836bf5c59434966a6c3b2211b29363f31ab",
                         "installed_by": ["modules"]
                     },
                     "hisat2/extractsplicesites": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
                         "installed_by": ["modules"]
                     },
                     "miranda": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80",
                         "installed_by": ["modules"]
                     },
                     "samtools/flagstat": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "570ec5bcfe19c49e16c9ca35a7a116563af6cc1c",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "samtools/idxstats": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "e662ab16e0c11f1e62983e21de9871f59371a639",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": ["bam_sort_stats_samtools", "modules"]
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "installed_by": ["modules", "bam_sort_stats_samtools"]
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": ["bam_sort_stats_samtools", "modules"]
+                        "git_sha": "a0f7be95788366c1923171e358da7d049eb440f9",
+                        "installed_by": ["modules", "bam_sort_stats_samtools"]
                     },
                     "samtools/stats": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "samtools/view": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "3ffae3598260a99e8db3207dead9f73f87f90d1f",
                         "installed_by": ["modules"]
                     },
                     "segemehl/align": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "segemehl/index": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "star/align": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "cc08a888069f67cab8120259bddab8032d4c0fe3",
                         "installed_by": ["modules"]
                     },
                     "star/genomegenerate": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "cc08a888069f67cab8120259bddab8032d4c0fe3",
                         "installed_by": ["modules"]
                     },
                     "stringtie/stringtie": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "trimgalore": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     }
                 }
@@ -146,12 +146,12 @@
                 "nf-core": {
                     "bam_sort_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "3911652a6b24249358f79e8b8466338d63efb2a2",
+                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
                         "installed_by": ["subworkflows"]
                     },
                     "bam_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "92eb5091ae5368a60cda58b3a0ced8b36d715b0f",
+                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
                         "installed_by": ["bam_sort_stats_samtools"]
                     }
                 }
diff --git a/modules/nf-core/bowtie/align/main.nf b/modules/nf-core/bowtie/align/main.nf
index 4cb6ca7a..082c0762 100644
--- a/modules/nf-core/bowtie/align/main.nf
+++ b/modules/nf-core/bowtie/align/main.nf
@@ -5,7 +5,7 @@ process BOWTIE_ALIGN {
     conda "bioconda::bowtie=1.3.0 bioconda::samtools=1.16.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:c84c7c55c45af231883d9ff4fe706ac44c479c36-0' :
-        'quay.io/biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:c84c7c55c45af231883d9ff4fe706ac44c479c36-0' }"
+        'biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:c84c7c55c45af231883d9ff4fe706ac44c479c36-0' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/nf-core/bowtie/build/main.nf b/modules/nf-core/bowtie/build/main.nf
index 85314ec7..6de02e6e 100644
--- a/modules/nf-core/bowtie/build/main.nf
+++ b/modules/nf-core/bowtie/build/main.nf
@@ -5,7 +5,7 @@ process BOWTIE_BUILD {
     conda "bioconda::bowtie=1.3.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bowtie:1.3.0--py38hed8969a_1' :
-        'quay.io/biocontainers/bowtie:1.3.0--py38hed8969a_1' }"
+        'biocontainers/bowtie:1.3.0--py38hed8969a_1' }"
 
     input:
     path fasta
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
+    "${task.process}":
+        bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/bwa/index/main.nf b/modules/nf-core/bwa/index/main.nf
index 7ccf3110..c30d194d 100644
--- a/modules/nf-core/bwa/index/main.nf
+++ b/modules/nf-core/bwa/index/main.nf
@@ -5,7 +5,7 @@ process BWA_INDEX {
     conda "bioconda::bwa=0.7.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bwa:0.7.17--hed695b0_7' :
-        'quay.io/biocontainers/bwa:0.7.17--hed695b0_7' }"
+        'biocontainers/bwa:0.7.17--hed695b0_7' }"
 
     input:
     tuple val(meta), path(fasta)
@@ -18,13 +18,14 @@ process BWA_INDEX {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${fasta.baseName}"
+    def args   = task.ext.args ?: ''
     """
     mkdir bwa
     bwa \\
         index \\
         $args \\
-        -p bwa/${fasta.baseName} \\
+        -p bwa/${prefix} \\
         $fasta
 
     cat <<-END_VERSIONS > versions.yml
@@ -34,14 +35,15 @@ process BWA_INDEX {
     """
 
     stub:
+    def prefix = task.ext.prefix ?: "${fasta.baseName}"
     """
     mkdir bwa
 
