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Dp24 pretext fix #283

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merged 11 commits into from
Mar 20, 2024
Merged

Dp24 pretext fix #283

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DLBPointon Mar 14, 2024
27c3c54
Adding the genome file as input to the pretextmap process, stops us r…
DLBPointon Mar 14, 2024
3ab21eb
Added the meta.type to a channel which was causing files to be overwr…
DLBPointon Mar 14, 2024
3009597
Updated to accept a tuple including a fasta and a fai file
DLBPointon Mar 14, 2024
fa2cb8b
Updated due to patch
DLBPointon Mar 14, 2024
48705fc
Prettier fixes as usual
DLBPointon Mar 14, 2024
54c4b40
Adding specific config for pretext in the config file for testing
DLBPointon Mar 15, 2024
c2c54c1
Update modules.config
DLBPointon Mar 18, 2024
07e130d
Added a boolean flag to controll the use of juicer
DLBPointon Mar 18, 2024
f17c29f
Adding a default value to the juicer
DLBPointon Mar 18, 2024
59bc432
Adding the values for juicer
DLBPointon Mar 18, 2024
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2 changes: 1 addition & 1 deletion conf/base.config
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Original file line number Diff line number Diff line change
Expand Up @@ -128,7 +128,7 @@ process {

withName: '.*:.*:GENE_ALIGNMENT:.*:MINIMAP2_ALIGN' {
cpus = { check_max( 6 * task.attempt, 'cpus' ) }
memory = { check_max( 1.GB * ( reference.size() < 2e9 ? 60 : Math.ceil( ( reference.size() / 1e+9 ) * 30 ) * Math.ceil( task.attempt * 1 ) ) , 'memory') }
memory = { check_max( 1.GB * ( reference.size() < 2e9 ? 64 : Math.ceil( ( reference.size() / 1e+9 ) * 45 ) * Math.ceil( task.attempt * 1 ) ) , 'memory') }
time = { check_max( 10.h * task.attempt, 'time' ) }
}

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4 changes: 2 additions & 2 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -328,12 +328,12 @@ process {
// normal = standard run, pi = "pre-ingestion", hr = High res
//
withName: PRETEXTMAP_STANDRD {
ext.args = { "${meta.map_order.equals("length") ? "--sortby length": "--sortby nosort" } --mapq 0 --memory ${task.memory.giga}G" }
ext.args = { "${meta.map_order.equals("length") ? "--sortby length": "--sortby nosort" } --mapq 0 --memory ${task.memory.giga}" }
ext.prefix = { "${meta.id}_normal_pi" }
}

withName: PRETEXTMAP_HIGHRES {
ext.args = { "${meta.map_order.equals("length") ? "--sortby length": "--sortby nosort" } --highRes --mapq 0 --memory ${task.memory.giga}G" }
ext.args = { "${meta.map_order.equals("length") ? "--sortby length": "--sortby nosort" } --highRes --mapq 0 --memory ${task.memory.giga}" }
ext.prefix = { "${meta.id}_hr_pi" }
}

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150 changes: 112 additions & 38 deletions modules.json
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Original file line number Diff line number Diff line change
Expand Up @@ -8,192 +8,266 @@
"bedtools/bamtobed": {
"branch": "master",
"git_sha": "1d1cb7bfef6cf67fbc7faafa6992ad8bdc3045b3",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"bedtools/genomecov": {
"branch": "master",
"git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"bedtools/intersect": {
"branch": "master",
"git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"bedtools/makewindows": {
"branch": "master",
"git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"bedtools/map": {
"branch": "master",
"git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"bedtools/merge": {
"branch": "master",
"git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"bedtools/sort": {
"branch": "master",
"git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"busco": {
"branch": "master",
"git_sha": "e3126f437c336c826f242842fe51769cfce0ec2d",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"bwamem2/index": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"cat/cat": {
"branch": "master",
"git_sha": "81f27e75847087865299cc46605deb3b09b4e0a2",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"cooler/cload": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"cooler/zoomify": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"custom/dumpsoftwareversions": {
"branch": "master",
"git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"custom/getchromsizes": {
"branch": "master",
"git_sha": "1b0ffa4e5aed5b7e3cd4311af31bd3b2c8345051",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/custom/getchromsizes/custom-getchromsizes.diff"
},
"fastk/fastk": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"gnu/sort": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"merquryfk/merquryfk": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"minimap2/align": {
"branch": "master",
"git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/minimap2/align/minimap2-align.diff"
},
"minimap2/index": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"miniprot/align": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"miniprot/index": {
"branch": "master",
"git_sha": "8d737766e8f3c1417212b4b56acb959f3c356d26",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"mummer": {
"branch": "master",
"git_sha": "9e51255c4f8ec69fb6ccf68593392835f14fecb8",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/mummer/mummer.diff"
},
"paftools/sam2paf": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"pretextmap": {
"branch": "master",
"git_sha": "decfb802f2e573efb7b44ff06b11ecf16853054d",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/pretextmap/pretextmap.diff"
},
"pretextsnapshot": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/pretextsnapshot/pretextsnapshot.diff"
},
"samtools/faidx": {
"branch": "master",
"git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"samtools/index": {
"branch": "master",
"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"samtools/markdup": {
"branch": "master",
"git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"samtools/merge": {
"branch": "master",
"git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"samtools/sort": {
"branch": "master",
"git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"samtools/view": {
"branch": "master",
"git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"seqtk/cutn": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"tabix/bgziptabix": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"ucsc/bedgraphtobigwig": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"ucsc/bedtobigbed": {
"branch": "master",
"git_sha": "9e51255c4f8ec69fb6ccf68593392835f14fecb8",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"windowmasker/mkcounts": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"windowmasker/ustat": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
}
}
},
Expand All @@ -202,4 +276,4 @@
}
}
}
}
}
6 changes: 3 additions & 3 deletions modules/nf-core/pretextmap/main.nf
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