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Update mirtop, process samples independently and join results #438

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3 changes: 2 additions & 1 deletion CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [[#427]](https://github.com/nf-core/smrnaseq/pull/427) - Add [nf-core pigz uncompress](https://github.com/nf-core/smrnaseq/issues/422) - replace local `mirdeep_pigz`
- [[#429]](https://github.com/nf-core/smrnaseq/pull/429) - Make [saving of intermediate files optional](https://github.com/nf-core/smrnaseq/issues/424) - Allows user to choose whether to save intermediate files or not. Replaces several params that referred to the same such as `params.save_aligned` and `params.save_aligned_mirna_quant`.
- [[#433]](https://github.com/nf-core/smrnaseq/pull/433) - Replace local instances of bowtie for nf-core [`bowtie2`](https://github.com/nf-core/smrnaseq/issues/434) and [`bowtie1`](https://github.com/nf-core/smrnaseq/issues/433) - Additionally adds a `bioawk` module that cleans fasta files.
- [[#432]](https://github.com/nf-core/smrnaseq/pull/432) - Update [MultiQC to latest version](https://github.com/nf-core/smrnaseq/issues/428) - Include UMIcollapse module in MultiQC.
- [[#432]](https://github.com/nf-core/smrnaseq/pull/432) - Update [MultiQC and all modules to latest version](https://github.com/nf-core/smrnaseq/issues/428) - Include UMIcollapse module in MultiQC.
- [[#435]](https://github.com/nf-core/smrnaseq/pull/435) - Update [Mirtop to latest version](https://github.com/nf-core/smrnaseq/issues/437) - Process samples separately and join results with `CSVTK_JOIN`.

## v2.3.1 - 2024-04-18 - Gray Zinc Dalmation Patch

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20 changes: 18 additions & 2 deletions conf/modules.config
Original file line number Diff line number Diff line change
Expand Up @@ -370,14 +370,30 @@ process {
]
}

withName: 'MIRTOP_COUNTS' {
withName: 'NFCORE_SMRNASEQ:MIRNA_QUANT:BAM_STATS_MIRNA_MIRTOP:MIRTOP_COUNTS' {
ext.args = '--add-extra'
publishDir = [ enabled: false ]
}

withName: 'NFCORE_SMRNASEQ:MIRNA_QUANT:BAM_STATS_MIRNA_MIRTOP:MIRTOP_STATS' {
publishDir = [ enabled: false ]
}

withName: 'MIRTOP_GFF' {
withName: 'NFCORE_SMRNASEQ:MIRNA_QUANT:BAM_STATS_MIRNA_MIRTOP:MIRTOP_GFF' {
publishDir = [
path: { "${params.outdir}/mirna_quant/mirtop/gff" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'NFCORE_SMRNASEQ:MIRNA_QUANT:CSVTK_JOIN' {
ext.args = "--fields 'UID,Read,miRNA,Variant,iso_5p,iso_3p,iso_add3p,iso_snp,iso_5p_nt,iso_3p_nt,iso_add3p_nt,iso_snp_nt' --tabs --outer-join --na \"0\" --out-delimiter \"\t\""
ext.prefix = "joined_samples_mirtop"
publishDir = [
path: { "${params.outdir}/mirna_quant/mirtop" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

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6 changes: 3 additions & 3 deletions docs/output.md
Original file line number Diff line number Diff line change
Expand Up @@ -140,9 +140,9 @@ If `--save_intermediates` is specified, these files will be placed in this direc

**Output directory: `results/mirtop`**

- `mirtop.gff`: [mirgff3](https://github.com/miRTop/mirGFF3) file
- `mirtop.tsv`: tabular file of the previous file for easy integration with downstream analysis.
- `mirtop_rawData.tsv`: File compatible with [isomiRs](http://lpantano.github.io/isomiRs/reference/IsomirDataSeqFromMirtop.html) Bioconductor package to perform isomiRs analysis.
- `gff/{sample.id}.gff`: [mirgff3](https://github.com/miRTop/mirGFF3) file
- `joined_samples_mirtop.tsv`: tabular file of the previous file for easy integration with downstream analysis.
- `export/{sample.id}_mirtop_rawData.tsv`: File compatible with [isomiRs](http://lpantano.github.io/isomiRs/reference/IsomirDataSeqFromMirtop.html) Bioconductor package to perform isomiRs analysis.
- `mirna.tsv`: tabular file with miRNA counts after summarizing unique isomiRs for each miRNA

## miRDeep2
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15 changes: 10 additions & 5 deletions modules.json
Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,11 @@
"git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["modules"]
},
"csvtk/join": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"fastp": {
"branch": "master",
"git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
Expand All @@ -53,22 +58,22 @@
},
"mirtop/counts": {
"branch": "master",
"git_sha": "43b2b702abd8ab2cb1aa1365763f518413ad5721",
"git_sha": "196062335bb9ec979075bf2212f64a369b927b0d",
"installed_by": ["bam_stats_mirna_mirtop"]
},
"mirtop/export": {
"branch": "master",
"git_sha": "43b2b702abd8ab2cb1aa1365763f518413ad5721",
"git_sha": "196062335bb9ec979075bf2212f64a369b927b0d",
"installed_by": ["bam_stats_mirna_mirtop"]
},
"mirtop/gff": {
"branch": "master",
"git_sha": "43b2b702abd8ab2cb1aa1365763f518413ad5721",
"git_sha": "196062335bb9ec979075bf2212f64a369b927b0d",
"installed_by": ["bam_stats_mirna_mirtop"]
},
"mirtop/stats": {
"branch": "master",
"git_sha": "43b2b702abd8ab2cb1aa1365763f518413ad5721",
"git_sha": "196062335bb9ec979075bf2212f64a369b927b0d",
"installed_by": ["bam_stats_mirna_mirtop"]
},
"mirtrace/qc": {
Expand Down Expand Up @@ -148,7 +153,7 @@
},
"bam_stats_mirna_mirtop": {
"branch": "master",
"git_sha": "43b2b702abd8ab2cb1aa1365763f518413ad5721",
"git_sha": "196062335bb9ec979075bf2212f64a369b927b0d",
"installed_by": ["subworkflows"]
},
"bam_stats_samtools": {
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2 changes: 1 addition & 1 deletion modules/local/datatable_merge/datatable_merge.nf
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ process TABLE_MERGE {
'biocontainers/r-data.table:1.12.2' }"

input:
path mirtop
tuple val(meta), path(mirtop)

output:
path "mirna.tsv" , emit: mirna_tsv
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5 changes: 5 additions & 0 deletions modules/nf-core/csvtk/join/environment.yml

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49 changes: 49 additions & 0 deletions modules/nf-core/csvtk/join/main.nf

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45 changes: 45 additions & 0 deletions modules/nf-core/csvtk/join/meta.yml

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64 changes: 64 additions & 0 deletions modules/nf-core/csvtk/join/tests/main.nf.test

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60 changes: 60 additions & 0 deletions modules/nf-core/csvtk/join/tests/main.nf.test.snap

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5 changes: 5 additions & 0 deletions modules/nf-core/csvtk/join/tests/nextflow.config

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2 changes: 2 additions & 0 deletions modules/nf-core/csvtk/join/tests/tags.yml

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10 changes: 7 additions & 3 deletions modules/nf-core/mirtop/counts/environment.yml

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4 changes: 1 addition & 3 deletions modules/nf-core/mirtop/counts/main.nf

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