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KBTools update to nf-core module #126

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merged 4 commits into from Jul 5, 2022
Merged

KBTools update to nf-core module #126

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a561f4b
Drop local Kbtools/count, update to latest module version
apeltzer Jul 5, 2022
9290e4c
Changelog
apeltzer Jul 5, 2022
aa7e256
Wrong module call
apeltzer Jul 5, 2022
f3ce79c
Should fix things
apeltzer Jul 5, 2022
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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

### Fixes

- Fixed Kallistobustools workflow [#123](https://github.com/nf-core/scrnaseq/issues/123) by upgrading to nf-core/modules module

## v2.0.0 - 2022-06-17 "Gray Nickel Beagle"

- Pipeline ported to dsl2
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9 changes: 6 additions & 3 deletions modules.json
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Expand Up @@ -22,13 +22,16 @@
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
"gunzip": {
"git_sha": "9aadd9a6d3f5964476582319b3a1c54a3e3fe7c9"
"git_sha": "fa37e0662690c4ec4260dae282fbce08777503e6"
},
"kallistobustools/count": {
"git_sha": "ed5594bee3eb38874cb282d288bc22ab6262a73e"
},
"kallistobustools/ref": {
"git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
"git_sha": "0f1e736212e5ae37036ac7e32b225087a8a9b154"
},
"multiqc": {
"git_sha": "e5f8924fabf4c8380f55fb7aee89fd2c268161b1"
"git_sha": "08376da6843b14c82d84d444784c0b3635bb7fd5"
},
"salmon/index": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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52 changes: 0 additions & 52 deletions modules/local/kallistobustools_count.nf
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10 changes: 10 additions & 0 deletions modules/nf-core/modules/gunzip/main.nf
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49 changes: 49 additions & 0 deletions modules/nf-core/modules/kallistobustools/count/main.nf
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67 changes: 67 additions & 0 deletions modules/nf-core/modules/kallistobustools/count/meta.yml
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6 changes: 3 additions & 3 deletions modules/nf-core/modules/kallistobustools/ref/main.nf
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4 changes: 2 additions & 2 deletions modules/nf-core/modules/multiqc/main.nf
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14 changes: 7 additions & 7 deletions subworkflows/local/kallisto_bustools.nf
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@@ -1,6 +1,6 @@
/* -- IMPORT LOCAL MODULES/SUBWORKFLOWS -- */
include { GENE_MAP } from '../../modules/local/gene_map'
include { KALLISTOBUSTOOLS_COUNT } from '../../modules/local/kallistobustools_count'
include {KALLISTOBUSTOOLS_COUNT } from '../../modules/nf-core/modules/kallistobustools/count/main'

/* -- IMPORT NF-CORE MODULES/SUBWORKFLOWS -- */
include { GUNZIP } from '../../modules/nf-core/modules/gunzip/main'
Expand Down Expand Up @@ -46,6 +46,8 @@ workflow KALLISTO_BUSTOOLS {
txp2gene = KALLISTOBUSTOOLS_REF.out.t2g.collect()
kallisto_index = KALLISTOBUSTOOLS_REF.out.index.collect()
ch_versions = ch_versions.mix(KALLISTOBUSTOOLS_REF.out.versions)
t1c = KALLISTOBUSTOOLS_REF.out.cdna_t2c.ifEmpty{ [] }
t2c = KALLISTOBUSTOOLS_REF.out.intron_t2c.ifEmpty{ [] }
}

/*
Expand All @@ -55,18 +57,16 @@ workflow KALLISTO_BUSTOOLS {
ch_fastq,
kallisto_index,
txp2gene,
[],
[],
false,
false,
kb_workflow,
t1c,
t2c,
protocol
)

ch_versions = ch_versions.mix(KALLISTOBUSTOOLS_COUNT.out.versions)

emit:
ch_versions
counts = KALLISTOBUSTOOLS_COUNT.out.counts
counts = KALLISTOBUSTOOLS_COUNT.out.count


}