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Allow ABACAS for multifasta #481

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fb35a1d
splitting the reference multifasta into individual fasta files, proce…
chaudb1998 Mar 25, 2025
470aa21
fix nf-core linting
cduong11 Mar 25, 2025
cc3d138
simplify seqtk split
cduong11 Mar 26, 2025
cacb5db
fix nf-core linting
cduong11 Mar 26, 2025
407dd34
remove seqkit_concat and seqkit_split, add test_illumina_fragmented p…
cduong11 Mar 26, 2025
662682c
update CI test
cduong11 Mar 27, 2025
6243f3b
fix linting
cduong11 Mar 27, 2025
78528a6
fix linting again
cduong11 Mar 27, 2025
03692eb
Apply prettier formatting
cduong11 Mar 28, 2025
203542c
adjust for better clarity
cduong11 Mar 28, 2025
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89 changes: 86 additions & 3 deletions conf/modules_illumina.config
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Original file line number Diff line number Diff line change
Expand Up @@ -872,14 +872,42 @@ if (!params.skip_assembly) {

if (!params.skip_abacas) {
process {
withName: '.*:.*:ASSEMBLY_SPADES:.*:ABACAS' {
withName: '.*:.*:ASSEMBLY_SPADES:.*:ABACAS_SINGLE' {
ext.args = '-m -p nucmer'
publishDir = [
path: { "${params.outdir}/assembly/spades/${params.spades_mode}/abacas" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: '.*:.*:ASSEMBLY_SPADES:.*:.*:ABACAS' {
ext.prefix = { "${meta.id}.${fasta.baseName}" }
ext.args = '-m -p nucmer'
publishDir = [
path: { "${params.outdir}/assembly/spades/${params.spades_mode}/abacas" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: '.*:.*:ASSEMBLY_SPADES:.*:.*:SEQKIT_SPLIT' {
ext.args = '-i'
publishDir = [
path: { "${params.outdir}/assembly/spades/${params.spades_mode}/seqkit/split" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: '.*:.*:ASSEMBLY_SPADES:.*:.*:SEQKIT_CONCAT' {
ext.args = '-f'
publishDir = [
path: { "${params.outdir}/assembly/spades/${params.spades_mode}/seqkit/concat" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
}
}

Expand Down Expand Up @@ -977,14 +1005,42 @@ if (!params.skip_assembly) {

if (!params.skip_abacas) {
process {
withName: '.*:.*:ASSEMBLY_UNICYCLER:.*:ABACAS' {
withName: '.*:.*:ASSEMBLY_UNICYCLER:.*:ABACAS_SINGLE' {
ext.args = '-m -p nucmer'
publishDir = [
path: { "${params.outdir}/assembly/unicycler/abacas" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: '.*:.*:ASSEMBLY_UNICYCLER:.*:.*:ABACAS' {
ext.prefix = { "${meta.id}.${fasta.baseName}" }
ext.args = '-m -p nucmer'
publishDir = [
path: { "${params.outdir}/assembly/unicycler/abacas" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: '.*:.*:ASSEMBLY_UNICYCLER:.*:.*:SEQKIT_SPLIT' {
ext.args = '-i'
publishDir = [
path: { "${params.outdir}/assembly/unicycler/seqkit/split" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: '.*:.*:ASSEMBLY_UNICYCLER:.*:.*:SEQKIT_CONCAT' {
ext.args = '-f'
publishDir = [
path: { "${params.outdir}/assembly/unicycler/seqkit/concat" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
}
}

Expand Down Expand Up @@ -1049,14 +1105,41 @@ if (!params.skip_assembly) {

if (!params.skip_abacas) {
process {
withName: '.*:.*:ASSEMBLY_MINIA:.*:ABACAS' {
withName: '.*:.*:ASSEMBLY_MINIA:.*:ABACAS_SINGLE' {
ext.args = '-m -p nucmer'
publishDir = [
path: { "${params.outdir}/assembly/minia/abacas" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
withName: '.*:.*:ASSEMBLY_MINIA:.*:.*:ABACAS' {
ext.prefix = { "${meta.id}.${fasta.baseName}" }
ext.args = '-m -p nucmer'
publishDir = [
path: { "${params.outdir}/assembly/minia/abacas" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: '.*:.*:ASSEMBLY_MINIA:.*:.*:SEQKIT_SPLIT' {
ext.args = '-i'
publishDir = [
path: { "${params.outdir}/assembly/minia/seqkit/split" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: '.*:.*:ASSEMBLY_MINIA:.*:.*:SEQKIT_CONCAT' {
ext.args = '-f'
publishDir = [
path: { "${params.outdir}/assembly/minia/seqkit/concat" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
}
}

Expand Down
7 changes: 7 additions & 0 deletions modules.json
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@
"artic/minion": {
"branch": "master",
"git_sha": "b44f728e80a1420b9f130061d91f7ff86673735a",
"installed_by": ["modules"],
"patch": "modules/nf-core/artic/minion/artic-minion.diff"
},
"bandage/image": {
Expand Down Expand Up @@ -108,6 +109,7 @@
"cutadapt": {
"branch": "master",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"],
"patch": "modules/nf-core/cutadapt/cutadapt.diff"
},
"fastp": {
Expand Down Expand Up @@ -250,6 +252,11 @@
"git_sha": "e9bca09da225e5132d45a32bf830a434843bb5be",
"installed_by": ["modules"]
},
"seqkit/concat": {
"branch": "master",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"spades": {
"branch": "master",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
Expand Down
39 changes: 39 additions & 0 deletions modules/local/seqkit_split.nf
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@@ -0,0 +1,39 @@
process SEQKIT_SPLIT {
tag "$fastx.baseName"
label 'process_low'

conda "bioconda::seqkit=2.9.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0':
'biocontainers/seqkit:2.9.0--h9ee0642_0' }"

input:
tuple val(meta), path(fastx)

output:
tuple val(meta), path("${fastx.baseName}*/*.{fasta,fastq,fa,fq,fas,fna,faa}") , emit: fastx
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when

script:
def args = task.ext.args ?: ''
def extension = "fastq"
if ("$fastx" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz|.+\.fsa|.+\.fsa.gz/ ) {
extension = "fasta"
}

"""
seqkit \\
split \\
--threads $task.cpus \\
$args \\
$fastx

cat <<-END_VERSIONS > versions.yml
"${task.process}":
seqkit: \$(seqkit version | cut -d' ' -f2)
END_VERSIONS
"""
}
7 changes: 7 additions & 0 deletions modules/nf-core/seqkit/concat/environment.yml
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46 changes: 46 additions & 0 deletions modules/nf-core/seqkit/concat/main.nf
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50 changes: 50 additions & 0 deletions modules/nf-core/seqkit/concat/meta.yml
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66 changes: 66 additions & 0 deletions modules/nf-core/seqkit/concat/tests/main.nf.test
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