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Merge pull request #209 from nf-core/module-version-bumps

Update all modules to make templaite compatible
This commit is contained in:
James A. Fellows Yates 2022-12-23 23:17:17 +01:00 committed by GitHub
commit 6dcf619518
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GPG key ID: 4AEE18F83AFDEB23
42 changed files with 124 additions and 106 deletions

View file

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

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@ -2,7 +2,7 @@ process ADAPTERREMOVAL {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::adapterremoval=2.3.2" : null) conda "bioconda::adapterremoval=2.3.2"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/adapterremoval:2.3.2--hb7ba0dd_0' : 'https://depot.galaxyproject.org/singularity/adapterremoval:2.3.2--hb7ba0dd_0' :
'quay.io/biocontainers/adapterremoval:2.3.2--hb7ba0dd_0' }" 'quay.io/biocontainers/adapterremoval:2.3.2--hb7ba0dd_0' }"

View file

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

View file

@ -2,14 +2,14 @@ process BOWTIE2_ALIGN {
tag "$meta.id" tag "$meta.id"
label "process_high" 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: input:
tuple val(meta), path(reads) tuple val(meta) , path(reads)
path index tuple val(meta2), path(index)
val save_unaligned val save_unaligned
val sort_bam val sort_bam
@ -40,8 +40,8 @@ process BOWTIE2_ALIGN {
def samtools_command = sort_bam ? 'sort' : 'view' 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 [ -z "\$INDEX" ] && echo "Bowtie2 index files not found" 1>&2 && exit 1
bowtie2 \\ bowtie2 \\

View file

@ -27,6 +27,11 @@ input:
description: | description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data, List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively. respectively.
- meta2:
type: map
description: |
Groovy Map containing reference information
e.g. [ id:'test', single_end:false ]
- index: - index:
type: file type: file
description: Bowtie2 genome index files description: Bowtie2 genome index files

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@ -2,17 +2,17 @@ process BOWTIE2_BUILD {
tag "$fasta" tag "$fasta"
label 'process_high' label 'process_high'
conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4' : null) conda "bioconda::bowtie2=2.4.4"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bowtie2:2.4.4--py39hbb4e92a_0' : 'https://depot.galaxyproject.org/singularity/bowtie2:2.4.4--py39hbb4e92a_0' :
'quay.io/biocontainers/bowtie2:2.4.4--py39hbb4e92a_0' }" 'quay.io/biocontainers/bowtie2:2.4.4--py39hbb4e92a_0' }"
input: input:
path fasta tuple val(meta), path(fasta)
output: output:
path 'bowtie2' , emit: index tuple val(meta), path('bowtie2') , emit: index
path "versions.yml" , emit: versions path "versions.yml" , emit: versions
when: when:
task.ext.when == null || task.ext.when task.ext.when == null || task.ext.when

View file

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

View file

@ -4,7 +4,7 @@ process BRACKEN_BRACKEN {
// WARN: Version information not provided by tool on CLI. // WARN: Version information not provided by tool on CLI.
// Please update version string below when bumping container versions. // Please update version string below when bumping container versions.
conda (params.enable_conda ? "bioconda::bracken=2.7" : null) conda "bioconda::bracken=2.7"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bracken:2.7--py39hc16433a_0': 'https://depot.galaxyproject.org/singularity/bracken:2.7--py39hc16433a_0':
'quay.io/biocontainers/bracken:2.7--py39hc16433a_0' }" 'quay.io/biocontainers/bracken:2.7--py39hc16433a_0' }"

View file

@ -2,7 +2,7 @@ process BRACKEN_COMBINEBRACKENOUTPUTS {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::bracken=2.7" : null) conda "bioconda::bracken=2.7"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bracken:2.7--py39hc16433a_0': 'https://depot.galaxyproject.org/singularity/bracken:2.7--py39hc16433a_0':
'quay.io/biocontainers/bracken:2.7--py39hc16433a_0' }" 'quay.io/biocontainers/bracken:2.7--py39hc16433a_0' }"

