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fq lint module update: exit on failed validation #7000

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fq lint module update: exit on failed validation #7000

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b3c6ecb
Have fq lint module exit on failed validation
oligomyeggo Nov 15, 2024
4e8ef40
Update subworkflow
oligomyeggo Nov 15, 2024
cc79afc
Add module output to subworkflow
oligomyeggo Nov 15, 2024
98a2105
Remove custom changes from fq lint main.nf
oligomyeggo Nov 18, 2024
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14 changes: 14 additions & 0 deletions subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@ include { BBMAP_BBSPLIT } from '../../../modules/nf-core/bbmap
include { CAT_FASTQ } from '../../../modules/nf-core/cat/fastq/main'
include { SORTMERNA } from '../../../modules/nf-core/sortmerna/main'
include { SORTMERNA as SORTMERNA_INDEX } from '../../../modules/nf-core/sortmerna/main'
include { FQ_LINT } from '../../../modules/nf-core/fq/lint/main'

include { FASTQ_SUBSAMPLE_FQ_SALMON } from '../fastq_subsample_fq_salmon'
include { FASTQ_FASTQC_UMITOOLS_TRIMGALORE } from '../fastq_fastqc_umitools_trimgalore'
Expand Down Expand Up @@ -106,6 +107,7 @@ workflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS {
umi_discard_read // integer: 0, 1 or 2
stranded_threshold // float: The fraction of stranded reads that must be assigned to a strandedness for confident assignment. Must be at least 0.5
unstranded_threshold // float: The difference in fraction of stranded reads assigned to 'forward' and 'reverse' below which a sample is classified as 'unstranded'
skip_linting // boolean: true/false

main:

Expand All @@ -114,6 +116,17 @@ workflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS {
ch_trim_read_count = Channel.empty()
ch_multiqc_files = Channel.empty()

//
// MODULE: Lint FastQ files
//
if(!skip_linting) {
FQ_LINT (
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ch_fastq_lint.map{ meta, fastqs -> [meta, fastqs.flatten()] }
)
ch_versions = ch_versions.mix(FQ_LINT.out.versions.first())
ch_lint_log = FQ_LINT.out.lint
}

ch_reads
.branch {
meta, fastqs ->
Expand Down Expand Up @@ -312,6 +325,7 @@ workflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS {

emit:

lint_log = ch_lint_log
reads = ch_strand_inferred_fastq
trim_read_count = ch_trim_read_count

Expand Down
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