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Add chopper and nanoq options for longread preprocessing #692

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Add chopper and nanoq options for longread preprocessing #692

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ad89172
install chopper from nf-core/chopper
muabnezor Oct 14, 2024
c614c01
Add nanoq from nf-core/nanoq, and add code in longread_preprocessing …
muabnezor Oct 14, 2024
7102af4
Fix config for modules nanoq and filtlong in modules.config
muabnezor Oct 14, 2024
9bc8156
Make it possible to use chopper as filtering tool as well
muabnezor Oct 15, 2024
59aa4ad
Merge branch 'dev' into add_chopper_nanoq
jfy133 Oct 29, 2024
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47 changes: 46 additions & 1 deletion conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -183,7 +183,8 @@ process {
"--min_length ${params.longreads_min_length}",
"--keep_percent ${params.longreads_keep_percent}",
"--trim",
"--length_weight ${params.longreads_length_weight}"
"--length_weight ${params.longreads_length_weight}",
params.longreads_min_quality ? "--min_mean_q ${params.longreads_min_quality}" : '',
].join(' ').trim()
publishDir = [
path: { "${params.outdir}/QC_longreads/Filtlong" },
Expand All @@ -194,11 +195,55 @@ process {
ext.prefix = { "${meta.id}_run${meta.run}_filtlong" }
}

withName: NANOQ {
ext.args = [
"--min-len ${params.longreads_min_length}",
params.longreads_min_quality ? "--min-qual ${params.longreads_min_quality}": '',
"-vv"
].join(' ').trim()
publishDir = [
[
path: { "${params.outdir}/QC_longreads/Nanoq" },
mode: params.publish_dir_mode,
pattern: "*_nanoq_filtered.fastq.gz",
enabled: params.save_filtered_reads
],
[
path: { "${params.outdir}/QC_longreads/Nanoq" },
mode: params.publish_dir_mode,
pattern: "*_nanoq_filtered.stats"
]
]
ext.prefix = { "${meta.id}_run${meta.run}_nanoq_filtered" }
}

withName: NANOLYSE {
publishDir = [[path: { "${params.outdir}/QC_longreads/NanoLyse" }, mode: params.publish_dir_mode, pattern: "*.log"], [path: { "${params.outdir}/QC_longreads/NanoLyse" }, mode: params.publish_dir_mode, pattern: "*_nanolyse.fastq.gz", enabled: params.save_lambdaremoved_reads]]
ext.prefix = { "${meta.id}_run${meta.run}_lambdafiltered" }
}

withName: CHOPPER {
ext.args2 = [
!params.keep_lambda ? "--contam ${params.lambda_reference}": "",
params.longreads_min_quality ? "--quality ${params.longreads_min_quality}": "",
params.longreads_min_length ? "--minlength ${params.longreads_min_length}": "",
].join(' ').trim()
Comment on lines +225 to +230
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I added the option to use chopper for filtering. Since the conditions in the subworkflow got a bit messy, i decided to put the logic in the modules.config. In this way if params.keep_phage is true, and params.longread_filtering_tool is chopper will run both phage removal and filtering. what do you think of this @jfy133?

publishDir = [
[
path: { "${params.outdir}/QC_longreads/Chopper" },
mode: params.publish_dir_mode,
pattern: "*.log"
],
[
path: { "${params.outdir}/QC_longreads/Chopper" },
mode: params.publish_dir_mode,
pattern: "*_chopper.fastq.gz",
enabled: params.save_lambdaremoved_reads
]
]
ext.prefix = { "${meta.id}_run${meta.run}_chopper" }
}

withName: NANOPLOT_RAW {
ext.prefix = 'raw'
ext.args = {
Expand Down
10 changes: 10 additions & 0 deletions modules.json
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Expand Up @@ -62,6 +62,11 @@
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"chopper": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"concoct/concoct": {
"branch": "master",
"git_sha": "baa30accc6c50ea8a98662417d4f42ed18966353",
Expand Down Expand Up @@ -212,6 +217,11 @@
"git_sha": "3135090b46f308a260fc9d5991d7d2f9c0785309",
"installed_by": ["modules"]
},
"nanoq": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"porechop/abi": {
"branch": "master",
"git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
Expand Down
5 changes: 5 additions & 0 deletions modules/nf-core/chopper/environment.yml
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42 changes: 42 additions & 0 deletions modules/nf-core/chopper/main.nf
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60 changes: 60 additions & 0 deletions modules/nf-core/chopper/meta.yml
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45 changes: 45 additions & 0 deletions modules/nf-core/chopper/tests/main.nf.test
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16 changes: 16 additions & 0 deletions modules/nf-core/chopper/tests/main.nf.test.snap
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2 changes: 2 additions & 0 deletions modules/nf-core/chopper/tests/tags.yml
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7 changes: 7 additions & 0 deletions modules/nf-core/nanoq/environment.yml
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49 changes: 49 additions & 0 deletions modules/nf-core/nanoq/main.nf
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63 changes: 63 additions & 0 deletions modules/nf-core/nanoq/meta.yml
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