View file

@ -2,7 +2,7 @@ process CAT_FASTQ {
tag "$meta.id" tag "$meta.id"
label 'process_single' label 'process_single'
conda (params.enable_conda ? "conda-forge::sed=4.7" : null) conda "conda-forge::sed=4.7"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'ubuntu:20.04' }" 'ubuntu:20.04' }"

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@ -2,7 +2,7 @@ process CENTRIFUGE_CENTRIFUGE {
tag "$meta.id" tag "$meta.id"
label 'process_high' label 'process_high'
conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null) conda "bioconda::centrifuge=1.0.4_beta"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4_beta--h9a82719_6' : 'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4_beta--h9a82719_6' :
'quay.io/biocontainers/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'" : '' def sam_output = sam_format ? "--out-fmt 'sam'" : ''
""" """
## we add "-no-name ._" to ensure silly Mac OSX metafiles files aren't included ## 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 \\ centrifuge \\
-x \$db_name \\ -x \$db_name \\
-p $task.cpus \\ -p $task.cpus \\

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@ -2,7 +2,7 @@ process CENTRIFUGE_KREPORT {
tag "$meta.id" tag "$meta.id"
label 'process_single' label 'process_single'
conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null) conda "bioconda::centrifuge=1.0.4_beta"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4_beta--h9a82719_6': 'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4_beta--h9a82719_6':
'quay.io/biocontainers/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 args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${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 centrifuge-kreport -x \$db_name ${report} > ${prefix}.txt
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml

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@ -2,7 +2,7 @@ process DIAMOND_BLASTX {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null) conda "bioconda::diamond=2.0.15"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' : 'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' :
'quay.io/biocontainers/diamond:2.0.15--hb97b32f_0' }" 'quay.io/biocontainers/diamond:2.0.15--hb97b32f_0' }"
@ -46,7 +46,7 @@ process DIAMOND_BLASTX {
break break
} }
""" """
DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'` DB=`find -L ./ -name "*.dmnd" | sed 's/\\.dmnd\$//'`
diamond \\ diamond \\
blastx \\ blastx \\

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@ -3,7 +3,7 @@ process FALCO {
label 'process_single' label 'process_single'
conda (params.enable_conda ? "bioconda::falco=1.2.1" : null) conda "bioconda::falco=1.2.1"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/falco:1.2.1--h867801b_3': 'https://depot.galaxyproject.org/singularity/falco:1.2.1--h867801b_3':
'quay.io/biocontainers/falco:1.2.1--h867801b_3' }" 'quay.io/biocontainers/falco:1.2.1--h867801b_3' }"

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@ -2,7 +2,7 @@ process FASTP {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? 'bioconda::fastp=0.23.2' : null) conda "bioconda::fastp=0.23.2"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/fastp:0.23.2--h79da9fb_0' : 'https://depot.galaxyproject.org/singularity/fastp:0.23.2--h79da9fb_0' :
'quay.io/biocontainers/fastp:0.23.2--h79da9fb_0' }" 'quay.io/biocontainers/fastp:0.23.2--h79da9fb_0' }"

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@ -2,7 +2,7 @@ process FILTLONG {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::filtlong=0.2.1" : null) conda "bioconda::filtlong=0.2.1"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/filtlong:0.2.1--h9a82719_0' : 'https://depot.galaxyproject.org/singularity/filtlong:0.2.1--h9a82719_0' :
'quay.io/biocontainers/filtlong:0.2.1--h9a82719_0' }" 'quay.io/biocontainers/filtlong:0.2.1--h9a82719_0' }"

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@ -2,7 +2,7 @@ process GUNZIP {
tag "$archive" tag "$archive"
label 'process_single' label 'process_single'
conda (params.enable_conda ? "conda-forge::sed=4.7" : null) conda "conda-forge::sed=4.7"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'ubuntu:20.04' }" 'ubuntu:20.04' }"

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@ -2,7 +2,7 @@ process KAIJU_KAIJU {
tag "$meta.id" tag "$meta.id"
label 'process_high' label 'process_high'
conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null) conda "bioconda::kaiju=1.8.2"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1': 'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1':
'quay.io/biocontainers/kaiju:1.8.2--h5b5514e_1' }" 'quay.io/biocontainers/kaiju:1.8.2--h5b5514e_1' }"

