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add fq lint #57

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1c37161
add fq_lint module
erkutilaslan Oct 29, 2024
0babe59
add fq_lint config
erkutilaslan Oct 30, 2024
5321066
add fq_lint documentation
erkutilaslan Oct 30, 2024
48eb720
fix fq_lint config typo
erkutilaslan Oct 30, 2024
2b75934
Merge branch 'dev' into fq_lint
erkutilaslan Oct 30, 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 @@ -10,6 +10,11 @@
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"fq/lint": {
"branch": "master",
"git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc",
"installed_by": ["modules"]
},
"multiqc": {
"branch": "master",
"git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
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5 changes: 5 additions & 0 deletions modules/nf-core/fq/lint/environment.yml
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33 changes: 33 additions & 0 deletions modules/nf-core/fq/lint/main.nf
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43 changes: 43 additions & 0 deletions modules/nf-core/fq/lint/meta.yml
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63 changes: 63 additions & 0 deletions modules/nf-core/fq/lint/tests/main.nf.test
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25 changes: 25 additions & 0 deletions modules/nf-core/fq/lint/tests/main.nf.test.snap
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2 changes: 2 additions & 0 deletions modules/nf-core/fq/lint/tests/tags.yml
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9 changes: 9 additions & 0 deletions workflows/seqinspector.nf
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Expand Up @@ -4,6 +4,7 @@
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
include { FASTQC } from '../modules/nf-core/fastqc/main'
include { FQ_LINT } from '../modules/nf-core/fq/lint/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 +40,14 @@ workflow SEQINSPECTOR {
ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip)
ch_versions = ch_versions.mix(FASTQC.out.versions.first())

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

//
// Collate and save software versions
//
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