From e5c6db96c89b2c2862aab8ee403949c9b1ce635d Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Fri, 23 Dec 2022 17:23:05 +0100 Subject: [PATCH] update all modules to make templaite compatible --- modules.json | 74 +++++++++---------- modules/nf-core/adapterremoval/main.nf | 2 +- modules/nf-core/bbmap/bbduk/main.nf | 8 +- modules/nf-core/bowtie2/align/main.nf | 16 ++-- modules/nf-core/bowtie2/align/meta.yml | 5 ++ modules/nf-core/bowtie2/build/main.nf | 8 +- modules/nf-core/bowtie2/build/meta.yml | 10 +++ modules/nf-core/bracken/bracken/main.nf | 2 +- .../bracken/combinebrackenoutputs/main.nf | 2 +- modules/nf-core/cat/fastq/main.nf | 2 +- modules/nf-core/centrifuge/centrifuge/main.nf | 4 +- modules/nf-core/centrifuge/kreport/main.nf | 4 +- modules/nf-core/diamond/blastx/main.nf | 4 +- modules/nf-core/falco/main.nf | 2 +- modules/nf-core/fastp/main.nf | 2 +- modules/nf-core/filtlong/main.nf | 2 +- modules/nf-core/gunzip/main.nf | 2 +- modules/nf-core/kaiju/kaiju/main.nf | 2 +- modules/nf-core/kaiju/kaiju2krona/main.nf | 2 +- modules/nf-core/kaiju/kaiju2table/main.nf | 2 +- modules/nf-core/kraken2/kraken2/main.nf | 2 +- .../krakentools/combinekreports/main.nf | 2 +- .../nf-core/krakentools/kreport2krona/main.nf | 2 +- .../nf-core/krona/ktimporttaxonomy/main.nf | 2 +- modules/nf-core/krona/ktimporttext/main.nf | 2 +- modules/nf-core/malt/run/main.nf | 2 +- modules/nf-core/megan/rma2info/main.nf | 2 +- .../metaphlan3/mergemetaphlantables/main.nf | 2 +- modules/nf-core/metaphlan3/metaphlan3/main.nf | 2 +- modules/nf-core/minimap2/align/main.nf | 8 +- modules/nf-core/minimap2/index/main.nf | 7 +- modules/nf-core/minimap2/index/meta.yml | 2 +- modules/nf-core/motus/merge/main.nf | 2 +- modules/nf-core/motus/profile/main.nf | 2 +- modules/nf-core/porechop/porechop/main.nf | 2 +- modules/nf-core/prinseqplusplus/main.nf | 2 +- modules/nf-core/samtools/bam2fq/main.nf | 6 +- modules/nf-core/samtools/index/main.nf | 6 +- modules/nf-core/samtools/stats/main.nf | 6 +- modules/nf-core/samtools/view/main.nf | 10 ++- modules/nf-core/untar/main.nf | 2 +- subworkflows/local/shortread_hostremoval.nf | 2 +- 42 files changed, 124 insertions(+), 106 deletions(-) diff --git a/modules.json b/modules.json index ab944fa..0ce4614 100644 --- a/modules.json +++ b/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"] } } diff --git a/modules/nf-core/adapterremoval/main.nf b/modules/nf-core/adapterremoval/main.nf index 643c141..324b4b0 100644 --- a/modules/nf-core/adapterremoval/main.nf +++ b/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' }" diff --git a/modules/nf-core/bbmap/bbduk/main.nf b/modules/nf-core/bbmap/bbduk/main.nf index 0ae005e..f33d937 100644 --- a/modules/nf-core/bbmap/bbduk/main.nf +++ b/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' : - '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 """ } diff --git a/modules/nf-core/bowtie2/align/main.nf b/modules/nf-core/bowtie2/align/main.nf index c74e376..3d85186 100644 --- a/modules/nf-core/bowtie2/align/main.nf +++ b/modules/nf-core/bowtie2/align/main.nf @@ -2,14 +2,14 @@ process BOWTIE2_ALIGN { tag "$meta.id" label "process_high" - conda (params.enable_conda ? "bioconda::bowtie2=2.4.4 bioconda::samtools=1.15.1 conda-forge::pigz=2.6" : null) - container "${ 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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' : + 'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' }" input: - tuple val(meta), path(reads) - path index + tuple val(meta) , path(reads) + tuple val(meta2), path(index) val save_unaligned val sort_bam @@ -40,8 +40,8 @@ process BOWTIE2_ALIGN { def samtools_command = sort_bam ? 'sort' : 'view' """ - INDEX=`find -L ./ -name "*.rev.1.bt2" | sed "s/.rev.1.bt2//"` - [ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed "s/.rev.1.bt2l//"` + INDEX=`find -L ./ -name "*.rev.1.bt2" | sed "s/\\.rev.1.bt2\$//"` + [ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed "s/\\.rev.1.bt2l\$//"` [ -z "\$INDEX" ] && echo "Bowtie2 index files not found" 1>&2 && exit 1 bowtie2 \\ diff --git a/modules/nf-core/bowtie2/align/meta.yml b/modules/nf-core/bowtie2/align/meta.yml index 42ba0f9..c8e9a00 100644 --- a/modules/nf-core/bowtie2/align/meta.yml +++ b/modules/nf-core/bowtie2/align/meta.yml @@ -27,6 +27,11 @@ input: description: | List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] - index: type: file description: Bowtie2 genome index files diff --git a/modules/nf-core/bowtie2/build/main.nf b/modules/nf-core/bowtie2/build/main.nf index a4da62d..551893a 100644 --- a/modules/nf-core/bowtie2/build/main.nf +++ b/modules/nf-core/bowtie2/build/main.nf @@ -2,17 +2,17 @@ process BOWTIE2_BUILD { tag "$fasta" label 'process_high' - conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4' : null) + conda "bioconda::bowtie2=2.4.4" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bowtie2:2.4.4--py39hbb4e92a_0' : 'quay.io/biocontainers/bowtie2:2.4.4--py39hbb4e92a_0' }" input: - path fasta + tuple val(meta), path(fasta) output: - path 'bowtie2' , emit: index - path "versions.yml" , emit: versions + tuple val(meta), path('bowtie2') , emit: index + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/bowtie2/build/meta.yml b/modules/nf-core/bowtie2/build/meta.yml index 2da9a21..0240224 100644 --- a/modules/nf-core/bowtie2/build/meta.yml +++ b/modules/nf-core/bowtie2/build/meta.yml @@ -16,10 +16,20 @@ tools: doi: 10.1038/nmeth.1923 licence: ["GPL-3.0-or-later"] input: + - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] - fasta: type: file description: Input genome fasta file output: + - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] - index: type: file description: Bowtie2 genome index files diff --git a/modules/nf-core/bracken/bracken/main.nf b/modules/nf-core/bracken/bracken/main.nf index ac7d1af..ddb2d6f 100644 --- a/modules/nf-core/bracken/bracken/main.nf +++ b/modules/nf-core/bracken/bracken/main.nf @@ -4,7 +4,7 @@ process BRACKEN_BRACKEN { // WARN: Version information not provided by tool on CLI. // Please update version string below when bumping container versions. - conda (params.enable_conda ? "bioconda::bracken=2.7" : null) + conda "bioconda::bracken=2.7" container "${ 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' }" diff --git a/modules/nf-core/bracken/combinebrackenoutputs/main.nf b/modules/nf-core/bracken/combinebrackenoutputs/main.nf index 977030c..c57e6a8 100644 --- a/modules/nf-core/bracken/combinebrackenoutputs/main.nf +++ b/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' }" diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf index 4fa365d..8a0b560 100644 --- a/modules/nf-core/cat/fastq/main.nf +++ b/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' }" diff --git a/modules/nf-core/centrifuge/centrifuge/main.nf b/modules/nf-core/centrifuge/centrifuge/main.nf index 3d23fc9..26c91ee 100644 --- a/modules/nf-core/centrifuge/centrifuge/main.nf +++ b/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 $task.cpus \\ diff --git a/modules/nf-core/centrifuge/kreport/main.nf b/modules/nf-core/centrifuge/kreport/main.nf index 8e5b741..6fcee55 100644 --- a/modules/nf-core/centrifuge/kreport/main.nf +++ b/modules/nf-core/centrifuge/kreport/main.nf @@ -2,7 +2,7 @@ process CENTRIFUGE_KREPORT { tag "$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} > ${prefix}.txt cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/diamond/blastx/main.nf b/modules/nf-core/diamond/blastx/main.nf index 1f4ff25..e305b57 100644 --- a/modules/nf-core/diamond/blastx/main.nf +++ b/modules/nf-core/diamond/blastx/main.nf @@ -2,7 +2,7 @@ process DIAMOND_BLASTX { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null) + conda "bioconda::diamond=2.0.15" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' : 'quay.io/biocontainers/diamond:2.0.15--hb97b32f_0' }" @@ -46,7 +46,7 @@ process DIAMOND_BLASTX { break } """ - DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'` + DB=`find -L ./ -name "*.dmnd" | sed 's/\\.dmnd\$//'` diamond \\ blastx \\ diff --git a/modules/nf-core/falco/main.nf b/modules/nf-core/falco/main.nf index b279c57..f0f131e 100644 --- a/modules/nf-core/falco/main.nf +++ b/modules/nf-core/falco/main.nf @@ -3,7 +3,7 @@ process FALCO { label 'process_single' - conda (params.enable_conda ? "bioconda::falco=1.2.1" : null) + conda "bioconda::falco=1.2.1" container "${ 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' }" diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf index 207258a..e1ed928 100644 --- a/modules/nf-core/fastp/main.nf +++ b/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' }" diff --git a/modules/nf-core/filtlong/main.nf