-    touch bwa/genome.amb
-    touch bwa/genome.ann
-    touch bwa/genome.bwt
-    touch bwa/genome.pac
-    touch bwa/genome.sa
+    touch bwa/${prefix}.amb
+    touch bwa/${prefix}.ann
+    touch bwa/${prefix}.bwt
+    touch bwa/${prefix}.pac
+    touch bwa/${prefix}.sa
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf
index 8a0b5600..5021e6fc 100644
--- a/modules/nf-core/cat/fastq/main.nf
+++ b/modules/nf-core/cat/fastq/main.nf
@@ -5,7 +5,7 @@ process CAT_FASTQ {
     conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'ubuntu:20.04' }"
+        'nf-core/ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(reads, stageAs: "input*/*")
diff --git a/modules/nf-core/cat/fastq/meta.yml b/modules/nf-core/cat/fastq/meta.yml
index c836598e..8a39e309 100644
--- a/modules/nf-core/cat/fastq/meta.yml
+++ b/modules/nf-core/cat/fastq/meta.yml
@@ -1,6 +1,7 @@
 name: cat_fastq
 description: Concatenates fastq files
 keywords:
+  - cat
   - fastq
   - concatenate
 tools:
@@ -16,7 +17,7 @@ input:
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
   - reads:
-      type: list
+      type: file
       description: |
         List of input FastQ files to be concatenated.
 output:
diff --git a/modules/nf-core/circexplorer2/annotate/main.nf b/modules/nf-core/circexplorer2/annotate/main.nf
index 335723a8..c2eda39a 100644
--- a/modules/nf-core/circexplorer2/annotate/main.nf
+++ b/modules/nf-core/circexplorer2/annotate/main.nf
@@ -5,7 +5,7 @@ process CIRCEXPLORER2_ANNOTATE {
     conda "bioconda::circexplorer2=2.3.8"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/circexplorer2:2.3.8--pyh864c0ab_1':
-        'quay.io/biocontainers/circexplorer2:2.3.8--pyh864c0ab_1' }"
+        'biocontainers/circexplorer2:2.3.8--pyh864c0ab_1' }"
 
     input:
     tuple val(meta), path(junctions)
diff --git a/modules/nf-core/circexplorer2/parse/main.nf b/modules/nf-core/circexplorer2/parse/main.nf
index 147a73f3..641c3146 100644
--- a/modules/nf-core/circexplorer2/parse/main.nf
+++ b/modules/nf-core/circexplorer2/parse/main.nf
@@ -5,7 +5,7 @@ process CIRCEXPLORER2_PARSE {
     conda "bioconda::circexplorer2=2.3.8"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/circexplorer2:2.3.8--pyh864c0ab_1':
-        'quay.io/biocontainers/circexplorer2:2.3.8--pyh864c0ab_1' }"
+        'biocontainers/circexplorer2:2.3.8--pyh864c0ab_1' }"
 
     input:
     tuple val(meta), path(fusions)
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
index ebc87273..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' :
-        '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/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/hisat2/align/main.nf b/modules/nf-core/hisat2/align/main.nf
index eefb5819..db8e8bb6 100644
--- a/modules/nf-core/hisat2/align/main.nf
+++ b/modules/nf-core/hisat2/align/main.nf
@@ -6,12 +6,12 @@ process HISAT2_ALIGN {
     conda "bioconda::hisat2=2.2.1 bioconda::samtools=1.16.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2cdf6bf1e92acbeb9b2834b1c58754167173a410-0' :
-        'quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2cdf6bf1e92acbeb9b2834b1c58754167173a410-0' }"
+        'biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2cdf6bf1e92acbeb9b2834b1c58754167173a410-0' }"
 
     input:
     tuple val(meta), path(reads)
-    path  index
-    path  splicesites
+    tuple val(meta2), path(index)
+    tuple val(meta3), path(splicesites)
 
     output:
     tuple val(meta), path("*.bam")                   , emit: bam
@@ -33,6 +33,7 @@ process HISAT2_ALIGN {
     } else if (meta.strandedness == 'reverse') {
         strandedness = meta.single_end ? '--rna-strandness R' : '--rna-strandness RF'
     }
+    ss = "$splicesites" ? "--known-splicesite-infile $splicesites" : ''
     def seq_center = params.seq_center ? "--rg-id ${prefix} --rg SM:$prefix --rg CN:${params.seq_center.replaceAll('\\s','_')}" : "--rg-id ${prefix} --rg SM:$prefix"
     if (meta.single_end) {
         def unaligned = params.save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
@@ -42,7 +43,7 @@ process HISAT2_ALIGN {
             -x \$INDEX \\
             -U $reads \\
             $strandedness \\
-            --known-splicesite-infile $splicesites \\
+            $ss \\
             --summary-file ${prefix}.hisat2.summary.log \\
             --threads $task.cpus \\
             $seq_center \\
@@ -65,7 +66,7 @@ process HISAT2_ALIGN {
             -1 ${reads[0]} \\
             -2 ${reads[1]} \\
             $strandedness \\
-            --known-splicesite-infile $splicesites \\
+            $ss \\
             --summary-file ${prefix}.hisat2.summary.log \\
             --threads $task.cpus \\
             $seq_center \\
diff --git a/modules/nf-core/hisat2/align/meta.yml b/modules/nf-core/hisat2/align/meta.yml
index 7550aefa..008a9611 100644
--- a/modules/nf-core/hisat2/align/meta.yml
+++ b/modules/nf-core/hisat2/align/meta.yml
@@ -25,10 +25,20 @@ input:
       description: |
         List of input FastQ files of size 1 and 2 for single-end and paired-end data,
         respectively.
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'genome' ]
   - index:
       type: file
       description: HISAT2 genome index file
       pattern: "*.ht2"
+  - meta3:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'genome' ]
   - splicesites:
       type: file
       description: Splices sites in gtf file
@@ -55,3 +65,4 @@ output:
 
 authors:
   - "@ntoda03"
+  - "@ramprasadn"
diff --git a/modules/nf-core/hisat2/build/main.nf b/modules/nf-core/hisat2/build/main.nf
index e0a7f652..90f8efcc 100644
--- a/modules/nf-core/hisat2/build/main.nf
+++ b/modules/nf-core/hisat2/build/main.nf
@@ -7,16 +7,16 @@ process HISAT2_BUILD {
     conda "bioconda::hisat2=2.2.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/hisat2:2.2.1--h1b792b2_3' :
-        'quay.io/biocontainers/hisat2:2.2.1--h1b792b2_3' }"
+        'biocontainers/hisat2:2.2.1--h1b792b2_3' }"
 
     input:
-    path fasta
-    path gtf
-    path splicesites
+    tuple val(meta), path(fasta)
+    tuple val(meta2), path(gtf)
+    tuple val(meta3), path(splicesites)
 
     output:
-    path "hisat2"       , emit: index
-    path "versions.yml" , emit: versions
+    tuple val(meta), path("hisat2") , emit: index
+    path "versions.yml"             , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -37,9 +37,9 @@ process HISAT2_BUILD {
     def hisat2_build_memory = params.hisat2_build_memory ? (params.hisat2_build_memory as nextflow.util.MemoryUnit).toGiga() : 0
     if (avail_mem >= hisat2_build_memory) {
         log.info "[HISAT2 index build] At least ${hisat2_build_memory} GB available, so using splice sites and exons to build HISAT2 index"
-        extract_exons = "hisat2_extract_exons.py $gtf > ${gtf.baseName}.exons.txt"
-        ss = "--ss $splicesites"
-        exon = "--exon ${gtf.baseName}.exons.txt"
+        extract_exons = gtf ? "hisat2_extract_exons.py $gtf > ${gtf.baseName}.exons.txt" : ""
+        ss = splicesites ? "--ss $splicesites" : ""
+        exon = gtf ? "--exon ${gtf.baseName}.exons.txt" : ""
     } else {
         log.info "[HISAT2 index build] Less than ${hisat2_build_memory} GB available, so NOT using splice sites and exons to build HISAT2 index."
         log.info "[HISAT2 index build] Use --hisat2_build_memory [small number] to skip this check."
diff --git a/modules/nf-core/hisat2/build/meta.yml b/modules/nf-core/hisat2/build/meta.yml
index a2e1fd67..e61bf2a3 100644
--- a/modules/nf-core/hisat2/build/meta.yml
+++ b/modules/nf-core/hisat2/build/meta.yml
@@ -15,28 +15,48 @@ tools:
       licence: ["MIT"]
 
 input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'genome' ]
   - fasta:
       type: file
       description: Reference fasta file
       pattern: "*.{fa,fasta,fna}"
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'genome' ]
   - gtf:
       type: file
       description: Reference gtf annotation file
       pattern: "*.{gtf}"
+  - meta3:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'genome' ]
   - splicesites:
       type: file
       description: Splices sites in gtf file
       pattern: "*.{txt}"
 
 output:
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'genome' ]
   - index:
       type: file
       description: HISAT2 genome index file
       pattern: "*.ht2"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
 
 authors:
   - "@ntoda03"
diff --git a/modules/nf-core/hisat2/extractsplicesites/main.nf b/modules/nf-core/hisat2/extractsplicesites/main.nf
index db6cbe6a..a6e59e20 100644
--- a/modules/nf-core/hisat2/extractsplicesites/main.nf
+++ b/modules/nf-core/hisat2/extractsplicesites/main.nf
@@ -6,14 +6,14 @@ process HISAT2_EXTRACTSPLICESITES {
     conda "bioconda::hisat2=2.2.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/hisat2:2.2.1--h1b792b2_3' :
-        'quay.io/biocontainers/hisat2:2.2.1--h1b792b2_3' }"
+        'biocontainers/hisat2:2.2.1--h1b792b2_3' }"
 
