mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-25 17:59:55 +00:00
Update taxpasta/merge module
This commit is contained in:
sofstam
parent
b93c7082b8
commit
58f09ed659
2 changed files with 131 additions and 47 deletions
170
modules.json
170
modules.json
|
|
@ -8,214 +8,298 @@
|
||||||
"adapterremoval": {
|
"adapterremoval": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"bbmap/bbduk": {
|
"bbmap/bbduk": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"bowtie2/align": {
|
"bowtie2/align": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"bowtie2/build": {
|
"bowtie2/build": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"bracken/bracken": {
|
"bracken/bracken": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"bracken/combinebrackenoutputs": {
|
"bracken/combinebrackenoutputs": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"cat/fastq": {
|
"cat/fastq": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"centrifuge/centrifuge": {
|
"centrifuge/centrifuge": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"centrifuge/kreport": {
|
"centrifuge/kreport": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"custom/dumpsoftwareversions": {
|
"custom/dumpsoftwareversions": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"diamond/blastx": {
|
"diamond/blastx": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"falco": {
|
"falco": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"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": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"fastqc": {
|
"fastqc": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"filtlong": {
|
"filtlong": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"gunzip": {
|
"gunzip": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"kaiju/kaiju": {
|
"kaiju/kaiju": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"kaiju/kaiju2krona": {
|
"kaiju/kaiju2krona": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"kaiju/kaiju2table": {
|
"kaiju/kaiju2table": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"kraken2/kraken2": {
|
"kraken2/kraken2": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"krakentools/combinekreports": {
|
"krakentools/combinekreports": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"krakentools/kreport2krona": {
|
"krakentools/kreport2krona": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"krakenuniq/preloadedkrakenuniq": {
|
"krakenuniq/preloadedkrakenuniq": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "a6eb17f65b3ee5761c25c075a6166c9f76733cee",
|
"git_sha": "a6eb17f65b3ee5761c25c075a6166c9f76733cee",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"krona/ktimporttaxonomy": {
|
"krona/ktimporttaxonomy": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"krona/ktimporttext": {
|
"krona/ktimporttext": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"malt/run": {
|
"malt/run": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"megan/rma2info": {
|
"megan/rma2info": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"metaphlan3/mergemetaphlantables": {
|
"metaphlan3/mergemetaphlantables": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"metaphlan3/metaphlan3": {
|
"metaphlan3/metaphlan3": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"minimap2/align": {
|
"minimap2/align": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"minimap2/index": {
|
"minimap2/index": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"motus/merge": {
|
"motus/merge": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"motus/profile": {
|
"motus/profile": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"multiqc": {
|
"multiqc": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "ee80d14721e76e2e079103b8dcd5d57129e584ba",
|
"git_sha": "ee80d14721e76e2e079103b8dcd5d57129e584ba",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"porechop/porechop": {
|
"porechop/porechop": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"],
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
],
|
||||||
"patch": "modules/nf-core/porechop/porechop/porechop-porechop.diff"
|
"patch": "modules/nf-core/porechop/porechop/porechop-porechop.diff"
|
||||||
},
|
},
|
||||||
"prinseqplusplus": {
|
"prinseqplusplus": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"samtools/bam2fq": {
|
"samtools/bam2fq": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"samtools/index": {
|
"samtools/index": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"samtools/stats": {
|
"samtools/stats": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"samtools/view": {
|
"samtools/view": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"taxpasta/merge": {
|
"taxpasta/merge": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "fe58454add6225d2b7468e6d72a3a1f6a3149638",
|
"git_sha": "23ff77e576b3930923229e7430dcdd0b51012c1d",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
},
|
},
|
||||||
"untar": {
|
"untar": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||||
"installed_by": ["modules"]
|
"installed_by": [
|
||||||
|
"modules"
|
||||||
|
]
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
|
||||||
6
modules/nf-core/taxpasta/merge/main.nf
generated
6
modules/nf-core/taxpasta/merge/main.nf
generated
|
|
@ -2,10 +2,10 @@ process TAXPASTA_MERGE {
|
||||||
tag "$meta.id"
|
tag "$meta.id"
|
||||||
label 'process_single'
|
label 'process_single'
|
||||||
|
|
||||||
conda "bioconda::taxpasta=0.2.0"
|
conda "bioconda::taxpasta=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/taxpasta:0.2.0--pyhdfd78af_0':
|
'https://depot.galaxyproject.org/singularity/taxpasta:0.2.1--pyhdfd78af_0':
|
||||||
'quay.io/biocontainers/taxpasta:0.2.0--pyhdfd78af_0' }"
|
'quay.io/biocontainers/taxpasta:0.2.1--pyhdfd78af_0' }"
|
||||||
|
|
||||||
|
|
||||||
input:
|
input:
|
||||||
|
|
|
||||||
Loading…
Reference in a new issue