update all modules to make templaite compatible

modules.json

@@ -7,47 +7,47 @@
                 "nf-core": {
                     "adapterremoval": {
                         "branch": "master",
-                        "git_sha": "ce7cf27e377fdacf7ebe8e75903ec70405ea1659",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "bbmap/bbduk": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "bowtie2/align": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "bowtie2/build": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "bracken/bracken": {
                         "branch": "master",
-                        "git_sha": "8cab56516076b23c6f8eb1ac20ba4ce9692c85e1",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "bracken/combinebrackenoutputs": {
                         "branch": "master",
-                        "git_sha": "9c87d5fdad182590a370ea43a4ecebd200a6f6fb",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "cat/fastq": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "centrifuge/centrifuge": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "centrifuge/kreport": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "custom/dumpsoftwareversions": {
@@ -57,18 +57,18 @@
                     },
                     "diamond/blastx": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "falco": {
                         "branch": "master",
-                        "git_sha": "fc959214036403ad83efe7a41d43d0606c445cda",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/falco/falco.diff"
                     },
                     "fastp": {
                         "branch": "master",
-                        "git_sha": "1e49f31e93c56a3832833eef90a02d3cde5a3f7e",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {
@@ -78,42 +78,42 @@
                     },
                     "filtlong": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "kaiju/kaiju": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "kaiju/kaiju2krona": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "kaiju/kaiju2table": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "kraken2/kraken2": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "krakentools/combinekreports": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "krakentools/kreport2krona": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "krakenuniq/preloadedkrakenuniq": {
@@ -123,52 +123,52 @@
                     },
                     "krona/ktimporttaxonomy": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "krona/ktimporttext": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "malt/run": {
                         "branch": "master",
-                        "git_sha": "6d9712f03ec2de8264a50ee4541a617e1e063b51",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "megan/rma2info": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "metaphlan3/mergemetaphlantables": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "metaphlan3/metaphlan3": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "minimap2/align": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "minimap2/index": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "motus/merge": {
                         "branch": "master",
-                        "git_sha": "3fce766123e71e82fb384db7d07b59180baa9ee9",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "motus/profile": {
                         "branch": "master",
-                        "git_sha": "3fce766123e71e82fb384db7d07b59180baa9ee9",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
@@ -178,37 +178,37 @@
                     },
                     "porechop/porechop": {
                         "branch": "master",
-                        "git_sha": "2a4e85eb81875a572bb58133e37f84ba3cc484d7",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "prinseqplusplus": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "samtools/bam2fq": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "samtools/stats": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "samtools/view": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     }
                 }

modules/nf-core/adapterremoval/main.nf

@@ -2,7 +2,7 @@ process ADAPTERREMOVAL {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::adapterremoval=2.3.2" : null)
+    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' }"

modules/nf-core/bbmap/bbduk/main.nf

@@ -2,10 +2,10 @@ process BBMAP_BBDUK {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::bbmap=38.90" : null)
+    conda "bioconda::bbmap=39.01"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bbmap:38.90--he522d1c_1' :
+        'https://depot.galaxyproject.org/singularity/bbmap:39.01--h5c4e2a8_0':
-        'quay.io/biocontainers/bbmap:38.90--he522d1c_1' }"
+        'quay.io/biocontainers/bbmap:39.01--h5c4e2a8_0' }"
 
     input:
     tuple val(meta), path(reads)
@@ -37,7 +37,7 @@ process BBMAP_BBDUK {
         &> ${prefix}.bbduk.log
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        bbmap: \$(bbversion.sh)
+        bbmap: \$(bbversion.sh | grep -v "Duplicate cpuset")
     END_VERSIONS
     """
 }

modules/nf-core/bowtie2/align/main.nf

@@ -2,14 +2,14 @@ process BOWTIE2_ALIGN {
     tag "$meta.id"
     label "process_high"
 
-    conda (params.enable_conda ? "bioconda::bowtie2=2.4.4 bioconda::samtools=1.15.1 conda-forge::pigz=2.6" : null)
+    conda "bioconda::bowtie2=2.4.4 bioconda::samtools=1.16.1 conda-forge::pigz=2.6"
-    container "${ workflow.containerEngine == "singularity" && !task.ext.singularity_pull_docker_container ?
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        "https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0" :
+        'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' :
-        "quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0" }"
+        'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' }"
 
     input:
-    tuple val(meta), path(reads)
+    tuple val(meta) , path(reads)
-    path  index
+    tuple val(meta2), path(index)
     val   save_unaligned
     val   sort_bam
 
@@ -40,8 +40,8 @@ process BOWTIE2_ALIGN {
     def samtools_command = sort_bam ? 'sort' : 'view'
 
