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refactor: Use fastx/collapser from nf-core #34

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Mar 31, 2024
Merged

refactor: Use fastx/collapser from nf-core #34

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8 changes: 8 additions & 0 deletions modules.json
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Original file line number Diff line number Diff line change
Expand Up @@ -59,6 +59,14 @@
"modules"
]
},
"fastx/collapser": {
"branch": "master",
"git_sha": "210e7c8f33f8ca0e35e027aa8889d03205a57b88",
"installed_by": [
"modules"
],
"patch": "modules/nf-core/fastx/collapser/fastx-collapser.diff"
},
"gunzip": {
"branch": "master",
"git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
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33 changes: 0 additions & 33 deletions modules/local/fastx_toolkit/collapser.nf
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9 changes: 9 additions & 0 deletions modules/nf-core/fastx/collapser/environment.yml
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14 changes: 14 additions & 0 deletions modules/nf-core/fastx/collapser/fastx-collapser.diff
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46 changes: 46 additions & 0 deletions modules/nf-core/fastx/collapser/main.nf
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51 changes: 51 additions & 0 deletions modules/nf-core/fastx/collapser/meta.yml
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61 changes: 61 additions & 0 deletions modules/nf-core/fastx/collapser/tests/main.nf.test
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68 changes: 68 additions & 0 deletions modules/nf-core/fastx/collapser/tests/main.nf.test.snap
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2 changes: 2 additions & 0 deletions modules/nf-core/fastx/collapser/tests/tags.yml
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4 changes: 2 additions & 2 deletions workflows/euryale.nf
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Expand Up @@ -36,7 +36,6 @@ ch_multiqc_custom_methods_description = params.multiqc_methods_description ? fil
//
// MODULES
//
include { FASTX_COLLAPSER } from '../modules/local/fastx_toolkit/collapser'

//
// SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
Expand All @@ -59,6 +58,7 @@ include { FUNCTIONAL } from '../subworkflows/local/functional'
// MODULE: Installed directly from nf-core/modules
//
include { GUNZIP } from '../modules/nf-core/gunzip/main'
include { FASTX_COLLAPSER } from '../modules/nf-core/fastx/collapser'
include { MULTIQC } from '../modules/nf-core/multiqc/main'
include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'

Expand Down Expand Up @@ -143,7 +143,7 @@ workflow EURYALE {
decompressed_reads
)

FASTX_COLLAPSER.out.collapsed.set { clean_reads }
FASTX_COLLAPSER.out.fasta.set { clean_reads }
}

if (!params.skip_alignment) {
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