Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

improve workflow logic for fastq_align_dedup_bismark #7005

Merged
merged 8 commits into from
Nov 18, 2024
Merged

improve workflow logic for fastq_align_dedup_bismark #7005

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
bde8f31
improve workflow logic
sateeshperi Nov 16, 2024
e0a5e61
Merge branch 'master' into fix/fastq_align_dedup_bismark
sateeshperi Nov 16, 2024
476f59b
add paired-end tests
sateeshperi Nov 17, 2024
d25b8a9
update meta.yml
sateeshperi Nov 17, 2024
9ee6851
minor formatting fix
sateeshperi Nov 17, 2024
c18a53e
apply suggestions from code review
sateeshperi Nov 18, 2024
70d9ea0
Merge branch 'master' into fix/fastq_align_dedup_bismark
sateeshperi Nov 18, 2024
775e596
Merge branch 'master' into fix/fastq_align_dedup_bismark
sateeshperi Nov 18, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
127 changes: 64 additions & 63 deletions subworkflows/nf-core/fastq_align_dedup_bismark/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
include { BISMARK_ALIGN } from '../../../modules/nf-core/bismark/align/main'
include { BISMARK_DEDUPLICATE } from '../../../modules/nf-core/bismark/deduplicate/main'
include { BISMARK_METHYLATIONEXTRACTOR } from '../../../modules/nf-core/bismark/methylationextractor/main'
include { BISMARK_COVERAGE2CYTOSINE } from '../../../modules/nf-core/bismark/coverage2cytosine/main'
include { BISMARK_REPORT } from '../../../modules/nf-core/bismark/report/main'
include { BISMARK_SUMMARY } from '../../../modules/nf-core/bismark/summary/main'
include { SAMTOOLS_SORT as SAMTOOLS_SORT_DEDUPLICATED } from '../../../modules/nf-core/samtools/sort/main'
include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_DEDUPLICATED } from '../../../modules/nf-core/samtools/index/main'
include { BISMARK_ALIGN } from '../../../modules/nf-core/bismark/align/main'
include { BISMARK_DEDUPLICATE } from '../../../modules/nf-core/bismark/deduplicate/main'
include { SAMTOOLS_SORT } from '../../../modules/nf-core/samtools/sort/main'
include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index/main'
include { BISMARK_METHYLATIONEXTRACTOR } from '../../../modules/nf-core/bismark/methylationextractor/main'
include { BISMARK_COVERAGE2CYTOSINE } from '../../../modules/nf-core/bismark/coverage2cytosine/main'
include { BISMARK_REPORT } from '../../../modules/nf-core/bismark/report/main'
include { BISMARK_SUMMARY } from '../../../modules/nf-core/bismark/summary/main'

workflow FASTQ_ALIGN_DEDUP_BISMARK {

Expand All @@ -17,18 +17,20 @@ workflow FASTQ_ALIGN_DEDUP_BISMARK {
cytosine_report // boolean: whether the run coverage2cytosine

main:
ch_versions = Channel.empty()
ch_coverage2cytosine_coverage = Channel.empty()
ch_coverage2cytosine_report = Channel.empty()
ch_coverage2cytosine_summary = Channel.empty()
ch_alignments = Channel.empty()
ch_alignment_reports = Channel.empty()
ch_methylation_bedgraph = Channel.empty()
ch_methylation_calls = Channel.empty()
ch_methylation_coverage = Channel.empty()
ch_methylation_report = Channel.empty()
ch_methylation_mbias = Channel.empty()
ch_coverage2cytosine_coverage = Channel.empty()
ch_coverage2cytosine_report = Channel.empty()
ch_coverage2cytosine_summary = Channel.empty()
ch_bismark_report = Channel.empty()
ch_bismark_summary = Channel.empty()
ch_multiqc_files = Channel.empty()
ch_versions = Channel.empty()