     """
-    INDEX=`find -L ./ -name "*.rev.1.bt2" | sed "s/.rev.1.bt2//"`
+    INDEX=`find -L ./ -name "*.rev.1.bt2" | sed "s/\\.rev.1.bt2\$//"`
-    [ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed "s/.rev.1.bt2l//"`
+    [ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed "s/\\.rev.1.bt2l\$//"`
     [ -z "\$INDEX" ] && echo "Bowtie2 index files not found" 1>&2 && exit 1
 
     bowtie2 \\

modules/nf-core/bowtie2/align/meta.yml

@@ -27,6 +27,11 @@ 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', single_end:false ]
   - index:
       type: file
       description: Bowtie2 genome index files

modules/nf-core/bowtie2/build/main.nf

@@ -2,16 +2,16 @@ process BOWTIE2_BUILD {
     tag "$fasta"
     label 'process_high'
 
-    conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4' : null)
+    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' }"
 
     input:
-    path fasta
+    tuple val(meta), path(fasta)
 
     output:
-    path 'bowtie2'      , emit: index
+    tuple val(meta), path('bowtie2')    , emit: index
     path "versions.yml"                 , emit: versions
 
     when:

modules/nf-core/bowtie2/build/meta.yml

@@ -16,10 +16,20 @@ tools:
       doi: 10.1038/nmeth.1923
       licence: ["GPL-3.0-or-later"]
 input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'test', single_end:false ]
   - fasta:
       type: file
       description: Input genome fasta file
 output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'test', single_end:false ]
   - index:
       type: file
       description: Bowtie2 genome index files

modules/nf-core/bracken/bracken/main.nf

@@ -4,7 +4,7 @@ process BRACKEN_BRACKEN {
 
     // WARN: Version information not provided by tool on CLI.
     // Please update version string below when bumping container versions.
-    conda (params.enable_conda ? "bioconda::bracken=2.7" : null)
+    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' }"

modules/nf-core/bracken/combinebrackenoutputs/main.nf

@@ -2,7 +2,7 @@ process BRACKEN_COMBINEBRACKENOUTPUTS {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::bracken=2.7" : null)
+    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' }"

modules/nf-core/cat/fastq/main.nf

@@ -2,7 +2,7 @@ process CAT_FASTQ {
     tag "$meta.id"
     label 'process_single'
 
-    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
+    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' }"

modules/nf-core/centrifuge/centrifuge/main.nf

@@ -2,7 +2,7 @@ process CENTRIFUGE_CENTRIFUGE {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null)
+    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' }"
@@ -41,7 +41,7 @@ process CENTRIFUGE_CENTRIFUGE {
     def sam_output = sam_format ? "--out-fmt 'sam'" : ''
     """
     ## we add "-no-name ._" to ensure silly Mac OSX metafiles files aren't included
-    db_name=`find -L ${db} -name "*.1.cf" -not -name "._*"  | sed 's/.1.cf//'`
+    db_name=`find -L ${db} -name "*.1.cf" -not -name "._*"  | sed 's/\\.1.cf\$//'`
     centrifuge \\
         -x \$db_name \\
         -p $task.cpus \\

modules/nf-core/centrifuge/kreport/main.nf

@@ -2,7 +2,7 @@ process CENTRIFUGE_KREPORT {
     tag "$meta.id"
     label 'process_single'
 
-    conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null)
+    conda "bioconda::centrifuge=1.0.4_beta"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4_beta--h9a82719_6':
         'quay.io/biocontainers/centrifuge:1.0.4_beta--h9a82719_6' }"
@@ -22,7 +22,7 @@ process CENTRIFUGE_KREPORT {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    db_name=`find -L ${db} -name "*.1.cf" -not -name "._*"  | sed 's/.1.cf//'`
+    db_name=`find -L ${db} -name "*.1.cf" -not -name "._*"  | sed 's/\\.1.cf\$//'`
     centrifuge-kreport -x \$db_name ${report} > ${prefix}.txt
 
     cat <<-END_VERSIONS > versions.yml

modules/nf-core/diamond/blastx/main.nf

@@ -2,7 +2,7 @@ process DIAMOND_BLASTX {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null)
+    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' }"
@@ -46,7 +46,7 @@ process DIAMOND_BLASTX {
             break
     }
     """
-    DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'`
+    DB=`find -L ./ -name "*.dmnd" | sed 's/\\.dmnd\$//'`
 
     diamond \\
         blastx \\

modules/nf-core/falco/main.nf

@@ -3,7 +3,7 @@ process FALCO {
     label 'process_single'
 