     input:
-    path gtf
+    tuple val(meta), path(gtf)
 
     output:
-    path "*.splice_sites.txt", emit: txt
-    path "versions.yml"      , emit: versions
+    tuple val(meta), path("*.splice_sites.txt"), emit: txt
+    path "versions.yml"                        , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/hisat2/extractsplicesites/meta.yml b/modules/nf-core/hisat2/extractsplicesites/meta.yml
index 7dc1bac8..f70de082 100644
--- a/modules/nf-core/hisat2/extractsplicesites/meta.yml
+++ b/modules/nf-core/hisat2/extractsplicesites/meta.yml
@@ -15,12 +15,22 @@ tools:
       licence: ["MIT"]
 
 input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'genome' ]
   - gtf:
       type: file
       description: Reference gtf annotation file
       pattern: "*.{gtf}"
 
 output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'genome' ]
   - versions:
       type: file
       description: File containing software versions
@@ -32,3 +42,4 @@ output:
 
 authors:
   - "@ntoda03"
+  - "@ramprasadn"
diff --git a/modules/nf-core/miranda/main.nf b/modules/nf-core/miranda/main.nf
index 2f32f788..eb7f6e76 100644
--- a/modules/nf-core/miranda/main.nf
+++ b/modules/nf-core/miranda/main.nf
@@ -5,7 +5,7 @@ process MIRANDA {
     conda "bioconda::miranda=3.3a"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/miranda:3.3a--h779adbc_3':
-        'quay.io/biocontainers/miranda:3.3a--h779adbc_3' }"
+        'biocontainers/miranda:3.3a--h779adbc_3' }"
 
     input:
     tuple val(meta), path(query)
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 1fc387be..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' :
-        '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/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf
index 2120cd7d..b75707ec 100644
--- a/modules/nf-core/samtools/flagstat/main.nf
+++ b/modules/nf-core/samtools/flagstat/main.nf
@@ -2,10 +2,10 @@ process SAMTOOLS_FLAGSTAT {
     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(bam), path(bai)
@@ -32,4 +32,15 @@ process SAMTOOLS_FLAGSTAT {
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.flagstat
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/samtools/flagstat/meta.yml b/modules/nf-core/samtools/flagstat/meta.yml
index 95269063..954225df 100644
--- a/modules/nf-core/samtools/flagstat/meta.yml
+++ b/modules/nf-core/samtools/flagstat/meta.yml
@@ -14,7 +14,7 @@ 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/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf
index a7b87d8b..83c7c34b 100644
--- a/modules/nf-core/samtools/idxstats/main.nf
+++ b/modules/nf-core/samtools/idxstats/main.nf
@@ -2,10 +2,10 @@ process SAMTOOLS_IDXSTATS {
     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(bam), path(bai)
@@ -33,4 +33,16 @@ process SAMTOOLS_IDXSTATS {
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    touch ${prefix}.idxstats
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/samtools/idxstats/meta.yml b/modules/nf-core/samtools/idxstats/meta.yml
index 3710ab88..dda87e1e 100644
--- a/modules/nf-core/samtools/idxstats/meta.yml
+++ b/modules/nf-core/samtools/idxstats/meta.yml
@@ -15,7 +15,7 @@ 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/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/sort/main.nf b/modules/nf-core/samtools/sort/main.nf
index 84c167cd..2b7753fd 100644
--- a/modules/nf-core/samtools/sort/main.nf
+++ b/modules/nf-core/samtools/sort/main.nf
@@ -2,10 +2,10 @@ process SAMTOOLS_SORT {
     tag "$meta.id"
     label 'process_medium'
 
