millironx/taxprofiler
1
0
Fork 0
mirror of https://github.com/MillironX/taxprofiler.git synced 2024-11-13 07:23:10 +00:00
Code Issues Releases Packages Activity

Updata taxpasta

Browse source
This commit is contained in:
sofstam 2023-03-13 08:58:59 +01:00
parent b93c7082b8
commit 213f4e4f23
3 changed files with 132 additions and 48 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

170
modules.json
View file

@ -8,214 +8,298 @@
"adapterremoval": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"bbmap/bbduk": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"bowtie2/align": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"bowtie2/build": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"bracken/bracken": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"bracken/combinebrackenoutputs": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"cat/fastq": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"centrifuge/centrifuge": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"centrifuge/kreport": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"custom/dumpsoftwareversions": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"diamond/blastx": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"falco": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/falco/falco.diff"
},
"fastp": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"fastqc": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"filtlong": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"gunzip": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"kaiju/kaiju": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"kaiju/kaiju2krona": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"kaiju/kaiju2table": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"kraken2/kraken2": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"krakentools/combinekreports": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"krakentools/kreport2krona": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"krakenuniq/preloadedkrakenuniq": {
"branch": "master",
"git_sha": "a6eb17f65b3ee5761c25c075a6166c9f76733cee",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"krona/ktimporttaxonomy": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"krona/ktimporttext": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"malt/run": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"megan/rma2info": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"metaphlan3/mergemetaphlantables": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"metaphlan3/metaphlan3": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"minimap2/align": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"minimap2/index": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"motus/merge": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"motus/profile": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"multiqc": {
"branch": "master",
"git_sha": "ee80d14721e76e2e079103b8dcd5d57129e584ba",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"porechop/porechop": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/porechop/porechop/porechop-porechop.diff"
},
"prinseqplusplus": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"samtools/bam2fq": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"samtools/index": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"samtools/stats": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"samtools/view": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"taxpasta/merge": {
"branch": "master",
"git_sha": "fe58454add6225d2b7468e6d72a3a1f6a3149638",
"installed_by": ["modules"]
"git_sha": "ffa9641ee18f88aff974257cb50ba3cf8f7d143c",
"installed_by": [
"modules"
]
},
"untar": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
}
}
}

6
modules/nf-core/taxpasta/merge/main.nf generated
View file

@ -2,10 +2,10 @@ process TAXPASTA_MERGE {
tag "$meta.id"
label 'process_single'
conda "bioconda::taxpasta=0.2.0"
conda "bioconda::taxpasta=0.2.3"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/taxpasta:0.2.0--pyhdfd78af_0':
'quay.io/biocontainers/taxpasta:0.2.0--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/taxpasta:0.2.3--pyhdfd78af_0':
'quay.io/biocontainers/taxpasta:0.2.3--pyhdfd78af_0' }"
input:

2
modules/nf-core/taxpasta/merge/meta.yml generated
View file

@ -14,7 +14,7 @@ tools:
homepage: "https://taxpasta.readthedocs.io/"
documentation: "https://taxpasta.readthedocs.io/"
tool_dev_url: "https://github.com/taxprofiler/taxpasta"
doi: ""
licence: "['Apache-2.0']"
input: