8000 Add 'final reads for profiling' saving mechanism by jfy133 · Pull Request #272 · nf-core/taxprofiler · GitHub
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Add 'final reads for profiling' saving mechanism #272

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Merged
merged 16 commits into from
Apr 21, 2023
Merged

Add 'final reads for profiling' saving mechanism #272

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f9af004
Add multi-run meta information
jfy133 Mar 17, 2023
68d131a
Remove leftover dump
jfy133 Mar 17, 2023
74bc6b7
Logical ordering and improved commenting
jfy133 Mar 17, 2023
3b90064
Start adding conditions in modules.conf - non-cat not working
jfy133 Mar 22, 2023
6895e45
Fix a few conditional bugs and related
jfy133 Mar 23, 2023
ca9c0cf
Further fixes
jfy133 Apr 4, 2023
e5e0aab
More tweaks
jfy133 Apr 4, 2023
94e88d7
Everywhere account when no-runmerging for single libs
jfy133 Apr 4, 2023
ce97a11
Add final documentation
jfy133 Apr 15, 2023
3f34603
Prettier
jfy133 Apr 15, 2023
ee031eb
Apply suggestions from code review
jfy133 Apr 20, 2023
105bac7
Apply suggestions from code review
jfy133 Apr 20, 2023
0245c48
Merge branch 'dev' into final-reads-saving
jfy133 Apr 20, 2023
5d90c77
Logic safety!
jfy133 Apr 20, 2023
31e3c21
Make all saveAs conditions consistent
jfy133 Apr 20, 2023
ee76a5f
Update conf/modules.config
jfy133 Apr 21, 2023
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Added`

- [#272](https://github.com/nf-core/taxprofiler/pull/272) - Add saving of final 'analysis-ready-reads' to dedicated directory. (❤️ to @alexhbnr for reporting, added by @jfy133)

### `Fixed`

- [#271](https://github.com/nf-core/taxprofiler/pull/271/files) Improved standardised table generation documentation nd mOTUs manual database download tutorial (♥ to @prototaxites for reporting, fix by @jfy133)
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192 changes: 145 additions & 47 deletions conf/modules.config
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Expand Up @@ -71,6 +71,14 @@ process {
path: { "${params.outdir}/fastp" },
mode: params.publish_dir_mode,
pattern: '*.{log,html,json}'
],
[
path: { "${params.outdir}/analysis_ready_fastqs" },
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.save_analysis_ready_fastqs,
// Don't know why `!` doesn't work here, but `== false` makes it work...
saveAs: { ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs ? it : null }
]
]
}
Expand Down Expand Up @@ -99,6 +107,13 @@ process {
path: { "${params.outdir}/fastp" },
mode: params.publish_dir_mode,
pattern: '*.{log,html,json}'
],
[
path: { "${params.outdir}/analysis_ready_fastqs" },
mode: params.publish_dir_mode,
pattern: params.shortread_qc_mergepairs ? '*merged.fastq.gz' : '*.fastp.fastq.gz',
enabled: params.save_analysis_ready_fastqs,
saveAs: { ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs ? it : null }
]
]
}
Expand All @@ -122,6 +137,13 @@ process {
path: { "${params.outdir}/adapterremoval" },
mode: params.publish_dir_mode,
pattern: '*.settings'
],
[
path: { "${params.outdir}/analysis_ready_fastqs" },
mode: params.publish_dir_mode,
pattern: '*truncated.fastq.gz',
enabled: params.save_analysis_ready_fastqs,
saveAs: { ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs ? it : null }
]
]
}
Expand All @@ -148,6 +170,27 @@ process {
path: { "${params.outdir}/adapterremoval" },
mode: params.publish_dir_mode,
pattern: '*.settings'
],
[
path: { "${params.outdir}/analysis_ready_fastqs" },
mode: params.publish_dir_mode,
pattern: '*{truncated.fastq,singleton.truncated}.gz',
enabled: params.save_analysis_ready_fastqs,
saveAs: { ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && !params.shortread_qc_mergepairs && params.save_analysis_ready_fastqs ? it : null}
]
]
}

