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decontamination workflow #72

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decontamination workflow #72

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cf04b6f
writing subworkflow for decontamination of genome and decontamination…
LaurenHuet Oct 28, 2024
67933fb
updated decontamination subworkflow
LaurenHuet Oct 28, 2024
8826420
decontamination subworkflow completed and passed testing
LaurenHuet Oct 29, 2024
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5 changes: 1 addition & 4 deletions assets/samplesheet.csv
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@@ -1,5 +1,2 @@
species,refseq,fasta,gff
Vespula_vulgaris,GCF_905475345.1,,
Vespa_velutina,GCF_912470025.1,,
Apis_mellifera,GCF_003254395.2,,
Osmia_bicornis,GCF_907164935.1,,
Saccharomyces_cerevisiae,,/workspace/FCS_combo_test.fa,/workspace/GCF_000146045.2_R64_genomic.gff.gz
41 changes: 41 additions & 0 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -64,6 +64,47 @@ process {
ext.args = "--minimum 5 --maximum 12"
}

withName: 'FCS_FCSADAPTOR' {
publishDir = [
path: { "${params.outdir}/decontamination/adaptor" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'FCS_CLEANADAPTOR' {
publishDir = [
path: { "${params.outdir}/decontamination/adaptor" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'FCS_FCSGX' {
publishDir = [
path: { "${params.outdir}/decontamination//NCBI" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'FCS_CLEANGENOME' {
publishDir = [
path: { "${params.outdir}/decontamination/NCBI" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'TIARA_TIARA' {
publishDir = [
path: { "${params.outdir}/decontamination/tiara" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}


withName: 'MULTIQC' {
ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
publishDir = [
Expand Down
257 changes: 118 additions & 139 deletions modules.json
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Original file line number Diff line number Diff line change
@@ -1,142 +1,121 @@
{
"name": "ecoflow/genomeqc",
"homePage": "https://github.com/ecoflow/genomeqc",
"repos": {
"https://github.com/nf-core/modules.git": {
"modules": {
"nf-core": {
"agat/spstatistics": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": [
"modules"
]
},
"busco/busco": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": [
"modules"
]
},
"fastqc": {
"branch": "master",
"git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
"installed_by": [
"modules"
]
},
"gffread": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": [
"modules"
]
},
"multiqc": {
"branch": "master",
"git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
"installed_by": [
"modules"
]
},
"ncbigenomedownload": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": [
"modules"
]
},
"orthofinder": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": [
"modules"
]
},
"pigz/uncompress": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": [
"modules"
]
},
"quast": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": [
"modules"
]
},
"seqkit/seq": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": [
"fasta_explore_search_plot_tidk"
]
},
"seqkit/sort": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": [
"fasta_explore_search_plot_tidk"
]
},
"tidk/explore": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": [
"fasta_explore_search_plot_tidk"
]
},
"tidk/plot": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": [
"fasta_explore_search_plot_tidk"
]
},
"tidk/search": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": [
"fasta_explore_search_plot_tidk"
]
}
}
},
"subworkflows": {
"nf-core": {
"fasta_explore_search_plot_tidk": {
"branch": "master",
"git_sha": "ab80a04707104a4baf39341581dfbced5da05479",
"installed_by": [
"subworkflows"
]
},
"utils_nextflow_pipeline": {
"branch": "master",
"git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
"installed_by": [
"subworkflows"
]
},
"utils_nfcore_pipeline": {
"branch": "master",
"git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
"installed_by": [
"subworkflows"
]
},
"utils_nfvalidation_plugin": {
"branch": "master",
"git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
"installed_by": [
"subworkflows"
]
}
}
}
"name": "ecoflow/genomeqc",
"homePage": "https://github.com/ecoflow/genomeqc",
"repos": {
"https://github.com/nf-core/modules.git": {
"modules": {
"nf-core": {
"agat/spstatistics": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"busco/busco": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"fastqc": {
"branch": "master",
"git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
"installed_by": ["modules"]
},
"fcs/fcsadaptor": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"fcs/fcsgx": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"gffread": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"multiqc": {
"branch": "master",
"git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
"installed_by": ["modules"]
},
"ncbigenomedownload": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"orthofinder": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"pigz/uncompress": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"quast": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"seqkit/seq": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["fasta_explore_search_plot_tidk"]
},
"seqkit/sort": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["fasta_explore_search_plot_tidk"]
},
"tiara/tiara": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"tidk/explore": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["fasta_explore_search_plot_tidk"]
},
"tidk/plot": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["fasta_explore_search_plot_tidk"]
},
"tidk/search": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["fasta_explore_search_plot_tidk"]
}
}
},
"subworkflows": {
"nf-core": {
"fasta_explore_search_plot_tidk": {
"branch": "master",
"git_sha": "ab80a04707104a4baf39341581dfbced5da05479",
"installed_by": ["subworkflows"]
},
"utils_nextflow_pipeline": {
"branch": "master",
"git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
"installed_by": ["subworkflows"]
},
"utils_nfcore_pipeline": {
"branch": "master",
"git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
"installed_by": ["subworkflows"]
},
"utils_nfvalidation_plugin": {
"branch": "master",
"git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
"installed_by": ["subworkflows"]
}
}
}
}
}
}
}
51 changes: 51 additions & 0 deletions modules/local/fcs/cleanadaptor/main.nf
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@@ -0,0 +1,51 @@
process FCS_CLEANADAPTOR {
tag "$meta.id"
label 'process_low'

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ncbi-fcs-gx:0.5.4--h4ac6f70_1':
'biocontainers/ncbi-fcs-gx:0.5.4--h4ac6f70_1' }"

input:
tuple val(meta), path(assembly), path(adaptor_report)

output:
tuple val(meta), path("${meta.id}.adapt-cleaned.fasta") , emit: cleaned
path("${meta.id}.adaptor-contam.fasta") , emit: contam

script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def FCSGX_VERSION = '0.5.4'

"""
python3 --version
#sed -i '1i ##[["FCS genome report",2,' "$adaptor_report"
gx clean-genome \\
--input ${assembly} \\
--action-report "${adaptor_report}" \\
--output "${meta.id}.adapt-cleaned.fasta" \\
--contam-fasta-out "${prefix}.adaptor-contam.fasta"

cat <<-END_VERSIONS > versions.yml
"${task.process}":
FCS-GX: $FCSGX_VERSION
END_VERSIONS
"""

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def FCSGX_VERSION = '0.5.4'

"""
touch ${meta.id}.adapt-cleaned.fasta"
touch "${prefix}.adaptor-contam.fasta"

cat <<-END_VERSIONS > versions.yml
"${task.process}":
FCS-GX: $FCSGX_VERSION
END_VERSIONS
"""
}
3 changes: 3 additions & 0 deletions modules/local/fcs/cleangenome/environment.yml
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@@ -0,0 +1,3 @@
channels:
- conda-forge
- bioconda
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