b/modules/nf-core/filtlong/main.nf index afaa938..e920fef 100644 --- a/modules/nf-core/filtlong/main.nf +++ b/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' }" diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf index fa6ba26..d906034 100644 --- a/modules/nf-core/gunzip/main.nf +++ b/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' }" diff --git a/modules/nf-core/kaiju/kaiju/main.nf b/modules/nf-core/kaiju/kaiju/main.nf index ae8f99e..1d24e64 100644 --- a/modules/nf-core/kaiju/kaiju/main.nf +++ b/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' }" diff --git a/modules/nf-core/kaiju/kaiju2krona/main.nf b/modules/nf-core/kaiju/kaiju2krona/main.nf index 3f35ce7..fb8da1e 100644 --- a/modules/nf-core/kaiju/kaiju2krona/main.nf +++ b/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' }" diff --git a/modules/nf-core/kaiju/kaiju2table/main.nf b/modules/nf-core/kaiju/kaiju2table/main.nf index 8648d56..52bd643 100644 --- a/modules/nf-core/kaiju/kaiju2table/main.nf +++ b/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' }" diff --git a/modules/nf-core/kraken2/kraken2/main.nf b/modules/nf-core/kraken2/kraken2/main.nf index 43a1679..1b9e760 100644 --- a/modules/nf-core/kraken2/kraken2/main.nf +++ b/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' }" diff --git a/modules/nf-core/krakentools/combinekreports/main.nf b/modules/nf-core/krakentools/combinekreports/main.nf index fdcc245..b4ea504 100644 --- a/modules/nf-core/krakentools/combinekreports/main.nf +++ b/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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/krakentools:1.2--pyh5e36f6f_0': 'quay.io/biocontainers/krakentools:1.2--pyh5e36f6f_0' }" diff --git a/modules/nf-core/krakentools/kreport2krona/main.nf b/modules/nf-core/krakentools/kreport2krona/main.nf index 8ed46f1..df439ac 100644 --- a/modules/nf-core/krakentools/kreport2krona/main.nf +++ b/modules/nf-core/krakentools/kreport2krona/main.nf @@ -3,7 +3,7 @@ process KRAKENTOOLS_KREPORT2KRONA { label 'process_single' // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. - conda (params.enable_conda ? "bioconda::krakentools=1.2" : null) + conda "bioconda::krakentools=1.2" container "${ 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' }" diff --git a/modules/nf-core/krona/ktimporttaxonomy/main.nf b/modules/nf-core/krona/ktimporttaxonomy/main.nf index 79c01d7..3a76f66 100644 --- a/modules/nf-core/krona/ktimporttaxonomy/main.nf +++ b/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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/krona:2.8--pl5262hdfd78af_2' : 'quay.io/biocontainers/krona:2.8--pl5262hdfd78af_2' }" diff --git a/modules/nf-core/krona/ktimporttext/main.nf b/modules/nf-core/krona/ktimporttext/main.nf index edf7aab..53f3026 100644 --- a/modules/nf-core/krona/ktimporttext/main.nf +++ b/modules/nf-core/krona/ktimporttext/main.nf @@ -2,7 +2,7 @@ process KRONA_KTIMPORTTEXT { tag "$meta.id" label 'process_single' - conda (params.enable_conda ? "bioconda::krona=2.8.1" : null) + conda "bioconda::krona=2.8.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/krona:2.8.1--pl5321hdfd78af_1': 'quay.io/biocontainers/krona:2.8.1--pl5321hdfd78af_1' }" diff --git a/modules/nf-core/malt/run/main.nf b/modules/nf-core/malt/run/main.nf index 2e75b4c..83987d9 100644 --- a/modules/nf-core/malt/run/main.nf +++ b/modules/nf-core/malt/run/main.nf @@ -2,7 +2,7 @@ process MALT_RUN { tag "$meta.id" label 'process_high' - conda (params.enable_conda ? "bioconda::malt=0.61" : null) + conda "bioconda::malt=0.61" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/malt:0.61--hdfd78af_0' : 'quay.io/biocontainers/malt:0.61--hdfd78af_0' }" diff --git a/modules/nf-core/megan/rma2info/main.nf b/modules/nf-core/megan/rma2info/main.nf index 9c6a094..a37a4d6 100644 --- a/modules/nf-core/megan/rma2info/main.nf +++ b/modules/nf-core/megan/rma2info/main.nf @@ -2,7 +2,7 @@ process MEGAN_RMA2INFO { tag "$meta.id" label 'process_single' - conda (params.enable_conda ? "bioconda::megan=6.21.7" : null) + conda "bioconda::megan=6.21.7" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/megan:6.21.7--h9ee0642_0': 'quay.io/biocontainers/megan:6.21.7--h9ee0642_0' }" diff --git a/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf b/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf index 7c37eca..5be6e4f 100644 --- a/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf +++ b/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf @@ -1,7 +1,7 @@ process METAPHLAN3_MERGEMETAPHLANTABLES { label 'process_single' - conda (params.enable_conda ? 