 
-    conda (params.enable_conda ? "bioconda::falco=1.2.1" : null)
+    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' }"

modules/nf-core/fastp/main.nf

@@ -2,7 +2,7 @@ process FASTP {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::fastp=0.23.2' : null)
+    conda "bioconda::fastp=0.23.2"
     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' }"

modules/nf-core/filtlong/main.nf

@@ -2,7 +2,7 @@ process FILTLONG {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::filtlong=0.2.1" : null)
+    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' }"

modules/nf-core/gunzip/main.nf

@@ -2,7 +2,7 @@ process GUNZIP {
     tag "$archive"
     label 'process_single'
 
-    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
+    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' }"

modules/nf-core/kaiju/kaiju/main.nf

@@ -2,7 +2,7 @@ process KAIJU_KAIJU {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null)
+    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' }"

modules/nf-core/kaiju/kaiju2krona/main.nf

@@ -2,7 +2,7 @@ process KAIJU_KAIJU2KRONA {
     tag "$meta.id"
     label 'process_single'
 
-    conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null)
+    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' }"

modules/nf-core/kaiju/kaiju2table/main.nf

@@ -2,7 +2,7 @@ process KAIJU_KAIJU2TABLE {
     tag "$meta.id"
     label 'process_single'
 
-    conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null)
+    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' }"

modules/nf-core/kraken2/kraken2/main.nf

@@ -2,7 +2,7 @@ process KRAKEN2_KRAKEN2 {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? 'bioconda::kraken2=2.1.2 conda-forge::pigz=2.6' : null)
+    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' }"

modules/nf-core/krakentools/combinekreports/main.nf

@@ -1,7 +1,7 @@
 process KRAKENTOOLS_COMBINEKREPORTS {
     label 'process_single'
 
-    conda (params.enable_conda ? "bioconda::krakentools=1.2" : null)
+    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' }"

modules/nf-core/krakentools/kreport2krona/main.nf

@@ -3,7 +3,7 @@ process KRAKENTOOLS_KREPORT2KRONA {
     label 'process_single'
 
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
-    conda (params.enable_conda ? "bioconda::krakentools=1.2" : null)
+    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' }"

modules/nf-core/krona/ktimporttaxonomy/main.nf

@@ -3,7 +3,7 @@ process KRONA_KTIMPORTTAXONOMY {
     label 'process_single'
 
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
-    conda (params.enable_conda ? "bioconda::krona=2.8" : null)
+    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' }"

modules/nf-core/krona/ktimporttext/main.nf

@@ -2,7 +2,7 @@ process KRONA_KTIMPORTTEXT {
     tag "$meta.id"
     label 'process_single'
 
-    conda (params.enable_conda ? "bioconda::krona=2.8.1" : null)
+    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' }"

modules/nf-core/malt/run/main.nf

@@ -2,7 +2,7 @@ process MALT_RUN {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? "bioconda::malt=0.61" : null)
+    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' }"

modules/nf-core/megan/rma2info/main.nf

@@ -2,7 +2,7 @@ process MEGAN_RMA2INFO {
     tag "$meta.id"
     label 'process_single'
 
-    conda (params.enable_conda ? "bioconda::megan=6.21.7" : null)
+    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' }"

modules/nf-core/metaphlan3/mergemetaphlantables/main.nf

@@ -1,7 +1,7 @@
 process METAPHLAN3_MERGEMETAPHLANTABLES {
     label 'process_single'
 
-    conda (params.enable_conda ? 'bioconda::metaphlan=3.0.12' : null)
+    conda "bioconda::metaphlan=3.0.12"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/metaphlan:3.0.12--pyhb7b1952_0' :
         'quay.io/biocontainers/metaphlan:3.0.12--pyhb7b1952_0' }"

modules/nf-core/metaphlan3/metaphlan3/main.nf

@@ -2,7 +2,7 @@ process METAPHLAN3_METAPHLAN3 {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? 'bioconda::metaphlan=3.0.12' : null)
+    conda "bioconda::metaphlan=3.0.12"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/metaphlan:3.0.12--pyhb7b1952_0' :
         'quay.io/biocontainers/metaphlan:3.0.12--pyhb7b1952_0' }"

