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Move long read preprocessing into a subworkflow #674

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merged 37 commits into from
Oct 11, 2024
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08445cf
Added modules porechop/abi and chopper for QC of long reads
Sep 20, 2024
5aa3049
Move long read preprocessing into subworkflow, and swapping porechop …
Sep 20, 2024
451612a
Remove module import from main workflow, and add PORECHOP_ABI in conf…
Sep 20, 2024
59ef702
Exchange local filtlong module to nf-core/filtlong
muabnezor Sep 24, 2024
cd5ce2f
Add filtlong and porechop logs to multiqc
muabnezor Sep 24, 2024
5820fb4
Added --longread_preprocessing_tools parameters, to let user specify …
muabnezor Sep 24, 2024
5335fc5
Merge branch 'dev' into move_lr_qc
muabnezor Sep 25, 2024
1496ce9
Update modules/nf-core/filtlong/main.nf
muabnezor Sep 25, 2024
c11601a
make subworkflow name more verbose
muabnezor Sep 30, 2024
31deb5c
make --longread_adaptertrimming_tool as enum porechop or porechop_abi
muabnezor Sep 30, 2024
b2da50b
Make prefix for porechop/porechop-abi more verbose
muabnezor Sep 30, 2024
8955e31
lint
muabnezor Sep 30, 2024
644e2b1
Change default search pattern for filtlong.log files for the filtlong…
muabnezor Oct 1, 2024
3e15502
Update CHANGELOG.md
muabnezor Oct 3, 2024
ec8538c
Update CHANGELOG.md
muabnezor Oct 3, 2024
c6fb9b3
Update nextflow_schema.json
muabnezor Oct 3, 2024
b24f52f
Update conf/modules.config
muabnezor Oct 3, 2024
fcf509c
Update conf/modules.config
muabnezor Oct 3, 2024
8f9cac6
Update conf/modules.config
muabnezor Oct 3, 2024
10ecdc5
Update nextflow_schema.json
muabnezor Oct 3, 2024
ea6f9a4
Update nextflow.config
muabnezor Oct 3, 2024
b43b9f6
Update subworkflows/local/longread_preprocessing.nf
muabnezor Oct 3, 2024
25981a1
Update subworkflows/local/longread_preprocessing.nf
muabnezor Oct 3, 2024
edf8dab
Update subworkflows/local/longread_preprocessing.nf
muabnezor Oct 3, 2024
0a06944
Merge branch 'dev' into move_lr_qc
muabnezor Oct 3, 2024
669a854
Linting fix
muabnezor Oct 3, 2024
a1098f3
make porechop-abi default long read adapter trimming tool
muabnezor Oct 3, 2024
17ba45c
Fix changelog
muabnezor Oct 4, 2024
f54c967
Fix porechop_abi pattern in modules.config
muabnezor Oct 4, 2024
110b5dd
Merge branch 'dev' into move_lr_qc
muabnezor Oct 4, 2024
3472c87
remove chopper citation for now
muabnezor Oct 4, 2024
ab5f482
retrigger checks
muabnezor Oct 4, 2024
2cfd5e5
Merge branch 'dev' into move_lr_qc
muabnezor Oct 4, 2024
7b31394
Apply suggestions from code review
jfy133 Oct 11, 2024
78edf25
Apply suggestions from code review
jfy133 Oct 11, 2024
3c3b46a
Add previouysly undocumented output files to docs
jfy133 Oct 11, 2024
7c7e954
[automated] Fix code linting
nf-core-bot Oct 11, 2024
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3 changes: 3 additions & 0 deletions assets/multiqc_config.yml
Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,8 @@ run_modules:
- quast
- kraken
- prokka
- porechop
- filtlong

## Module order
top_modules:
Expand All @@ -35,6 +37,7 @@ top_modules:
- "fastp"
- "adapterRemoval"
- "porechop"
- "filtlong"
- "fastqc":
name: "FastQC: after preprocessing"
info: "After trimming and, if requested, contamination removal."
Expand Down
28 changes: 22 additions & 6 deletions conf/modules.config
Original file line number Diff line number Diff line change
Expand Up @@ -177,14 +177,30 @@ process {
ext.prefix = { "${meta.id}_run${meta.run}_trimmed" }
}

withName: PORECHOP_ABI {
publishDir = [
path: { "${params.outdir}/QC_longreads/porechop" },
mode: params.publish_dir_mode,
pattern: "*_trimmed.fastq",
enabled: params.save_porechop_reads
]
ext.prefix = { "${meta.id}_run${meta.run}_trimmed" }
}

withName: FILTLONG {
ext.args = [
"--min_length ${params.longreads_min_length}",
"--keep_percent ${params.longreads_keep_percent}",
"--trim",
"--length_weight ${params.longreads_length_weight}"
].join(' ').trim()
publishDir = [
path: { "${params.outdir}/QC_longreads/Filtlong" },
mode: params.publish_dir_mode,
pattern: "*_lr_filtlong.fastq.gz",
enabled: params.save_filtlong_reads
]
ext.prefix = { "${meta.id}_run${meta.run}_lengthfiltered" }
path: { "${params.outdir}/QC_longreads/Filtlong" },
mode: params.publish_dir_mode,
pattern: "*_lr_filtlong.fastq.gz",
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enabled: params.save_filtlong_reads
]
ext.prefix = { "${meta.id}_run${meta.run}_lr_filtlong" }
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The _lr is not necessary here

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(even if it was in the old module)

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}

withName: NANOLYSE {
Expand Down
15 changes: 15 additions & 0 deletions modules.json
Original file line number Diff line number Diff line change
Expand Up @@ -62,6 +62,11 @@
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"chopper": {
"branch": "master",
"git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["modules"]
},
"concoct/concoct": {
"branch": "master",
"git_sha": "baa30accc6c50ea8a98662417d4f42ed18966353",
Expand Down Expand Up @@ -107,6 +112,11 @@
"git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
"installed_by": ["modules"]
},
"filtlong": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"freebayes": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
Expand Down Expand Up @@ -202,6 +212,11 @@
"git_sha": "3135090b46f308a260fc9d5991d7d2f9c0785309",
"installed_by": ["modules"]
},
"porechop/abi": {
"branch": "master",
"git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["modules"]
},
"porechop/porechop": {
"branch": "master",
"git_sha": "1d68c7f248d1a480c5959548a9234602b771199e",
Expand Down
33 changes: 0 additions & 33 deletions modules/local/filtlong.nf

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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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53 changes: 53 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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5 changes: 5 additions & 0 deletions modules/nf-core/filtlong/environment.yml

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39 changes: 39 additions & 0 deletions modules/nf-core/filtlong/main.nf

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