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@ -2,7 +2,7 @@ process KAIJU_KAIJU2KRONA {
tag "$meta.id" tag "$meta.id"
label 'process_single' label 'process_single'
conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null) conda "bioconda::kaiju=1.8.2"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1': 'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1':
'quay.io/biocontainers/kaiju:1.8.2--h5b5514e_1' }" 'quay.io/biocontainers/kaiju:1.8.2--h5b5514e_1' }"

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@ -2,7 +2,7 @@ process KAIJU_KAIJU2TABLE {
tag "$meta.id" tag "$meta.id"
label 'process_single' label 'process_single'
conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null) conda "bioconda::kaiju=1.8.2"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1': 'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1':
'quay.io/biocontainers/kaiju:1.8.2--h2e03b76_0' }" 'quay.io/biocontainers/kaiju:1.8.2--h2e03b76_0' }"

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@ -2,7 +2,7 @@ process KRAKEN2_KRAKEN2 {
tag "$meta.id" tag "$meta.id"
label 'process_high' 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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0' : 'https://depot.galaxyproject.org/singularity/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0' :
'quay.io/biocontainers/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0' }" 'quay.io/biocontainers/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0' }"

View file

@ -1,7 +1,7 @@
process KRAKENTOOLS_COMBINEKREPORTS { process KRAKENTOOLS_COMBINEKREPORTS {
label 'process_single' label 'process_single'
conda (params.enable_conda ? "bioconda::krakentools=1.2" : null) conda "bioconda::krakentools=1.2"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/krakentools:1.2--pyh5e36f6f_0': 'https://depot.galaxyproject.org/singularity/krakentools:1.2--pyh5e36f6f_0':
'quay.io/biocontainers/krakentools:1.2--pyh5e36f6f_0' }" 'quay.io/biocontainers/krakentools:1.2--pyh5e36f6f_0' }"

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@ -3,7 +3,7 @@ process KRAKENTOOLS_KREPORT2KRONA {
label 'process_single' label 'process_single'
// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. // 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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/krakentools:1.2--pyh5e36f6f_0': 'https://depot.galaxyproject.org/singularity/krakentools:1.2--pyh5e36f6f_0':
'quay.io/biocontainers/krakentools:1.2--pyh5e36f6f_0' }" 'quay.io/biocontainers/krakentools:1.2--pyh5e36f6f_0' }"

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@ -3,7 +3,7 @@ process KRONA_KTIMPORTTAXONOMY {
label 'process_single' label 'process_single'
// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. // 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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/krona:2.8--pl5262hdfd78af_2' : 'https://depot.galaxyproject.org/singularity/krona:2.8--pl5262hdfd78af_2' :
'quay.io/biocontainers/krona:2.8--pl5262hdfd78af_2' }" 'quay.io/biocontainers/krona:2.8--pl5262hdfd78af_2' }"

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@ -2,7 +2,7 @@ process KRONA_KTIMPORTTEXT {
tag "$meta.id" tag "$meta.id"
label 'process_single' label 'process_single'
conda (params.enable_conda ? "bioconda::krona=2.8.1" : null) conda "bioconda::krona=2.8.1"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/krona:2.8.1--pl5321hdfd78af_1': 'https://depot.galaxyproject.org/singularity/krona:2.8.1--pl5321hdfd78af_1':
'quay.io/biocontainers/krona:2.8.1--pl5321hdfd78af_1' }" 'quay.io/biocontainers/krona:2.8.1--pl5321hdfd78af_1' }"

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@ -2,7 +2,7 @@ process MALT_RUN {
tag "$meta.id" tag "$meta.id"
label 'process_high' label 'process_high'
conda (params.enable_conda ? "bioconda::malt=0.61" : null) conda "bioconda::malt=0.61"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/malt:0.61--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/malt:0.61--hdfd78af_0' :
'quay.io/biocontainers/malt:0.61--hdfd78af_0' }" 'quay.io/biocontainers/malt:0.61--hdfd78af_0' }"

