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Adds FASTQE for summarising FASTQ scores as emojis #66

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Adds FASTQE for summarising FASTQ scores as emojis #66

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4d807e7
Adds FASTQE for summarising FASTQ scores as emojis
adamrtalbot Nov 1, 2024
7ae7132
fixup
adamrtalbot Nov 1, 2024
1110e8b
Update seqinspector.nf
adamrtalbot Nov 1, 2024
7c33aca
Merge branch 'dev' into add_fastqe_module
adamrtalbot Dec 17, 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"]
},
"fastqe": {
"branch": "master",
"git_sha": "cab0b8fdc4f785810f49423d8141a0773c21eb3b",
"installed_by": ["modules"]
},
"multiqc": {
"branch": "master",
"git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
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7 changes: 7 additions & 0 deletions modules/nf-core/fastqe/environment.yml
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48 changes: 48 additions & 0 deletions modules/nf-core/fastqe/main.nf
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50 changes: 50 additions & 0 deletions modules/nf-core/fastqe/meta.yml
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100 changes: 100 additions & 0 deletions modules/nf-core/fastqe/tests/main.nf.test
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142 changes: 142 additions & 0 deletions modules/nf-core/fastqe/tests/main.nf.test.snap
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14 changes: 12 additions & 2 deletions workflows/seqinspector.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@

include { SEQTK_SAMPLE } from '../modules/nf-core/seqtk/sample/main'
include { FASTQC } from '../modules/nf-core/fastqc/main'
include { FASTQE } from '../modules/nf-core/fastqe/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 All @@ -28,8 +29,8 @@ workflow SEQINSPECTOR {
main:

ch_versions = Channel.empty()
ch_multiqc_files = Channel.empty()
ch_multiqc_extra_files = Channel.empty()
ch_multiqc_files = Channel.empty()
ch_multiqc_extra_files = Channel.empty()
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Why the extra spaces?

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Oh alignment. My editor is still messed up. Can you put it back please?

ch_multiqc_reports = Channel.empty()

//
Expand Down Expand Up @@ -58,6 +59,15 @@ workflow SEQINSPECTOR {
ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip)
ch_versions = ch_versions.mix(FASTQC.out.versions.first())

// FASTQE
FASTQE(
ch_sample_sized.map {
meta, subsampled -> [meta, subsampled]
}
)
ch_multiqc_files = ch_multiqc_files.mix(FASTQE.out.tsv)
ch_versions = ch_versions.mix(FASTQE.out.versions.first())

//
// Collate and save software versions
//
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