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‎main.nf‎

Lines changed: 65 additions & 62 deletions
Original file line numberDiff line numberDiff line change
@@ -15,6 +15,8 @@
1515
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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*/
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18+
nextflow.preview.types = true
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1820
include { FASTA_INDEX_BISMARK_BWAMETH } from './subworkflows/nf-core/fasta_index_bismark_bwameth/main'
1921
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_methylseq_pipeline'
2022
include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_methylseq_pipeline'
@@ -23,6 +25,7 @@ include { METHYLSEQ } from './workflows/methylseq/'
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2426
include { Sample } from './utils/types.nf'
2527
include { MethylseqParams } from './workflows/methylseq/'
28+
include { MethylseqResult } from './workflows/methylseq/'
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -293,7 +296,7 @@ workflow NFCORE_METHYLSEQ {
293296
bismark_index = params_index.bismark_index ?: bismarkIndex(params_methylseq.aligner)
294297
bwameth_index = params_index.bwameth_index ?: (getGenomeAttribute('bwameth', params) ? file(getGenomeAttribute('bwameth', params)) : null)
295298

296-
FASTA_INDEX_BISMARK_BWAMETH(
299+
indices = FASTA_INDEX_BISMARK_BWAMETH(
297300
fasta,
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fasta_index,
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bismark_index,
@@ -306,24 +309,24 @@ workflow NFCORE_METHYLSEQ {
306309
// WORKFLOW: Run pipeline
307310
//
308311

309-
METHYLSEQ (
312+
methylseq = METHYLSEQ (
310313
ch_samples,
311-
FASTA_INDEX_BISMARK_BWAMETH.out.fasta,
312-
FASTA_INDEX_BISMARK_BWAMETH.out.fasta_index,
313-
FASTA_INDEX_BISMARK_BWAMETH.out.bismark_index,
314-
FASTA_INDEX_BISMARK_BWAMETH.out.bwameth_index,
314+
indices.fasta,
315+
indices.fasta_index,
316+
indices.bismark_index,
317+
indices.bwameth_index,
315318
params_methylseq
316319
)
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318321
emit:
319-
fasta_index = FASTA_INDEX_BISMARK_BWAMETH.out.fasta_index
320-
bismark_index = FASTA_INDEX_BISMARK_BWAMETH.out.bismark_index
321-
bwameth_index = FASTA_INDEX_BISMARK_BWAMETH.out.bwameth_index
322-
results = METHYLSEQ.out.results
323-
bismark_summary = METHYLSEQ.out.bismark_summary
324-
reference_dict = METHYLSEQ.out.reference_dict
325-
intervallist = METHYLSEQ.out.intervallist
326-
multiqc_report = METHYLSEQ.out.multiqc_report
322+
fasta_index = indices.fasta_index
323+
bismark_index = indices.bismark_index
324+
bwameth_index = indices.bwameth_index
325+
results = methylseq.results
326+
bismark_summary = methylseq.bismark_summary
327+
reference_dict = methylseq.reference_dict
328+
intervallist = methylseq.intervallist
329+
multiqc_report = methylseq.multiqc_report
327330

328331
}
329332

@@ -354,7 +357,7 @@ workflow {
354357
//
355358
// SUBWORKFLOW: Run initialisation tasks
356359
//
357-
PIPELINE_INITIALISATION (
360+
ch_samples = PIPELINE_INITIALISATION (
358361
params.input,
359362
params.version,
360363
params.validate_params,
@@ -366,8 +369,8 @@ workflow {
366369
//
367370
// WORKFLOW: Run main workflow
368371
//
369-
NFCORE_METHYLSEQ (
370-
PIPELINE_INITIALISATION.out.samplesheet,
372+
methylseq = NFCORE_METHYLSEQ (
373+
ch_samples,
371374
params,
372375
params
373376
)
@@ -381,94 +384,94 @@ workflow {
381384
params.outdir,
382385
params.monochrome_logs,
383386
params.hook_url,
384-
NFCORE_METHYLSEQ.out.multiqc_report
387+
methylseq.multiqc_report
385388
)
386389

387390
publish:
388-
fasta_index = NFCORE_METHYLSEQ.out.fasta_index
389-
bismark_index = NFCORE_METHYLSEQ.out.bismark_index
390-
bwameth_index = NFCORE_METHYLSEQ.out.bwameth_index
391-
samples = NFCORE_METHYLSEQ.out.results
392-
bismark_summary = NFCORE_METHYLSEQ.out.bismark_summary
393-
reference_dict = NFCORE_METHYLSEQ.out.reference_dict
394-
intervallist = NFCORE_METHYLSEQ.out.intervallist
395-
multiqc_report = NFCORE_METHYLSEQ.out.multiqc_report
391+
fasta_index = methylseq.fasta_index
392+
bismark_index = methylseq.bismark_index
393+
bwameth_index = methylseq.bwameth_index
394+
samples = methylseq.results
395+
bismark_summary = methylseq.bismark_summary
396+
reference_dict = methylseq.reference_dict
397+
intervallist = methylseq.intervallist
398+
multiqc_report = methylseq.multiqc_report
396399
}
397400

398401
output {
399-
fasta_index {
402+
fasta_index: Path {
400403
path "${params.aligner}/reference_genome"
401404
enabled params.save_reference
402405
}
403406

404-
bismark_index {
407+
bismark_index: Path {
405408
path "${params.aligner}/reference_genome"
406409
enabled params.save_reference
407410
}
408411

409-
bwameth_index {
412+
bwameth_index: Path {
410413
path "${params.aligner}/reference_genome"
411414
enabled params.save_reference
412415
}
413416