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@ -2,7 +2,7 @@ process MEGAN_RMA2INFO {
tag "$meta.id" tag "$meta.id"
label 'process_single' label 'process_single'
conda (params.enable_conda ? "bioconda::megan=6.21.7" : null) conda "bioconda::megan=6.21.7"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/megan:6.21.7--h9ee0642_0': 'https://depot.galaxyproject.org/singularity/megan:6.21.7--h9ee0642_0':
'quay.io/biocontainers/megan:6.21.7--h9ee0642_0' }" 'quay.io/biocontainers/megan:6.21.7--h9ee0642_0' }"

View file

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

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

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@ -2,7 +2,8 @@ process MINIMAP2_ALIGN {
tag "$meta.id" tag "$meta.id"
label 'process_medium' 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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' : 'https://depot.galaxyproject.org/singularity/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' :
'quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' }" 'quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' }"
@ -25,7 +26,6 @@ process MINIMAP2_ALIGN {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${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 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 cigar_paf = cigar_paf_format && !bam_format ? "-c" : ''
def set_cigar_bam = cigar_bam && bam_format ? "-L" : '' def set_cigar_bam = cigar_bam && bam_format ? "-L" : ''
@ -33,8 +33,8 @@ process MINIMAP2_ALIGN {
minimap2 \\ minimap2 \\
$args \\ $args \\
-t $task.cpus \\ -t $task.cpus \\
$reference \\ "${reference ?: reads}" \\
$input_reads \\ "$reads" \\
$cigar_paf \\ $cigar_paf \\
$set_cigar_bam \\ $set_cigar_bam \\
$bam_output $bam_output

View file

@ -1,10 +1,11 @@
process MINIMAP2_INDEX { process MINIMAP2_INDEX {
label 'process_medium' 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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ 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: input:
tuple val(meta), path(fasta) tuple val(meta), path(fasta)

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

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@ -2,7 +2,7 @@ process MOTUS_MERGE {
tag "$meta.id" tag "$meta.id"
label 'process_single' label 'process_single'
conda (params.enable_conda ? "bioconda::motus=3.0.3" : null) conda "bioconda::motus=3.0.3"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/motus:3.0.3--pyhdfd78af_0': 'https://depot.galaxyproject.org/singularity/motus:3.0.3--pyhdfd78af_0':
'quay.io/biocontainers/motus:3.0.3--pyhdfd78af_0' }" 'quay.io/biocontainers/motus:3.0.3--pyhdfd78af_0' }"

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@ -2,7 +2,7 @@ process MOTUS_PROFILE {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::motus=3.0.3" : null) conda "bioconda::motus=3.0.3"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/motus:3.0.3--pyhdfd78af_0': 'https://depot.galaxyproject.org/singularity/motus:3.0.3--pyhdfd78af_0':
'quay.io/biocontainers/motus:3.0.3--pyhdfd78af_0' }" 'quay.io/biocontainers/motus:3.0.3--pyhdfd78af_0' }"

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@ -2,7 +2,7 @@ process PORECHOP_PORECHOP {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::porechop=0.2.4" : null) conda "bioconda::porechop=0.2.4"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/porechop:0.2.4--py39h7cff6ad_2' : 'https://depot.galaxyproject.org/singularity/porechop:0.2.4--py39h7cff6ad_2' :
'quay.io/biocontainers/porechop:0.2.4--py39h7cff6ad_2' }" 'quay.io/biocontainers/porechop:0.2.4--py39h7cff6ad_2' }"

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@ -2,7 +2,7 @@ process PRINSEQPLUSPLUS {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::prinseq-plus-plus=1.2.3" : null) conda "bioconda::prinseq-plus-plus=1.2.3"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/prinseq-plus-plus:1.2.3--hc90279e_1': 'https://depot.galaxyproject.org/singularity/prinseq-plus-plus:1.2.3--hc90279e_1':
'quay.io/biocontainers/prinseq-plus-plus:1.2.3--hc90279e_1' }" 'quay.io/biocontainers/prinseq-plus-plus:1.2.3--hc90279e_1' }"

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

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

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

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

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@ -2,7 +2,7 @@ process UNTAR {
tag "$archive" tag "$archive"
label 'process_single' label 'process_single'
conda (params.enable_conda ? "conda-forge::sed=4.7" : null) conda "conda-forge::sed=4.7"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'ubuntu:20.04' }" 'ubuntu:20.04' }"

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