-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
1 parent
2a93a2d
commit 0b6ce07
Showing
12 changed files
with
257 additions
and
90 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,8 @@ | ||
| process { | ||
| withLabel: ubuntu { container = 'nanozoo/template:3.8--e13dfeb' } | ||
| withLabel: bakta { container = 'nanozoo/bakta:1.2.1--bf38720' } | ||
| withLabel: bakta { container = 'nanozoo/bakta:1.6.1--c012822' } | ||
| withLabel: prokka { container = 'nanozoo/prokka:1.14.6--c99ff65' } | ||
| withLabel: eggnog { container = 'nanozoo/eggnog-mapper:2.1.9--4f2b6c0' } | ||
| withLabel: pgap { container = 'ncbi/pgap:2022-10-03.build6384' } | ||
| withLabel: pgap { container = 'ncbi/pgap:2022-10-03.build6384' } | ||
| withLabel: r { container = 'nanozoo/ggplot2:3.4.0--3367007' } | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,10 +1,10 @@ | ||
| process.executor = 'local' | ||
|
|
||
| process { | ||
| withLabel: ubuntu { cpus = 2 } | ||
| withLabel: ubuntu { cpus = params.cores } | ||
| withLabel: prokka { cpus = params.cores } | ||
| withLabel: bakta { cpus = params.cores } | ||
| withLabel: eggnog { cpus = params.cores } | ||
| withLabel: pgap { cpus = params.cores } | ||
|
|
||
| withLabel: r { cpus = params.cores } | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,8 @@ | ||
| process { | ||
| withLabel: ubuntu { cpus = 2; memory = '2 GB' } | ||
| withLabel: ubuntu { cpus = 8; memory = '16 GB' } | ||
| withLabel: bakta { cpus = 8; memory = '16 GB' } | ||
| withLabel: prokka { cpus = 8; memory = '16 GB' } | ||
| withLabel: eggnog { cpus = 8; memory = '16 GB' } | ||
| withLabel: pgap { cpus = 8; memory = '16 GB' } | ||
| withLabel: r { cpus = 8; memory = '16 GB' } | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,18 +1,69 @@ | ||
| include { analysis } from './process/analyis.nf' | ||
|
|
||
| workflow analysis{ | ||
| include { analysis} from './process/analysis.nf' | ||
| include { analysis as analysis_org} from './process/analysis.nf' | ||
| include { analysis as analysis_noise} from './process/analysis.nf' | ||
| include { analysis as analysis_split} from './process/analysis.nf' | ||
| workflow analysis_wf{ | ||
| take: | ||
| combined_annotation_ch | ||
| combined | ||
| main: | ||
| //OTHER APPROACH | ||
| // branched_ch = combined.branch { | ||
| // original: it[1][0] == "original" | ||
| // noise: it[1][0] == "noise" | ||
| // split: it[1][0] == "split" | ||
| // } | ||
|
|
||
| //WIP filter channel to only contain original, noise, split for analysis | ||
| combined_annotation_ch.filter( | ||
| // original_grouped = branched_ch.original.groupTuple(by:0).view() | ||
| // noise_grouped = branched_ch.noise.groupTuple(by:0) | ||
| // split_grouped = branched_ch.split.groupTuple(by:0) | ||
| // analysis(original_grouped) | ||
| //END OF OTHER APPROACH | ||
| //org_ch=combined.filter{ it -> it[1][0][0] == 'noise'}.view() | ||
| //gives prokka | ||
| //combined.map { it -> tuple (it[1]) }.view() | ||
| //gives bakta | ||
| //combined.map { it -> tuple (it[2]) }.view() | ||
|
|
||
| original=combined.map { it -> | ||
| tuple( it[0], it[1].findAll { it.first() == "original" },it[2].findAll { it.first() == "original" }, | ||
| it[3].findAll { it.first() == "original" },it[4].findAll { it.first() == "original" } ) | ||
| } | ||
|
|
||
| analysis(combined_annotation_ch) | ||
| noise=combined.map { it -> | ||
| tuple( it[0], it[1].findAll { it.first() == "noise" },it[2].findAll { it.first() == "noise" }, | ||
| it[3].findAll { it.first() == "noise" },it[4].findAll { it.first() == "noise" } ) | ||
| } | ||
|
|
||
| split=combined.map { it -> | ||
| tuple( it[0], it[1].findAll { it.first() == "split" },it[2].findAll { it.first() == "split" }, | ||
| it[3].findAll { it.first() == "split" },it[4].findAll { it.first() == "split" } ) | ||
| } | ||
| original_proc=original.map { it -> tuple(it[0], | ||
| it[1].flatten()[1],it[1].flatten()[2],it[1].flatten()[3], | ||
| it[2].flatten()[1],it[2].flatten()[2],it[2].flatten()[3], | ||
| it[3].flatten()[1],it[3].flatten()[2],it[3].flatten()[3], | ||
| it[4].flatten()[1],it[4].flatten()[2],it[4].flatten()[3])} | ||
|
|
||
| noise=noise.map { it -> tuple(it[0], | ||
| it[1].flatten()[1],it[1].flatten()[2],it[1].flatten()[3], | ||
| it[2].flatten()[1],it[2].flatten()[2],it[2].flatten()[3], | ||
| it[3].flatten()[1],it[3].flatten()[2],it[3].flatten()[3], | ||
| it[4].flatten()[1],it[4].flatten()[2],it[4].flatten()[3])} | ||
|
|
||
| split=split.map { it -> tuple(it[0], | ||
| it[1].flatten()[1],it[1].flatten()[2],it[1].flatten()[3], | ||
| it[2].flatten()[1],it[2].flatten()[2],it[2].flatten()[3], | ||
| it[3].flatten()[1],it[3].flatten()[2],it[3].flatten()[3], | ||
| it[4].flatten()[1],it[4].flatten()[2],it[4].flatten()[3])} | ||
|
|
||
| report_original=analysis_org(original_proc,'original') | ||
| report_noise=analysis_noise(noise,'noise') | ||
| report_split=analysis_split(split,'split') | ||
|
|
||
| //emit: | ||
| report_original.mix(report_noise).mix(report_split).collectFile(name: 'collected_reports.csv', keepHeader: true ,storeDir: '${params.output}/final_report/') | ||
|
|
||
| emit: | ||
| combined | ||
|
|
||
| } | ||
|
|
Oops, something went wrong.