414-
samples {
417+
samples: Channel<MethylseqResult> {
415418
path { r ->
416-
r.fastqc_html >> "fastqc"
417-
r.fastqc_zip >> "fastqc/zips"
419+
r.fastqc_html >> "fastqc/"
420+
r.fastqc_zip >> "fastqc/zips/"
418421

419-
r.trim_reads >> (params.save_trimmed ? "trimgalore" : null)
420-
r.trim_log >> "trimgalore/logs"
421-
r.trim_unpaired >> (params.save_trimmed ? "trimgalore" : null)
422-
r.trim_html >> "trimgalore/fastqc"
423-
r.trim_zip >> "trimgalore/fastqc/zips"
422+
r.trim_reads >> (params.save_trimmed ? "trimgalore/" : null)
423+
r.trim_log >> "trimgalore/logs/"
424+
r.trim_unpaired >> (params.save_trimmed ? "trimgalore/" : null)
425+
r.trim_html >> "trimgalore/fastqc/"
426+
r.trim_zip >> "trimgalore/fastqc/zips/"
424427

425-
r.bam >> (params.save_align_intermeds ? "${params.aligner}/alignments" : null)
428+
r.bam >> (params.save_align_intermeds ? "${params.aligner}/alignments/" : null)
426429
r.bai >> (params.skip_deduplication ? "${params.aligner}/alignments/" : "${params.aligner}/deduplicated/")
427430

428-
r.align_report >> "${params.aligner}/alignments/logs"
429-
r.unmapped >> "${params.aligner}/alignments/unmapped"
430-
r.dedup_report >> "${params.aligner}/deduplicated/logs"
431-
r.coverage2cytosine_coverage >> "bismark/coverage2cytosine/coverage"
432-
r.coverage2cytosine_report >> "bismark/coverage2cytosine/reports"
433-
r.coverage2cytosine_summary >> "bismark/coverage2cytosine/summaries"
434-
r.methylation_bedgraph >> "${params.aligner}/methylation_calls/bedGraph"
435-
r.methylation_calls >> "${params.aligner}/methylation_calls/methylation_calls"
436-
r.methylation_coverage >> "${params.aligner}/methylation_calls/methylation_coverage"
437-
r.methylation_report >> "${params.aligner}/methylation_calls/splitting_report"
438-
r.methylation_mbias >> "${params.aligner}/methylation_calls/mbias"
439-
r.bismark_report >> "${params.aligner}/reports"
431+
r.align_report >> "${params.aligner}/alignments/logs/"
432+
r.unmapped >> "${params.aligner}/alignments/unmapped/"
433+
r.dedup_report >> "${params.aligner}/deduplicated/logs/"
434+
r.coverage2cytosine_coverage >> "bismark/coverage2cytosine/coverage/"
435+
r.coverage2cytosine_report >> "bismark/coverage2cytosine/reports/"
436+
r.coverage2cytosine_summary >> "bismark/coverage2cytosine/summaries/"
437+
r.methylation_bedgraph >> "${params.aligner}/methylation_calls/bedGraph/"
438+
r.methylation_calls >> "${params.aligner}/methylation_calls/methylation_calls/"
439+
r.methylation_coverage >> "${params.aligner}/methylation_calls/methylation_coverage/"
440+
r.methylation_report >> "${params.aligner}/methylation_calls/splitting_report/"
441+
r.methylation_mbias >> "${params.aligner}/methylation_calls/mbias/"
442+
r.bismark_report >> "${params.aligner}/reports/"
440443

441444
r.samtools_flagstat >> "${params.aligner}/alignments/samtools_stats/"
442445
r.samtools_stats >> "${params.aligner}/alignments/samtools_stats/"
443-
r.methydackel_extract_bedgraph >> "methyldackel"
444-
r.methydackel_extract_methylkit >> "methyldackel"
445-
r.methyldackel_mbias >> "methyldackel/mbias"
446-
r.picard_metrics >> "${params.aligner}/deduplicated/picard_metrics"
446+
r.methydackel_extract_bedgraph >> "methyldackel/"
447+
r.methydackel_extract_methylkit >> "methyldackel/"
448+
r.methyldackel_mbias >> "methyldackel/mbias/"
449+
r.picard_metrics >> "${params.aligner}/deduplicated/picard_metrics/"
447450

448451
r.qualimap_bamqc >> "${params.aligner}/qualimap/bamqc/"
449452

450-
r.bedgraph_intersect >> (params.aligner == 'bismark' ? "bismark/methylation_calls/bedGraph" : "methyldackel")
451-
r.picard_hsmetrics >> "enrichment_metrics"
453+
r.bedgraph_intersect >> (params.aligner == 'bismark' ? "bismark/methylation_calls/bedGraph/" : "methyldackel/")
454+
r.picard_hsmetrics >> "enrichment_metrics/"
452455

453-
r.lc_extrap >> "${params.aligner}/preseq"
454-
r.lc_log >> "${params.aligner}/preseq/log"
456+
r.lc_extrap >> "${params.aligner}/preseq/"
457+
r.lc_log >> "${params.aligner}/preseq/log/"
455458
}
456459
}
457460

458-
bismark_summary {
461+
bismark_summary: Set<Path> {
459462
path "${params.aligner}/summary"
460463
}
461464

462-
reference_dict {
465+
reference_dict: Record {
463466
path "${params.aligner}/reference_genome"
464467
enabled params.save_reference
465468
}
466469

467-
intervallist {
470+
intervallist: Record {
468471
path "enrichment_metrics"
469472
}
470473

471-
multiqc_report {
474+
multiqc_report: Path {
472475
path "multiqc/${params.aligner}"
473476
}
474477
}

‎modules/nf-core/bedtools/intersect/main.nf‎

Lines changed: 20 additions & 20 deletions
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‎modules/nf-core/bismark/align/main.nf‎

Lines changed: 18 additions & 18 deletions
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