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add bbmap clumpify #52

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6dc45ac
add module bbmap/clumpify
erkutilaslan Oct 28, 2024
445edd1
cleanup code
erkutilaslan Oct 28, 2024
ba4bac0
fix lint errors
erkutilaslan Oct 28, 2024
b0e2558
fix comment
erkutilaslan Oct 29, 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 @@ -5,6 +5,11 @@
"https://github.com/nf-core/modules.git": {
"modules": {
"nf-core": {
"bbmap/clumpify": {
"branch": "master",
"git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc",
"installed_by": ["modules"]
},
"fastqc": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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5 changes: 5 additions & 0 deletions modules/nf-core/bbmap/clumpify/environment.yml
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38 changes: 38 additions & 0 deletions modules/nf-core/bbmap/clumpify/main.nf
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56 changes: 56 additions & 0 deletions modules/nf-core/bbmap/clumpify/meta.yml
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72 changes: 72 additions & 0 deletions modules/nf-core/bbmap/clumpify/tests/main.nf.test
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49 changes: 49 additions & 0 deletions modules/nf-core/bbmap/clumpify/tests/main.nf.test.snap
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11 changes: 11 additions & 0 deletions workflows/seqinspector.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,8 @@
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
include { FASTQC } from '../modules/nf-core/fastqc/main'
include { BBMAP_CLUMPIFY } from '../modules/nf-core/bbmap/clumpify/main'


include { MULTIQC as MULTIQC_GLOBAL } from '../modules/nf-core/multiqc/main'
include { MULTIQC as MULTIQC_PER_TAG } from '../modules/nf-core/multiqc/main'
Expand Down Expand Up @@ -39,6 +41,15 @@ workflow SEQINSPECTOR {
ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip)
ch_versions = ch_versions.mix(FASTQC.out.versions.first())

//
// MODULE: Run BBMAP_CLUMPIFY
//
BBMAP_CLUMPIFY (
ch_samplesheet
)
ch_versions = ch_versions.mix(BBMAP_CLUMPIFY.out.versions)


//
// Collate and save software versions
//
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