/*
* Align with bismark
Expand All @@ -38,28 +40,44 @@ workflow FASTQ_ALIGN_DEDUP_BISMARK {
ch_fasta,
ch_bismark_index
)
ch_alignments = BISMARK_ALIGN.out.bam
ch_alignment_reports = BISMARK_ALIGN.out.report.map{ meta, report -> [ meta, report, [] ] }
ch_versions = ch_versions.mix(BISMARK_ALIGN.out.versions)

if (skip_deduplication) {
alignments = BISMARK_ALIGN.out.bam
alignment_reports = BISMARK_ALIGN.out.report.map{ meta, report -> [ meta, report, [] ] }
} else {
if (!skip_deduplication) {
/*
* Run deduplicate_bismark
*/
BISMARK_DEDUPLICATE (
BISMARK_ALIGN.out.bam
)
alignments = BISMARK_DEDUPLICATE.out.bam
alignment_reports = BISMARK_ALIGN.out.report.join(BISMARK_DEDUPLICATE.out.report)
ch_versions = ch_versions.mix(BISMARK_DEDUPLICATE.out.versions)
ch_alignments = BISMARK_DEDUPLICATE.out.bam
ch_alignment_reports = BISMARK_ALIGN.out.report.join(BISMARK_DEDUPLICATE.out.report)
ch_versions = ch_versions.mix(BISMARK_DEDUPLICATE.out.versions)
}

/*
* MODULE: Run samtools sort on aligned or deduplicated bam
*/
SAMTOOLS_SORT (
ch_alignments,
[[:],[]] // [ [meta], [fasta]]
)
ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions)

/*
* MODULE: Run samtools index on aligned or deduplicated bam
*/
SAMTOOLS_INDEX (
SAMTOOLS_SORT.out.bam
)
ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions)

/*
* Run bismark_methylation_extractor
*/
BISMARK_METHYLATIONEXTRACTOR (
alignments,
ch_alignments,
ch_bismark_index
)
ch_methylation_bedgraph = BISMARK_METHYLATIONEXTRACTOR.out.bedgraph
Expand All @@ -74,7 +92,7 @@ workflow FASTQ_ALIGN_DEDUP_BISMARK {
*/
if (cytosine_report) {
BISMARK_COVERAGE2CYTOSINE (
BISMARK_METHYLATIONEXTRACTOR.out.coverage,
ch_methylation_coverage,
ch_fasta,
ch_bismark_index
)
Expand All @@ -88,7 +106,7 @@ workflow FASTQ_ALIGN_DEDUP_BISMARK {
* Generate bismark sample reports
*/
BISMARK_REPORT (
alignment_reports
ch_alignment_reports
.join(ch_methylation_report)
.join(ch_methylation_mbias)
)
Expand All @@ -100,54 +118,37 @@ workflow FASTQ_ALIGN_DEDUP_BISMARK {
*/
BISMARK_SUMMARY (
BISMARK_ALIGN.out.bam.collect{ meta, bam -> bam.name },
alignment_reports.collect{ meta, align_report, dedup_report -> align_report },
alignment_reports.collect{ meta, align_report, dedup_report -> dedup_report }.ifEmpty([]),
BISMARK_METHYLATIONEXTRACTOR.out.report.collect{ meta, report -> report },
BISMARK_METHYLATIONEXTRACTOR.out.mbias.collect{ meta, mbias -> mbias }
ch_alignment_reports.collect{ meta, align_report, dedup_report -> align_report },
ch_alignment_reports.collect{ meta, align_report, dedup_report -> dedup_report }.ifEmpty([]),
ch_methylation_report.collect{ meta, report -> report },
ch_methylation_mbias.collect{ meta, mbias -> mbias }
)
ch_bismark_summary = BISMARK_SUMMARY.out.summary
ch_versions = ch_versions.mix(BISMARK_SUMMARY.out.versions)

/*
* MODULE: Run samtools sort on dedup bam
*/
SAMTOOLS_SORT_DEDUPLICATED (
alignments,
[[:],[]] // [ [meta], [fasta]]
)
ch_versions = ch_versions.mix(SAMTOOLS_SORT_DEDUPLICATED.out.versions)

/*
* MODULE: Run samtools index on dedup bam
*/
SAMTOOLS_INDEX_DEDUPLICATED (
SAMTOOLS_SORT_DEDUPLICATED.out.bam
)
ch_versions = ch_versions.mix(SAMTOOLS_INDEX_DEDUPLICATED.out.versions)