// AdapterRemoval separate output merging
withName: CAT_FASTQ {
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
[
path: { "${params.outdir}/analysis_ready_fastqs" },
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.save_analysis_ready_fastqs,
saveAs: { ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs ? it : null }
]
]
}
Expand All @@ -165,6 +208,13 @@ process {
path: { "${params.outdir}/porechop" },
mode: params.publish_dir_mode,
pattern: '*.log'
],
[
path: { "${params.outdir}/analysis_ready_fastqs" },
mode: params.publish_dir_mode,
pattern: '*_porechopped.fastq.gz',
enabled: params.save_analysis_ready_fastqs,
saveAs: { ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && !params.perform_longread_hostremoval && params.longread_qc_skipqualityfilter && !params.longread_qc_skipadaptertrim && params.perform_longread_qc && params.save_analysis_ready_fastqs ? it : null }
]
]
}
Expand All @@ -188,16 +238,82 @@ process {
path: { "${params.outdir}/filtlong" },
mode: params.publish_dir_mode,
pattern: '*.log'
],
[
path: { "${params.outdir}/analysis_ready_fastqs" },
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.save_analysis_ready_fastqs,
saveAs: { ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && !params.perform_longread_hostremoval && !params.longread_qc_skipqualityfilter && params.perform_longread_qc && params.save_analysis_ready_fastqs ? it : null }
]
]
}

withName: BBMAP_BBDUK {
ext.args = [
"entropy=${params.shortread_complexityfilter_entropy}",
"entropywindow=${params.shortread_complexityfilter_bbduk_windowsize}",
params.shortread_complexityfilter_bbduk_mask ? "entropymask=t" : "entropymask=f"
].join(' ').trim()
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
[
path: { "${params.outdir}/bbduk/" },
mode: params.publish_dir_mode,
pattern: '*.{fastq.gz}',
enabled: params.save_complexityfiltered_reads
],
[
path: { "${params.outdir}/bbduk/" },
mode: params.publish_dir_mode,
pattern: '*.log'
],
[
path: { "${params.outdir}/analysis_ready_fastqs" },
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.save_analysis_ready_fastqs,
saveAs: { ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && !params.perform_shortread_hostremoval && params.shortread_complexityfilter_tool && params.save_analysis_ready_fastqs ? it : null }
]
]
}

withName: PRINSEQPLUSPLUS {
ext.args = [
params.shortread_complexityfilter_prinseqplusplus_mode == 'dust' ? "-lc_dust=${params.shortread_complexityfilter_prinseqplusplus_dustscore}" : "-lc_entropy=${params.shortread_complexityfilter_entropy}",
"-trim_qual_left=0 -trim_qual_left=0 -trim_qual_window=0 -trim_qual_step=0",
].join(' ').trim()
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
[
path: { "${params.outdir}/prinseqplusplus/" },
mode: params.publish_dir_mode,
pattern: '*{_good_out.fastq.gz,_good_out_R1.fastq.gz,_good_out_R2.fastq.gz}',
enabled: params.save_complexityfiltered_reads
],
[
path: { "${params.outdir}/prinseqplusplus/" },
mode: params.publish_dir_mode,
pattern: '*.log'
],
[
path: { "${params.outdir}/analysis_ready_fastqs" },
mode: params.publish_dir_mode,
pattern: '*{_good_out.fastq.gz,_good_out_R1.fastq.gz,_good_out_R2.fastq.gz}',
enabled: params.save_analysis_ready_fastqs,
saveAs: { ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && !params.perform_shortread_hostremoval && params.shortread_complexityfilter_tool && params.save_analysis_ready_fastqs ? it : null }
]
]
}

withName: BOWTIE2_BUILD {
publishDir = [
[
path: { "${params.outdir}/bowtie2/build" },
mode: params.publish_dir_mode,
pattern: 'bowtie2',
enabled: params.save_hostremoval_index
]
]
}

