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@xiaoli-dong
xiaoli-dong committed Nov 14, 2024
1 parent 415fdac commit 842eddb
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1,055 changes: 489 additions & 566 deletions conf/modules.config
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312 changes: 155 additions & 157 deletions conf/modules_illumina.config
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Original file line number Diff line number Diff line change
Expand Up @@ -10,183 +10,181 @@
----------------------------------------------------------------------------------------
*/

if(!params.skip_illumina_reads_assembly){
process {


withName: SKESA {
publishDir = [
path: { "${params.outdir}/${meta.id}/assembly/illumina/skesa" },
process {


withName: SKESA {
publishDir = [
path: { "${params.outdir}/${meta.id}/assembly/illumina/skesa" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
pattern: "*"
]

}
withName: STATS_SKESA {
//ext.prefix = { "${meta.id}.contigs_stats" }
ext.args = '-t'
publishDir = [
path: { "${params.outdir}/${meta.id}/assembly/illumina/skesa" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
pattern: "*"
]

}
withName: STATS_SKESA {
//ext.prefix = { "${meta.id}.contigs_stats" }
ext.args = '-t'
publishDir = [
path: { "${params.outdir}/${meta.id}/assembly/illumina/skesa" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
pattern: "*",
enabled: false
]

}
withName: STATS_SKESA_FORMATASSEMBLYSTATS {
ext.prefix = { "${meta.id}.contigs_stats" }
publishDir = [
path: { "${params.outdir}/${meta.id}/assembly/illumina/skesa" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
pattern: "*"
]

}
withName: SPADES {
ext.args = "--careful --only-assembler --cov-cutoff auto"
publishDir = [
path: { "${params.outdir}/${meta.id}/assembly/illumina/spades" },
pattern: "*",
enabled: false
]

}
withName: STATS_SKESA_FORMATASSEMBLYSTATS {
ext.prefix = { "${meta.id}.contigs_stats" }
publishDir = [
path: { "${params.outdir}/${meta.id}/assembly/illumina/skesa" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
pattern: "*"
]

}
withName: STATS_SPADES {
//ext.prefix = { "${meta.id}.contigs_stats" }
ext.args = '-t'
publishDir = [
path: { "${params.outdir}/${meta.id}/assembly/illumina/spades" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
pattern: "*",
enabled: false
]

}
withName: STATS_SPADES_FORMATASSEMBLYSTATS {
ext.prefix = { "${meta.id}.contigs_stats" }
//ext.args = '-t'
publishDir = [
path: { "${params.outdir}/${meta.id}/assembly/illumina/spades" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
pattern: "*"
]

}
withName: UNICYCLER {
ext.args = "--no_correct --mode conservative --keep 0 --min_fasta_length 200 "
publishDir = [
path: { "${params.outdir}/${meta.id}/assembly/illumina/unicycler" },
]

}
withName: SPADES {
ext.args = "--careful --only-assembler --cov-cutoff auto"
publishDir = [
path: { "${params.outdir}/${meta.id}/assembly/illumina/spades" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
pattern: "*"
]

}
withName: STATS_SPADES {
//ext.prefix = { "${meta.id}.contigs_stats" }
ext.args = '-t'
publishDir = [
path: { "${params.outdir}/${meta.id}/assembly/illumina/spades" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
pattern: "*",
enabled: false
]

}
withName: STATS_SPADES_FORMATASSEMBLYSTATS {
ext.prefix = { "${meta.id}.contigs_stats" }
//ext.args = '-t'
publishDir = [
path: { "${params.outdir}/${meta.id}/assembly/illumina/spades" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
pattern: "*"
]

}
withName: STATS_UNICYCLER {
//ext.prefix = { "${meta.id}.contig_stats" }
ext.args = '-t'
publishDir = [
path: { "${params.outdir}/${meta.id}/assembly/illumina/unicycler" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
pattern: "*",
enabled: false
]


}
withName: STATS_UNICYCLER_FORMATASSEMBLYSTATS {
ext.prefix = { "${meta.id}.contigs_stats" }
publishDir = [
path: { "${params.outdir}/${meta.id}/assembly/illumina/unicycler" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
pattern: "*"
]

