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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
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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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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?

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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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