-    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(bam)
@@ -23,7 +23,13 @@ process SAMTOOLS_SORT {
     def prefix = task.ext.prefix ?: "${meta.id}"
     if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
-    samtools sort $args -@ $task.cpus -o ${prefix}.bam -T $prefix $bam
+    samtools sort \\
+        $args \\
+        -@ $task.cpus \\
+        -o ${prefix}.bam \\
+        -T $prefix \\
+        $bam
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
diff --git a/modules/nf-core/samtools/sort/meta.yml b/modules/nf-core/samtools/sort/meta.yml
index 09289751..07328431 100644
--- a/modules/nf-core/samtools/sort/meta.yml
+++ b/modules/nf-core/samtools/sort/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/segemehl/align/main.nf b/modules/nf-core/segemehl/align/main.nf
index 3e7fe4c7..768cd384 100644
--- a/modules/nf-core/segemehl/align/main.nf
+++ b/modules/nf-core/segemehl/align/main.nf
@@ -5,7 +5,7 @@ process SEGEMEHL_ALIGN {
     conda "bioconda::segemehl=0.3.4"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/segemehl:0.3.4--hc2ea5fd_5':
-        'quay.io/biocontainers/segemehl:0.3.4--hc2ea5fd_5' }"
+        'biocontainers/segemehl:0.3.4--hc2ea5fd_5' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/nf-core/segemehl/align/meta.yml b/modules/nf-core/segemehl/align/meta.yml
index bb5ac49f..7059cee8 100644
--- a/modules/nf-core/segemehl/align/meta.yml
+++ b/modules/nf-core/segemehl/align/meta.yml
@@ -39,7 +39,7 @@ output:
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
   - results:
-      type: folder
+      type: directory
       description: |
         Directory containing genomic alignments in SAM format
           (please add "-b" flag to task.ext.args for BAM)
diff --git a/modules/nf-core/segemehl/index/main.nf b/modules/nf-core/segemehl/index/main.nf
index f545c448..4a9146fe 100644
--- a/modules/nf-core/segemehl/index/main.nf
+++ b/modules/nf-core/segemehl/index/main.nf
@@ -5,7 +5,7 @@ process SEGEMEHL_INDEX {
     conda "bioconda::segemehl=0.3.4"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/segemehl:0.3.4--hc2ea5fd_5':
-        'quay.io/biocontainers/segemehl:0.3.4--hc2ea5fd_5' }"
+        'biocontainers/segemehl:0.3.4--hc2ea5fd_5' }"
 
     input:
     path fasta
diff --git a/modules/nf-core/segemehl/index/meta.yml b/modules/nf-core/segemehl/index/meta.yml
index a154dad7..de23592e 100644
--- a/modules/nf-core/segemehl/index/meta.yml
+++ b/modules/nf-core/segemehl/index/meta.yml
@@ -1,5 +1,6 @@
 name: "segemehl_index"
 description: Generate genome indices for segemehl align
+keywords:
   - index
   - circrna
   - splicing
diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf
index 0e3bd713..d0e20384 100644
--- a/modules/nf-core/star/align/main.nf
+++ b/modules/nf-core/star/align/main.nf
@@ -5,30 +5,34 @@ process STAR_ALIGN {
     conda "bioconda::star=2.7.10a bioconda::samtools=1.16.1 conda-forge::gawk=5.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' :
-        'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' }"
+        'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' }"
 
     input:
-    tuple val(meta), path(reads)
-    path index
-    path gtf
+    tuple val(meta), path(reads, stageAs: "input*/*")
+    tuple val(meta2), path(index)
+    tuple val(meta3), path(gtf)
     val star_ignore_sjdbgtf
     val seq_platform
     val seq_center
 
     output:
-    tuple val(meta), path('*d.out.bam')       , emit: bam
     tuple val(meta), path('*Log.final.out')   , emit: log_final
     tuple val(meta), path('*Log.out')         , emit: log_out
     tuple val(meta), path('*Log.progress.out'), emit: log_progress
     path  "versions.yml"                      , emit: versions
 
+    tuple val(meta), path('*d.out.bam')              , optional:true, emit: bam
     tuple val(meta), path('*sortedByCoord.out.bam')  , optional:true, emit: bam_sorted
     tuple val(meta), path('*toTranscriptome.out.bam'), optional:true, emit: bam_transcript
     tuple val(meta), path('*Aligned.unsort.out.bam') , optional:true, emit: bam_unsorted
     tuple val(meta), path('*fastq.gz')               , optional:true, emit: fastq
     tuple val(meta), path('*.tab')                   , optional:true, emit: tab
+    tuple val(meta), path('*.SJ.out.tab')            , optional:true, emit: spl_junc_tab
+    tuple val(meta), path('*.ReadsPerGene.out.tab')  , optional:true, emit: read_per_gene_tab
     tuple val(meta), path('*.out.junction')          , optional:true, emit: junction
     tuple val(meta), path('*.out.sam')               , optional:true, emit: sam
+    tuple val(meta), path('*.wig')                   , optional:true, emit: wig
+    tuple val(meta), path('*.bg')                    , optional:true, emit: bedgraph
 