}
withName: MEGAHIT {
publishDir = [
path: { "${params.outdir}/${meta.id}/assembly/illumina/megahit" },
]

}
withName: UNICYCLER {
ext.args = "--no_correct --mode conservative --keep 0 --min_fasta_length 200 "
publishDir = [
path: { "${params.outdir}/${meta.id}/assembly/illumina/unicycler" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
pattern: "*"
]

}
withName: STATS_UNICYCLER {
//ext.prefix = { "${meta.id}.contig_stats" }
ext.args = '-t'
publishDir = [
path: { "${params.outdir}/${meta.id}/assembly/illumina/unicycler" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
pattern: "*",
enabled: false
]


}
withName: STATS_UNICYCLER_FORMATASSEMBLYSTATS {
ext.prefix = { "${meta.id}.contigs_stats" }
publishDir = [
path: { "${params.outdir}/${meta.id}/assembly/illumina/unicycler" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
pattern: "*"
]

}
withName: STATS_MEGAHIT {
//ext.prefix = { "${meta.id}.contigs_stats" }
ext.args = '-t'
publishDir = [
path: { "${params.outdir}/${meta.id}/assembly/illumina/megahit" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
pattern: "*",
enabled: false
]

}
withName: STATS_MEGAHIT_FORMATASSEMBLYSTATS {
ext.prefix = { "${meta.id}.contigs_stats" }
publishDir = [
path: { "${params.outdir}/${meta.id}/assembly/illumina/megahit" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
pattern: "*"
]

}
withName: SHOVILL {

// ext.args = '--assembler megahit --gsize 2800000'
ext.args = '--assembler spades'
]

}
withName: MEGAHIT {
publishDir = [
path: { "${params.outdir}/${meta.id}/assembly/illumina/megahit" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
pattern: "*"
]

publishDir = [
path: { "${params.outdir}/${meta.id}/assembly/illumina/shovill" },
}
withName: STATS_MEGAHIT {
//ext.prefix = { "${meta.id}.contigs_stats" }
ext.args = '-t'
publishDir = [
path: { "${params.outdir}/${meta.id}/assembly/illumina/megahit" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
pattern: "*",
enabled: false
]

}
withName: STATS_MEGAHIT_FORMATASSEMBLYSTATS {
ext.prefix = { "${meta.id}.contigs_stats" }
publishDir = [
path: { "${params.outdir}/${meta.id}/assembly/illumina/megahit" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
pattern: "*"
]

}
withName: STATS_SHOVILL {
//ext.prefix = { "${meta.id}.contigs_stats" }
ext.args = '-t'
publishDir = [
path: { "${params.outdir}/${meta.id}/assembly/illumina/shovill" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
pattern: "*",
enabled: false
]
}
withName: STATS_SHOVILL_FORMATASSEMBLYSTATS {
ext.prefix = { "${meta.id}.contigs_stats" }
publishDir = [
path: { "${params.outdir}/${meta.id}/assembly/illumina/shovill" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
pattern: "*"
]

}
]

}
withName: SHOVILL {

withName: CSVTK_CONCAT_STATS_ASM{
publishDir = [
path: { "${params.outdir}/report" },
// ext.args = '--assembler megahit --gsize 2800000'
ext.args = '--assembler spades'

publishDir = [
path: { "${params.outdir}/${meta.id}/assembly/illumina/shovill" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
pattern: "*"
]

}
withName: STATS_SHOVILL {
//ext.prefix = { "${meta.id}.contigs_stats" }
ext.args = '-t'
publishDir = [
path: { "${params.outdir}/${meta.id}/assembly/illumina/shovill" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
pattern: "*",
enabled: false
]
}
withName: STATS_SHOVILL_FORMATASSEMBLYSTATS {
ext.prefix = { "${meta.id}.contigs_stats" }
publishDir = [
path: { "${params.outdir}/${meta.id}/assembly/illumina/shovill" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },

]
}
pattern: "*"
]

}

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

]
}


}

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