'bioconda::metaphlan=3.0.12' : null) + conda "bioconda::metaphlan=3.0.12" container "${ 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' }" diff --git a/modules/nf-core/metaphlan3/metaphlan3/main.nf b/modules/nf-core/metaphlan3/metaphlan3/main.nf index 1453466..34f8705 100644 --- a/modules/nf-core/metaphlan3/metaphlan3/main.nf +++ b/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' }" diff --git a/modules/nf-core/minimap2/align/main.nf b/modules/nf-core/minimap2/align/main.nf index 08ac6ee..430dbab 100644 --- a/modules/nf-core/minimap2/align/main.nf +++ b/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 \\ - $input_reads \\ + "${reference ?: reads}" \\ + "$reads" \\ $cigar_paf \\ $set_cigar_bam \\ $bam_output diff --git a/modules/nf-core/minimap2/index/main.nf b/modules/nf-core/minimap2/index/main.nf index 25e9429..73dd4ee 100644 --- a/modules/nf-core/minimap2/index/main.nf +++ b/modules/nf-core/minimap2/index/main.nf @@ -1,10 +1,11 @@ process MINIMAP2_INDEX { label 'process_medium' - conda (params.enable_conda ? 'bioconda::minimap2=2.21' : null) + // Note: the versions here need to match the versions used in minimap2/align + conda "bioconda::minimap2=2.24" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/minimap2:2.21--h5bf99c6_0' : - '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) diff --git a/modules/nf-core/minimap2/index/meta.yml b/modules/nf-core/minimap2/index/meta.yml index 603c651..b58f35c 100644 --- a/modules/nf-core/minimap2/index/meta.yml +++ b/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" diff --git a/modules/nf-core/motus/merge/main.nf b/modules/nf-core/motus/merge/main.nf index 5041cf0..23d2a49 100644 --- a/modules/nf-core/motus/merge/main.nf +++ b/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' }" diff --git a/modules/nf-core/motus/profile/main.nf b/modules/nf-core/motus/profile/main.nf index 8a76250..1491c46 100644 --- a/modules/nf-core/motus/profile/main.nf +++ b/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' }" diff --git a/modules/nf-core/porechop/porechop/main.nf b/modules/nf-core/porechop/porechop/main.nf index f946417..5267910 100644 --- a/modules/nf-core/porechop/porechop/main.nf +++ b/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' }" diff --git a/modules/nf-core/prinseqplusplus/main.nf b/modules/nf-core/prinseqplusplus/main.nf index ebd8c58..f6c1c5b 100644 --- a/modules/nf-core/prinseqplusplus/main.nf +++ b/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' }" diff --git a/modules/nf-core/samtools/bam2fq/main.nf b/modules/nf-core/samtools/bam2fq/main.nf index 9301d1d..0b06352 100644 --- a/modules/nf-core/samtools/bam2fq/main.nf +++ b/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' : - '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) diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index e04e63e..8b95687 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -2,10 +2,10 @@ process SAMTOOLS_INDEX { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) + conda "bioconda::samtools=1.16.1" container "${ 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) diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index 9b0c386..0a2a364 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/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' : - '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) diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf index 94da5d6..729c85e 100644 --- a/modules/nf-core/samtools/view/main.nf +++ b/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' : - '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}": diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index 71eea7b..16bccc9 100644 --- a/modules/nf-core/untar/main.nf +++ b/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' }" diff --git a/subworkflows/local/shortread_hostremoval.nf b/subworkflows/local/shortread_hostremoval.nf index 04c8556..71ebb08 100644 --- a/subworkflows/local/shortread_hostremoval.nf +++ b/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()