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Addseqtk #2

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merged 3 commits into from
Jun 19, 2024
Merged

Addseqtk #2

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8498a70
installed and run seqtk successfully
U13bs1125 Jun 18, 2024
dfb7e54
Effected the changes of Seqtk workflow to run on each channel individ…
U13bs1125 Jun 18, 2024
57fd146
Update pairgenomealign.nf
U13bs1125 Jun 19, 2024
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5 changes: 5 additions & 0 deletions modules.json
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Original file line number Diff line number Diff line change
Expand Up @@ -49,6 +49,11 @@
"branch": "master",
"git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
"installed_by": ["modules"]
},
"seqtk/cutn": {
"branch": "master",
"git_sha": "7f88aae93c69586c0789322b77743ee0ef469502",
"installed_by": ["modules"]
}
}
},
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7 changes: 7 additions & 0 deletions modules/nf-core/seqtk/cutn/environment.yml
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49 changes: 49 additions & 0 deletions modules/nf-core/seqtk/cutn/main.nf
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41 changes: 41 additions & 0 deletions modules/nf-core/seqtk/cutn/meta.yml
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57 changes: 57 additions & 0 deletions modules/nf-core/seqtk/cutn/tests/main.nf.test
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70 changes: 70 additions & 0 deletions modules/nf-core/seqtk/cutn/tests/main.nf.test.snap
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2 changes: 2 additions & 0 deletions modules/nf-core/seqtk/cutn/tests/tags.yml
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16 changes: 16 additions & 0 deletions workflows/pairgenomealign.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,8 @@

include { ASSEMBLYSCAN } from '../modules/nf-core/assemblyscan/main'
include { PAIRALIGN_M2M } from '../subworkflows/local/pairalign_m2m/main'
include { SEQTK_CUTN as SEQTK_CUTN_TARGET } from '../modules/nf-core/seqtk/cutn/main'
include { SEQTK_CUTN as SEQTK_CUTN_QUERY } from '../modules/nf-core/seqtk/cutn/main'
include { PAIRALIGN_M2O } from '../subworkflows/local/pairalign_m2o/main'
include { MULTIQC } from '../modules/nf-core/multiqc/main'
include { paramsSummaryMap } from 'plugin/nf-validation'
Expand All @@ -30,6 +32,20 @@ workflow PAIRGENOMEALIGN {
ch_versions = Channel.empty()
ch_multiqc_files = Channel.empty()

//
// MODULE: seqtk_cutn_target
//
SEQTK_CUTN_TARGET (
ch_targetgenome
)

//
// MODULE: seqtk_cutn_query
//
SEQTK_CUTN_QUERY (
ch_samplesheet
)

//
// MODULE: assembly-scan
//
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