/*
* Collect MultiQC inputs
*/
ch_multiqc_files = BISMARK_SUMMARY.out.summary
.mix(alignment_reports.collect{ meta, align_report, dedup_report -> align_report })
.mix(alignment_reports.collect{ meta, align_report, dedup_report -> dedup_report })
.mix(BISMARK_METHYLATIONEXTRACTOR.out.report.collect{ meta, report -> report })
.mix(BISMARK_METHYLATIONEXTRACTOR.out.mbias.collect{ meta, mbias -> mbias })
.mix(BISMARK_REPORT.out.report.collect{ meta, report -> report })
ch_multiqc_files = ch_bismark_summary
.mix(ch_alignment_reports.collect{ meta, align_report, dedup_report -> align_report })
.mix(ch_alignment_reports.collect{ meta, align_report, dedup_report -> dedup_report })
.mix(ch_methylation_report.collect{ meta, report -> report })
.mix(ch_methylation_mbias.collect{ meta, mbias -> mbias })
.mix(ch_bismark_report.collect{ meta, report -> report })

emit:
dedup_bam = SAMTOOLS_SORT_DEDUPLICATED.out.bam // channel: [ val(meta), [ bam ] ]
dedup_bam_index = SAMTOOLS_INDEX_DEDUPLICATED.out.bai // channel: [ val(meta), [ bai ] ]
coverage2cytosine_coverage = ch_coverage2cytosine_coverage // channel: [ val(meta), [ coverage ] ]
coverage2cytosine_report = ch_coverage2cytosine_report // channel: [ val(meta), [ report ] ]
coverage2cytosine_summary = ch_coverage2cytosine_summary // channel: [ val(meta), [ summary ] ]
methylation_bedgraph = ch_methylation_bedgraph // channel: [ val(meta), [ bedgraph ] ]
methylation_calls = ch_methylation_calls // channel: [ val(meta), [ methylation_calls ] ]
methylation_coverage = ch_methylation_coverage // channel: [ val(meta), [ coverage ] ]
methylation_report = ch_methylation_report // channel: [ val(meta), [ report ] ]
methylation_mbias = ch_methylation_mbias // channel: [ val(meta), [ mbias ] ]
bismark_report = ch_bismark_report // channel: [ val(meta), [ report ] ]
bismark_summary = ch_bismark_summary // channel: [ val(meta), [ summary ] ]
multiqc = ch_multiqc_files // path: *{html,txt}
versions = ch_versions // path: *.version.txt
bam = SAMTOOLS_SORT.out.bam // channel: [ val(meta), [ bam ] ]
bai = SAMTOOLS_INDEX.out.bai // channel: [ val(meta), [ bai ] ]
coverage2cytosine_coverage = ch_coverage2cytosine_coverage // channel: [ val(meta), [ coverage ] ]
coverage2cytosine_report = ch_coverage2cytosine_report // channel: [ val(meta), [ report ] ]
coverage2cytosine_summary = ch_coverage2cytosine_summary // channel: [ val(meta), [ summary ] ]
methylation_bedgraph = ch_methylation_bedgraph // channel: [ val(meta), [ bedgraph ] ]
methylation_calls = ch_methylation_calls // channel: [ val(meta), [ methylation_calls ] ]
methylation_coverage = ch_methylation_coverage // channel: [ val(meta), [ coverage ] ]
methylation_report = ch_methylation_report // channel: [ val(meta), [ report ] ]
methylation_mbias = ch_methylation_mbias // channel: [ val(meta), [ mbias ] ]
bismark_report = ch_bismark_report // channel: [ val(meta), [ report ] ]
bismark_summary = ch_bismark_summary // channel: [ val(meta), [ summary ] ]
multiqc = ch_multiqc_files // path: *{html,txt}
versions = ch_versions // path: *.version.txt
}
10 changes: 5 additions & 5 deletions subworkflows/nf-core/fastq_align_dedup_bismark/meta.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ input:
description: |
Structure: [ val(meta), path(fasta) ]
pattern: "*.{fa,fa.gz}"
- ch_index:
- ch_bismark_index:
description: |
Bismark genome index files
Structure: [ val(meta), path(index) ]
Expand All @@ -46,16 +46,16 @@ input:
description: |
Produce coverage2cytosine reports that relates methylation calls back to genomic cytosine contexts
output:
- dedup_bam:
- bam:
type: file
description: |
Channel containing deduplicated BAM files.
Channel containing aligned or deduplicated BAM files.
Structure: [ val(meta), path(bam) ]
pattern: "*.bam"
- dedup_bam_index:
- bai:
type: file
description: |
Channel containing deduplicated BAM index files.
Channel containing aligned or deduplicated BAM index files.
Structure: [ val(meta), path(bam.bai) ]
pattern: "*.bai"
- coverage2cytosine_coverage:
Expand Down
Loading
Loading