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Code Issues Releases Packages Activity

update all modules to make templaite compatible

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This commit is contained in:
James Fellows Yates 2022-12-23 17:23:05 +01:00
parent 75a95d5ed8
commit e5c6db96c8
42 changed files with 124 additions and 106 deletions
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74
modules.json
View file

@ -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"]
}
}

2
modules/nf-core/adapterremoval/main.nf generated
View file

@ -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' }"

8
modules/nf-core/bbmap/bbduk/main.nf generated
View file

@ -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' :
'quay.io/biocontainers/bbmap:38.90--he522d1c_1' }"
'https://depot.galaxyproject.org/singularity/bbmap:39.01--h5c4e2a8_0':
'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
"""
}

14
modules/nf-core/bowtie2/align/main.nf generated
View file

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

5
modules/nf-core/bowtie2/align/meta.yml generated
View file

@ -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

6
modules/nf-core/bowtie2/build/main.nf generated
View file

@ -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:

10
modules/nf-core/bowtie2/build/meta.yml generated
View file

@ -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

2
modules/nf-core/bracken/bracken/main.nf generated
View file

@ -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' }"

2
modules/nf-core/bracken/combinebrackenoutputs/main.nf generated
View file

@ -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' }"

2
modules/nf-core/cat/fastq/main.nf generated
View file

@ -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' }"

4
modules/nf-core/centrifuge/centrifuge/main.nf generated
View file

@ -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 \\

4
modules/nf-core/centrifuge/kreport/main.nf generated
View file

@ -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

4
modules/nf-core/diamond/blastx/main.nf generated
View file

@ -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 \\

2
modules/nf-core/falco/main.nf generated
View file

@ -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' }"

2
modules/nf-core/fastp/main.nf generated
View file

@ -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' }"

2
modules/nf-core/filtlong/main.nf generated
View file

@ -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' }"

2
modules/nf-core/gunzip/main.nf generated
View file

@ -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' }"

2
modules/nf-core/kaiju/kaiju/main.nf generated
View file

@ -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' }"

2
modules/nf-core/kaiju/kaiju2krona/main.nf generated
View file

@ -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' }"

2
modules/nf-core/kaiju/kaiju2table/main.nf generated
View file

@ -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' }"

2
modules/nf-core/kraken2/kraken2/main.nf generated
View file

@ -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' }"

2
modules/nf-core/krakentools/combinekreports/main.nf generated
View file

@ -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' }"

2
modules/nf-core/krakentools/kreport2krona/main.nf generated
View file

@ -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' }"

2
modules/nf-core/krona/ktimporttaxonomy/main.nf generated
View file

@ -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' }"

2
modules/nf-core/krona/ktimporttext/main.nf generated
View file

@ -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' }"

2
modules/nf-core/malt/run/main.nf generated
View file

@ -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' }"

2
modules/nf-core/megan/rma2info/main.nf generated
View file

@ -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' }"

2
modules/nf-core/metaphlan3/mergemetaphlantables/main.nf generated
View file

@ -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' }"

2
modules/nf-core/metaphlan3/metaphlan3/main.nf generated
View file

@ -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' }"

8
modules/nf-core/minimap2/align/main.nf generated
View file

@ -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 \\
$input_reads \\
"${reference ?: reads}" \\
"$reads" \\
$cigar_paf \\
$set_cigar_bam \\
$bam_output

7
modules/nf-core/minimap2/index/main.nf generated
View file

@ -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' :
'quay.io/biocontainers/minimap2:2.21--h5bf99c6_0' }"
'https://depot.galaxyproject.org/singularity/minimap2:2.24--h7132678_1' :
'quay.io/biocontainers/minimap2:2.24--h7132678_1' }"
input:
tuple val(meta), path(fasta)

2
modules/nf-core/minimap2/index/meta.yml generated
View file

@ -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"

2
modules/nf-core/motus/merge/main.nf generated
View file

@ -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' }"

2
modules/nf-core/motus/profile/main.nf generated
View file

@ -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' }"

2
modules/nf-core/porechop/porechop/main.nf generated
View file

@ -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' }"

2
modules/nf-core/prinseqplusplus/main.nf generated
View file

@ -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' }"

6
modules/nf-core/samtools/bam2fq/main.nf generated
View file

@ -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' :
'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' :
'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }"
input:
tuple val(meta), path(inputbam)

6
modules/nf-core/samtools/index/main.nf generated
View file

@ -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' :
'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' :
'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }"
input:
tuple val(meta), path(input)

6
modules/nf-core/samtools/stats/main.nf generated
View file

@ -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' :
'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' :
'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }"
input:
tuple val(meta), path(input), path(input_index)

10
modules/nf-core/samtools/view/main.nf generated
View file

@ -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' :
'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' :
'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}":

2
modules/nf-core/untar/main.nf generated
View file

@ -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' }"

2
subworkflows/local/shortread_hostremoval.nf
View file

@ -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()