     when:
     task.ext.when == null || task.ext.when
@@ -36,20 +40,23 @@ process STAR_ALIGN {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def reads1 = [], reads2 = []
+    meta.single_end ? [reads].flatten().each{reads1 << it} : reads.eachWithIndex{ v, ix -> ( ix & 1 ? reads2 : reads1) << v }
     def ignore_gtf      = star_ignore_sjdbgtf ? '' : "--sjdbGTFfile $gtf"
     def seq_platform    = seq_platform ? "'PL:$seq_platform'" : ""
-    def seq_center      = seq_center ? "--outSAMattrRGline ID:$prefix 'CN:$seq_center' 'SM:$prefix' $seq_platform " : "--outSAMattrRGline ID:$prefix 'SM:$prefix' $seq_platform "
+    def seq_center      = seq_center ? "'CN:$seq_center'" : ""
+    def attrRG          = args.contains("--outSAMattrRGline") ? "" : "--outSAMattrRGline 'ID:$prefix' $seq_center 'SM:$prefix' $seq_platform"
     def out_sam_type    = (args.contains('--outSAMtype')) ? '' : '--outSAMtype BAM Unsorted'
     def mv_unsorted_bam = (args.contains('--outSAMtype BAM Unsorted SortedByCoordinate')) ? "mv ${prefix}.Aligned.out.bam ${prefix}.Aligned.unsort.out.bam" : ''
     """
     STAR \\
         --genomeDir $index \\
-        --readFilesIn $reads  \\
+        --readFilesIn ${reads1.join(",")} ${reads2.join(",")} \\
         --runThreadN $task.cpus \\
         --outFileNamePrefix $prefix. \\
         $out_sam_type \\
         $ignore_gtf \\
-        $seq_center \\
+        $attrRG \\
         $args
 
     $mv_unsorted_bam
@@ -81,11 +88,16 @@ process STAR_ALIGN {
     touch ${prefix}.sortedByCoord.out.bam
     touch ${prefix}.toTranscriptome.out.bam
     touch ${prefix}.Aligned.unsort.out.bam
+    touch ${prefix}.Aligned.sortedByCoord.out.bam
     touch ${prefix}.unmapped_1.fastq.gz
     touch ${prefix}.unmapped_2.fastq.gz
     touch ${prefix}.tab
+    touch ${prefix}.SJ.out.tab
+    touch ${prefix}.ReadsPerGene.out.tab
     touch ${prefix}.Chimeric.out.junction
     touch ${prefix}.out.sam
+    touch ${prefix}.Signal.UniqueMultiple.str1.out.wig
+    touch ${prefix}.Signal.UniqueMultiple.str1.out.bg
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/star/align/meta.yml b/modules/nf-core/star/align/meta.yml
index 7ee10f1c..3d8fed0c 100644
--- a/modules/nf-core/star/align/meta.yml
+++ b/modules/nf-core/star/align/meta.yml
@@ -25,10 +25,34 @@ input:
       description: |
         List of input FastQ files of size 1 and 2 for single-end and paired-end data,
         respectively.
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'test' ]
   - index:
       type: directory
       description: STAR genome index
       pattern: "star"
+  - meta3:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'test' ]
+  - gtf:
+      type: file
+      description: Annotation GTF file
+      pattern: "*.{gtf}"
+  - star_ignore_sjdbgtf:
+      type: boolean
+      description: Ignore annotation GTF file
+  - seq_platform:
+      type: string
+      description: Sequencing platform
+  - seq_center:
+      type: string
+      description: Sequencing center
+
 output:
   - bam:
       type: file
@@ -74,6 +98,14 @@ output:
       type: file
       description: STAR chimeric junction output file (optional)
       pattern: "*.out.junction"
+  - wig:
+      type: file
+      description: STAR output wiggle format file(s) (optional)
+      pattern: "*.wig"
+  - bedgraph:
+      type: file
+      description: STAR output bedGraph format file(s) (optional)
+      pattern: "*.bg"
 
 authors:
   - "@kevinmenden"
diff --git a/modules/nf-core/star/genomegenerate/main.nf b/modules/nf-core/star/genomegenerate/main.nf
index 91462489..43424042 100644
--- a/modules/nf-core/star/genomegenerate/main.nf
+++ b/modules/nf-core/star/genomegenerate/main.nf
@@ -5,15 +5,15 @@ process STAR_GENOMEGENERATE {
     conda "bioconda::star=2.7.10a bioconda::samtools=1.16.1 conda-forge::gawk=5.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' :
-        'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' }"
+        'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' }"
 
     input:
-    path fasta
-    path gtf
+    tuple val(meta), path(fasta)
+    tuple val(meta2), path(gtf)
 
     output:
-    path "star"        , emit: index
-    path "versions.yml", emit: versions
+    tuple val(meta), path("star")  , emit: index
+    path "versions.yml"            , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/star/genomegenerate/meta.yml b/modules/nf-core/star/genomegenerate/meta.yml
index 8181157a..eba2d9cf 100644
--- a/modules/nf-core/star/genomegenerate/meta.yml
+++ b/modules/nf-core/star/genomegenerate/meta.yml
@@ -15,14 +15,29 @@ tools:
       doi: 10.1093/bioinformatics/bts635
       licence: ["MIT"]
 input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - fasta:
       type: file
       description: Fasta file of the reference genome
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'test' ]
   - gtf:
       type: file
       description: GTF file of the reference genome
 
 output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - index:
       type: directory
       description: Folder containing the star index files
diff --git a/modules/nf-core/stringtie/stringtie/main.nf b/modules/nf-core/stringtie/stringtie/main.nf
index 2d5b035f..d0f8b563 100644
--- a/modules/nf-core/stringtie/stringtie/main.nf
+++ b/modules/nf-core/stringtie/stringtie/main.nf
@@ -5,7 +5,7 @@ process STRINGTIE_STRINGTIE {
     conda "bioconda::stringtie=2.2.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' :
-        'quay.io/biocontainers/stringtie:2.2.1--hecb563c_2' }"
+        'biocontainers/stringtie:2.2.1--hecb563c_2' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf
index ab8bb14e..dcb77ae7 100644
--- a/modules/nf-core/trimgalore/main.nf
+++ b/modules/nf-core/trimgalore/main.nf
@@ -5,19 +5,18 @@ process TRIMGALORE {
     conda "bioconda::trim-galore=0.6.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/trim-galore:0.6.7--hdfd78af_0' :
-        'quay.io/biocontainers/trim-galore:0.6.7--hdfd78af_0' }"
+        'biocontainers/trim-galore:0.6.7--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(reads)
 
     output:
-    tuple val(meta), path("*{trimmed,val}*.fq.gz"), emit: reads
-    tuple val(meta), path("*report.txt")          , emit: log
-    path "versions.yml"                           , emit: versions
-
-    tuple val(meta), path("*unpaired*.fq.gz")     , emit: unpaired, optional: true
-    tuple val(meta), path("*.html")               , emit: html    , optional: true
-    tuple val(meta), path("*.zip")                , emit: zip     , optional: true
+    tuple val(meta), path("*{3prime,5prime,trimmed,val}*.fq.gz"), emit: reads
+    tuple val(meta), path("*report.txt")                        , emit: log     , optional: true
+    tuple val(meta), path("*unpaired*.fq.gz")                   , emit: unpaired, optional: true
+    tuple val(meta), path("*.html")                             , emit: html    , optional: true
+    tuple val(meta), path("*.zip")                              , emit: zip     , optional: true
+    path "versions.yml"                                         , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -38,10 +37,12 @@ process TRIMGALORE {
     // Added soft-links to original fastqs for consistent naming in MultiQC
     def prefix = task.ext.prefix ?: "${meta.id}"
     if (meta.single_end) {
+        def args_list = args.split("\\s(?=--)").toList()
+        args_list.removeAll { it.toLowerCase().contains('_r2 ') }
         """
         [ ! -f  ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
         trim_galore \\
-            $args \\
+            ${args_list.join(' ')} \\
             --cores $cores \\
             --gzip \\
             ${prefix}.fastq.gz
diff --git a/modules/nf-core/trimgalore/meta.yml b/modules/nf-core/trimgalore/meta.yml
index 439f566d..f84c4d77 100644
--- a/modules/nf-core/trimgalore/meta.yml
+++ b/modules/nf-core/trimgalore/meta.yml
@@ -36,7 +36,7 @@ output:
       description: |
         List of input adapter trimmed FastQ files of size 1 and 2 for
         single-end and paired-end data, respectively.
-      pattern: "*.{fq.gz}"
+      pattern: "*{3prime,5prime,trimmed,val}*.fq.gz"
   - unpaired:
       type: file
       description: |
diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/main.nf b/subworkflows/nf-core/bam_sort_stats_samtools/main.nf
index 617871fe..fc1c652b 100644
--- a/subworkflows/nf-core/bam_sort_stats_samtools/main.nf
+++ b/subworkflows/nf-core/bam_sort_stats_samtools/main.nf
@@ -9,7 +9,7 @@ include { BAM_STATS_SAMTOOLS } from '../bam_stats_samtools/main'
 workflow BAM_SORT_STATS_SAMTOOLS {
     take:
     ch_bam   // channel: [ val(meta), [ bam ] ]
-    ch_fasta // channel: [ fasta ]
+    ch_fasta // channel: [ val(meta), path(fasta) ]
 
     main:
 
diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/meta.yml b/subworkflows/nf-core/bam_sort_stats_samtools/meta.yml
index 131065be..69c16be4 100644
--- a/subworkflows/nf-core/bam_sort_stats_samtools/meta.yml
+++ b/subworkflows/nf-core/bam_sort_stats_samtools/meta.yml
@@ -1,3 +1,4 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: bam_sort_stats_samtools
 description: Sort SAM/BAM/CRAM file
 keywords:
@@ -5,12 +6,13 @@ keywords:
   - bam
   - sam
   - cram
-modules:
+components:
   - samtools/sort
   - samtools/index
   - samtools/stats
   - samtools/idxstats
   - samtools/flagstat
+  - bam_stats_samtools
 input:
   - meta:
       type: map
diff --git a/subworkflows/nf-core/bam_stats_samtools/main.nf b/subworkflows/nf-core/bam_stats_samtools/main.nf
index cfcc48dd..44d4c010 100644
--- a/subworkflows/nf-core/bam_stats_samtools/main.nf
+++ b/subworkflows/nf-core/bam_stats_samtools/main.nf
@@ -8,25 +8,25 @@ include { SAMTOOLS_FLAGSTAT } from '../../../modules/nf-core/samtools/flagstat/m
 