Expand All @@ -221,6 +337,14 @@ process {
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.save_hostremoval_unmapped
],
[
path: { "${params.outdir}/analysis_ready_fastqs" },
mode: params.publish_dir_mode,
enabled: params.perform_shortread_hostremoval,
pattern: '*.fastq.gz',
enabled: params.save_analysis_ready_fastqs,
saveAs: { ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && params.perform_shortread_hostremoval && params.save_analysis_ready_fastqs ? it : null }
]
]
}
Expand Down Expand Up @@ -253,10 +377,19 @@ process {
withName: SAMTOOLS_FASTQ {
ext.prefix = { "${meta.id}_${meta.run_accession}.unmapped" }
publishDir = [
path: { "${params.outdir}/samtools/fastq" },
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.save_hostremoval_unmapped
[
path: { "${params.outdir}/samtools/fastq" },
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.save_hostremoval_unmapped
],
[
path: { "${params.outdir}/analysis_ready_fastqs" },
mode: params.publish_dir_mode,
pattern: '*.fq.gz',
enabled: params.save_analysis_ready_fastqs,
saveAs: { ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun) ) && params.perform_longread_hostremoval && params.save_analysis_ready_fastqs ? it : null }
]
]
}

Expand All @@ -269,59 +402,24 @@ process {
]
}

withName: BBMAP_BBDUK {
ext.args = [
"entropy=${params.shortread_complexityfilter_entropy}",
"entropywindow=${params.shortread_complexityfilter_bbduk_windowsize}",
params.shortread_complexityfilter_bbduk_mask ? "entropymask=t" : "entropymask=f"
].join(' ').trim()
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
[
path: { "${params.outdir}/bbduk/" },
mode: params.publish_dir_mode,
pattern: '*.{fastq.gz,log}',
enabled: params.save_complexityfiltered_reads
],
[
path: { "${params.outdir}/bbduk/" },
mode: params.publish_dir_mode,
pattern: '*.log'
]
]
}

withName: PRINSEQPLUSPLUS {
ext.args = [
params.shortread_complexityfilter_prinseqplusplus_mode == 'dust' ? "-lc_dust=${params.shortread_complexityfilter_prinseqplusplus_dustscore}" : "-lc_entropy=${params.shortread_complexityfilter_entropy}",
"-trim_qual_left=0 -trim_qual_left=0 -trim_qual_window=0 -trim_qual_step=0",
].join(' ').trim()
ext.prefix = { "${meta.id}_${meta.run_accession}" }
withName: MERGE_RUNS {
ext.prefix = { "${meta.id}" }
publishDir = [
[
path: { "${params.outdir}/prinseqplusplus/" },
path: { "${params.outdir}/run_merging/" },
mode: params.publish_dir_mode,
pattern: '*{_good_out.fastq.gz,_good_out_R1.fastq.gz,_good_out_R2.fastq.gz}',
enabled: params.save_complexityfiltered_reads
pattern: '*.fastq.gz',
enabled: params.save_runmerged_reads
],
[
path: { "${params.outdir}/prinseqplusplus/" },
path: { "${params.outdir}/analysis_ready_fastqs" },
mode: params.publish_dir_mode,
pattern: '*.log'
pattern: '*.fastq.gz',
enabled: params.perform_runmerging && params.save_analysis_ready_fastqs
]
]
}

withName: CAT_FASTQ {
ext.prefix = { "${meta.id}" }
publishDir = [
path: { "${params.outdir}/run_merging/" },
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.save_runmerged_reads
]
}

withName: MALT_RUN {
ext.args = { "${meta.db_params} -m ${params.malt_mode}" }
// one run with multiple samples, so fix ID to just db name to ensure clean log name
Expand Down
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