Deepbgcdownload (#2010)

* deepbgc_download first version

* with test.yml

* Apply suggestions from code review

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Apply suggestions from code review

* delete trailing whitespace main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
This commit is contained in:
louperelo 2022-09-05 16:51:21 +02:00 committed by GitHub
parent 30102f3b20
commit 04dfb65335
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@ -0,0 +1,31 @@
process DEEPBGC_DOWNLOAD {
tag "download"
label 'process_low'
conda (params.enable_conda ? "bioconda::deepbgc=0.1.30" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/deepbgc:0.1.30--pyhb7b1952_1':
'quay.io/biocontainers/deepbgc:0.1.30--pyhb7b1952_1' }"
output:
path "deepbgc_db" , emit: db
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
"""
export DEEPBGC_DOWNLOADS_DIR='./deepbgc_db'
deepbgc \\
download
cat <<-END_VERSIONS > versions.yml
"${task.process}":
deepbgc: \$(echo \$(deepbgc info 2>&1 /dev/null/ | grep 'version' | cut -d " " -f3) )
END_VERSIONS
"""
}

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@ -0,0 +1,34 @@
name: "deepbgc_download"
description: database to detect BGCs in bacterial and fungal genomes using deep learning
keywords:
- database
- download
- BGC
- Biosynthetic Gene Cluster
- deep learning
- neural network
- random forrest
- genomes
- bacteria
- fungi
tools:
- "deepbgc":
description: "DeepBGC - Biosynthetic Gene Cluster detection and classification"
homepage: "https://github.com/Merck/deepbgc"
documentation: "https://github.com/Merck/deepbgc"
tool_dev_url: "https://github.com/Merck/deepbgc"
doi: "10.1093/nar/gkz654"
licence: "['MIT']"
output:
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- deepbgc_db:
type: directory
description: contains files of reference db from 'deepbgc download'
pattern: "*db"
authors:
- "@louperelo"

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@ -599,6 +599,10 @@ deeparg/predict:
- modules/deeparg/predict/**
- tests/modules/deeparg/predict/**
deepbgc/download:
- modules/deepbgc/download/**
- tests/modules/deepbgc/download/**
deeptools/bamcoverage:
- modules/deeptools/bamcoverage/**
- tests/modules/deeptools/bamcoverage/**

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@ -0,0 +1,10 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { DEEPBGC_DOWNLOAD } from '../../../../modules/deepbgc/download/main.nf'
workflow test_deepbgc_download {
DEEPBGC_DOWNLOAD ( )
}

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@ -0,0 +1,5 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
}

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@ -0,0 +1,30 @@
- name: deepbgc download test_deepbgc_download
command: nextflow run ./tests/modules/deepbgc/download -entry test_deepbgc_download -c ./tests/config/nextflow.config -c ./tests/modules/deepbgc/download/nextflow.config
tags:
- deepbgc
- deepbgc/download
files:
- path: output/deepbgc/deepbgc_db/0.1.0/classifier/product_activity.pkl
md5sum: 90f0c010460e9df882cb057664a49f30
- path: output/deepbgc/deepbgc_db/0.1.0/classifier/product_class.pkl
md5sum: f78a2eda240403d2f40643d42202f3ac
- path: output/deepbgc/deepbgc_db/0.1.0/detector/clusterfinder_geneborder.pkl
md5sum: ca4be7031ae9f70780f17c616a4fa5b5
- path: output/deepbgc/deepbgc_db/0.1.0/detector/clusterfinder_original.pkl
md5sum: 2ca2429bb9bc99a401d1093c376b37aa
- path: output/deepbgc/deepbgc_db/0.1.0/detector/clusterfinder_retrained.pkl
md5sum: 65679a3b61c562ff4b84bdb574bb6d93
- path: output/deepbgc/deepbgc_db/0.1.0/detector/deepbgc.pkl
md5sum: 7e9218be79ba45bc9adb23bed3845dc1
- path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.clans.tsv
md5sum: a0a4590ffb2b33b83ef2b28f6ead886b
- path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.hmm
md5sum: 79a3328e4c95b13949a4489b19959fc5
- path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.hmm.h3f
md5sum: cbca323cf8dd4e5e7c109114ec444162
- path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.hmm.h3i
md5sum: 5242332a3f6a60cd1ab634cd9331afd6
- path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.hmm.h3m
md5sum: 1fe946fa2b3bcde1d4b2bad732bce612
- path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.hmm.h3p
md5sum: 27b98a1ded123b6a1ef72db01927017c