modules/nf-core/minimap2/align/main.nf

@@ -2,7 +2,8 @@ process MINIMAP2_ALIGN {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::minimap2=2.21 bioconda::samtools=1.12' : null)
+    // Note: the versions here need to match the versions used in the mulled container below and minimap2/index
+    conda "bioconda::minimap2=2.24 bioconda::samtools=1.14"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' :
         'quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' }"
@@ -25,7 +26,6 @@ process MINIMAP2_ALIGN {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def input_reads = meta.single_end ? "$reads" : "${reads[0]} ${reads[1]}"
     def bam_output = bam_format ? "-a | samtools sort | samtools view -@ ${task.cpus} -b -h -o ${prefix}.bam" : "-o ${prefix}.paf"
     def cigar_paf = cigar_paf_format && !bam_format ? "-c" : ''
     def set_cigar_bam = cigar_bam && bam_format ? "-L" : ''
@@ -33,8 +33,8 @@ process MINIMAP2_ALIGN {
     minimap2 \\
         $args \\
         -t $task.cpus \\
-        $reference \\
+        "${reference ?: reads}" \\
-        $input_reads \\
+        "$reads" \\
         $cigar_paf \\
         $set_cigar_bam \\
         $bam_output

modules/nf-core/minimap2/index/main.nf

@@ -1,10 +1,11 @@
 process MINIMAP2_INDEX {
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::minimap2=2.21' : null)
+    // Note: the versions here need to match the versions used in minimap2/align
+    conda "bioconda::minimap2=2.24"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/minimap2:2.21--h5bf99c6_0' :
+        'https://depot.galaxyproject.org/singularity/minimap2:2.24--h7132678_1' :
-        'quay.io/biocontainers/minimap2:2.21--h5bf99c6_0' }"
+        'quay.io/biocontainers/minimap2:2.24--h7132678_1' }"
 
     input:
     tuple val(meta), path(fasta)

modules/nf-core/minimap2/index/meta.yml

@@ -27,7 +27,7 @@ output:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - mmi:
+  - index:
       type: file
       description: Minimap2 fasta index.
       pattern: "*.mmi"

modules/nf-core/motus/merge/main.nf

@@ -2,7 +2,7 @@ process MOTUS_MERGE {
     tag "$meta.id"
     label 'process_single'
 
-    conda (params.enable_conda ? "bioconda::motus=3.0.3" : null)
+    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' }"

modules/nf-core/motus/profile/main.nf

@@ -2,7 +2,7 @@ process MOTUS_PROFILE {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::motus=3.0.3" : null)
+    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' }"

modules/nf-core/porechop/porechop/main.nf

@@ -2,7 +2,7 @@ process PORECHOP_PORECHOP {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::porechop=0.2.4" : null)
+    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' }"

modules/nf-core/prinseqplusplus/main.nf

@@ -2,7 +2,7 @@ process PRINSEQPLUSPLUS {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::prinseq-plus-plus=1.2.3" : null)
+    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' }"

modules/nf-core/samtools/bam2fq/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_BAM2FQ {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
+    conda "bioconda::samtools=1.16.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' :
-        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
+        'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }"
 
     input:
     tuple val(meta), path(inputbam)

modules/nf-core/samtools/index/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_INDEX {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
+    conda "bioconda::samtools=1.16.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' :
-        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
+        'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }"
 
     input:
     tuple val(meta), path(input)

modules/nf-core/samtools/stats/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_STATS {
     tag "$meta.id"
     label 'process_single'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
+    conda "bioconda::samtools=1.16.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' :
-        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
+        'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }"
 
     input:
     tuple val(meta), path(input), path(input_index)

modules/nf-core/samtools/view/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_VIEW {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
+    conda "bioconda::samtools=1.16.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' :
-        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
+        'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }"
 
     input:
     tuple val(meta), path(input), path(index)
@@ -26,6 +26,7 @@ process SAMTOOLS_VIEW {
 
     script:
     def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def reference = fasta ? "--reference ${fasta}" : ""
     def readnames = qname ? "--qname-file ${qname}": ""
@@ -42,7 +43,8 @@ process SAMTOOLS_VIEW {
         ${readnames} \\
         $args \\
         -o ${prefix}.${file_type} \\
-        $input
+        $input \\
+        $args2
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/untar/main.nf

@@ -2,7 +2,7 @@ process UNTAR {
     tag "$archive"
     label 'process_single'
 
-    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
+    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' }"

subworkflows/local/shortread_hostremoval.nf

@@ -19,7 +19,7 @@ workflow SHORTREAD_HOSTREMOVAL {
     ch_multiqc_files  = Channel.empty()
 
     if ( !params.shortread_hostremoval_index ) {
-        ch_bowtie2_index = BOWTIE2_BUILD ( reference ).index
+        ch_bowtie2_index = BOWTIE2_BUILD ( [ [], reference ] ).index
         ch_versions      = ch_versions.mix( BOWTIE2_BUILD.out.versions )
     } else {
         ch_bowtie2_index = index.first()