 workflow BAM_STATS_SAMTOOLS {
     take:
-    bam_bai // channel: [ val(meta), [ bam/cram ], [bai/csi] ]
-    fasta   // channel: [ fasta ]
+    ch_bam_bai // channel: [ val(meta), path(bam), path(bai) ]
+    ch_fasta   // channel: [ val(meta), path(fasta) ]
 
     main:
     ch_versions = Channel.empty()
 
-    SAMTOOLS_STATS ( bam_bai, fasta )
+    SAMTOOLS_STATS ( ch_bam_bai, ch_fasta )
     ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions)
 
-    SAMTOOLS_FLAGSTAT ( bam_bai )
+    SAMTOOLS_FLAGSTAT ( ch_bam_bai )
     ch_versions = ch_versions.mix(SAMTOOLS_FLAGSTAT.out.versions)
 
-    SAMTOOLS_IDXSTATS ( bam_bai )
+    SAMTOOLS_IDXSTATS ( ch_bam_bai )
     ch_versions = ch_versions.mix(SAMTOOLS_IDXSTATS.out.versions)
 
     emit:
-    stats    = SAMTOOLS_STATS.out.stats       // channel: [ val(meta), [ stats ] ]
-    flagstat = SAMTOOLS_FLAGSTAT.out.flagstat // channel: [ val(meta), [ flagstat ] ]
-    idxstats = SAMTOOLS_IDXSTATS.out.idxstats // channel: [ val(meta), [ idxstats ] ]
+    stats    = SAMTOOLS_STATS.out.stats       // channel: [ val(meta), path(stats) ]
+    flagstat = SAMTOOLS_FLAGSTAT.out.flagstat // channel: [ val(meta), path(flagstat) ]
+    idxstats = SAMTOOLS_IDXSTATS.out.idxstats // channel: [ val(meta), path(idxstats) ]
 
-    versions = ch_versions                    // channel: [ versions.yml ]
+    versions = ch_versions                    // channel: [ path(versions.yml) ]
 }
diff --git a/subworkflows/nf-core/bam_stats_samtools/meta.yml b/subworkflows/nf-core/bam_stats_samtools/meta.yml
index 5252b0e4..87863b11 100644
--- a/subworkflows/nf-core/bam_stats_samtools/meta.yml
+++ b/subworkflows/nf-core/bam_stats_samtools/meta.yml
@@ -1,3 +1,4 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: bam_stats_samtools
 description: Produces comprehensive statistics from SAM/BAM/CRAM file
 keywords:
@@ -6,49 +7,35 @@ keywords:
   - bam
   - sam
   - cram
-modules:
+components:
   - samtools/stats
   - samtools/idxstats
   - samtools/flagstat
 input:
-  - meta:
-      type: map
+  - ch_bam_bai:
       description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - bam:
-      type: file
-      description: BAM/CRAM/SAM file
-      pattern: "*.{bam,cram,sam}"
-  - bai:
-      type: file
-      description: Index for BAM/CRAM/SAM file
-      pattern: "*.{bai,crai,sai}"
-  - fasta:
-      type: file
-      description: Reference genome fasta file
-      pattern: "*.{fasta,fa}"
-output:
-  - meta:
-      type: map
+        The input channel containing the BAM/CRAM and it's index
+        Structure: [ val(meta), path(bam), path(bai) ]
+  - ch_fasta:
       description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
+        Reference genome fasta file
+        Structure: [ path(fasta) ]
+output:
   - stats:
-      type: file
-      description: File containing samtools stats output
-      pattern: "*.{stats}"
+      description: |
+        File containing samtools stats output
+        Structure: [ val(meta), path(stats) ]
   - flagstat:
-      type: file
-      description: File containing samtools flagstat output
-      pattern: "*.{flagstat}"
+      description: |
+        File containing samtools flagstat output
+        Structure: [ val(meta), path(flagstat) ]
   - idxstats:
-      type: file
-      description: File containing samtools idxstats output
-      pattern: "*.{idxstats}"
+      description: |
+        File containing samtools idxstats output
+        Structure: [ val(meta), path(idxstats)]
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      description: |
+        Files containing software versions
+        Structure: [ path(versions.yml) ]
 authors:
   - "@drpatelh"