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Intervals #609

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merged 9 commits into from
Jun 28, 2022
Merged

Intervals #609

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e13f188
remove meta
FriederikeHanssen Jun 28, 2022
d0d5b4e
if no_intervals than intervals-combined is empty
FriederikeHanssen Jun 28, 2022
1000d6f
don't write no intervals in subfodler
FriederikeHanssen Jun 28, 2022
cca8089
update Changelog
FriederikeHanssen Jun 28, 2022
b8256ff
fix mapping of no_intervals output
FriederikeHanssen Jun 28, 2022
74aa00a
intervals not needed for annotation
FriederikeHanssen Jun 28, 2022
458c4dc
Sort tests alphabetically, also stub run for cf, fixing a big
FriederikeHanssen Jun 28, 2022
984e4cf
fix syntax
FriederikeHanssen Jun 28, 2022
b66c573
Some renaming because of stub run
FriederikeHanssen Jun 28, 2022
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3 changes: 2 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -104,7 +104,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#599](https://github.com/nf-core/sarek/pull/599) - Add checks for correct data type for `params.step`
- [#599](https://github.com/nf-core/sarek/pull/599) - Add checks for no empty `--tools` with `--step variant_calling` or `--step annotation`
- [#600](https://github.com/nf-core/sarek/pull/600) - Remove `nf-core lint` warnings
- [#602](https://github.com/nf-core/sarek/pull/602/) - Fixed bug in `alignment_to_fastq` and added tests
- [#602](https://github.com/nf-core/sarek/pull/602) - Fixed bug in `alignment_to_fastq` and added tests
- [#609](https://github.com/nf-core/sarek/pull/609) - Remove unused intervals code, reorganize combined intervals file

### Deprecated

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9 changes: 6 additions & 3 deletions subworkflows/local/pair_variant_calling.nf
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Expand Up @@ -81,16 +81,16 @@ workflow PAIR_VARIANT_CALLING {
[meta, tumor_cram, intervals]
}
RUN_MPILEUP_NORMAL(cram_normal_intervals_no_index, fasta)
mpileup_normal = RUN_MPILEUP_NORMAL.out.mpileup
RUN_MPILEUP_TUMOR(cram_tumor_intervals_no_index, fasta)

mpileup_normal = RUN_MPILEUP_NORMAL.out.mpileup
mpileup_tumor = RUN_MPILEUP_TUMOR.out.mpileup
ch_versions = ch_versions.mix(RUN_MPILEUP_NORMAL.out.versions)
ch_versions = ch_versions.mix(RUN_MPILEUP_TUMOR.out.versions)

controlfreec_input = mpileup_normal.cross(mpileup_tumor)
.map{ normal, tumor ->
[normal[0], normal[1], tumor[1], [], [], [], []]
}

RUN_CONTROLFREEC_SOMATIC(controlfreec_input,
fasta,
fasta_fai,
Expand All @@ -99,6 +99,9 @@ workflow PAIR_VARIANT_CALLING {
chr_files,
mappability,
intervals_bed_combined)

ch_versions = ch_versions.mix(RUN_MPILEUP_NORMAL.out.versions)
ch_versions = ch_versions.mix(RUN_MPILEUP_TUMOR.out.versions)
ch_versions = ch_versions.mix(RUN_CONTROLFREEC_SOMATIC.out.versions)
}

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54 changes: 22 additions & 32 deletions subworkflows/local/prepare_intervals.nf
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Expand Up @@ -6,11 +6,10 @@
// For all modules here:
// A when clause condition is defined in the conf/modules.config to determine if the module should be run

include { BUILD_INTERVALS } from '../../modules/local/build_intervals/main'
include { CREATE_INTERVALS_BED } from '../../modules/local/create_intervals_bed/main'
include { GATK4_INTERVALLISTTOBED } from '../../modules/nf-core/modules/gatk4/intervallisttobed/main'
include { TABIX_BGZIPTABIX as TABIX_BGZIPTABIX_INTERVAL_SPLIT } from '../../modules/nf-core/modules/tabix/bgziptabix/main'
include { TABIX_BGZIPTABIX as TABIX_BGZIPTABIX_INTERVAL_ALL } from '../../modules/nf-core/modules/tabix/bgziptabix/main'
include { BUILD_INTERVALS } from '../../modules/local/build_intervals/main'
include { CREATE_INTERVALS_BED } from '../../modules/local/create_intervals_bed/main'
include { GATK4_INTERVALLISTTOBED } from '../../modules/nf-core/modules/gatk4/intervallisttobed/main'
include { TABIX_BGZIPTABIX as TABIX_BGZIPTABIX_INTERVAL_SPLIT } from '../../modules/nf-core/modules/tabix/bgziptabix/main'

workflow PREPARE_INTERVALS {
take:
Expand All @@ -20,9 +19,9 @@ workflow PREPARE_INTERVALS {

ch_versions = Channel.empty()

ch_intervals = Channel.empty()
ch_intervals_bed_gz_tbi = Channel.empty()
ch_intervals_combined_bed_gz_tbi = Channel.empty() // Create bed.gz and bed.gz.tbi for input/or created interval file. Contains ALL regions.
ch_intervals = Channel.empty() // List of bed files, one for each region
ch_intervals_bed_gz_tbi = Channel.empty() // List of bed.gz, bed,gz.tbi, one for each region
ch_intervals_combined = Channel.empty() // Bed file containing all intervals

if (params.no_intervals) {
file("${params.outdir}/no_intervals.bed").text = "no_intervals\n"
Expand All @@ -35,46 +34,37 @@ workflow PREPARE_INTERVALS {
ch_intervals_bed_gz_tbi = Channel.fromPath(file("${params.outdir}/no_intervals.bed.{gz,gz.tbi}"))
.collect().map{ it -> [it, 0]}

ch_intervals_combined_bed_gz_tbi = Channel.fromPath(file("${params.outdir}/no_intervals.bed.{gz,gz.tbi}"))
.collect()
ch_intervals_combined = Channel.fromPath(file("${params.outdir}/no_intervals.bed")).collect().map{ it -> [[id:it.simpleName], it]}

} else if (params.step != 'annotate' && params.step != 'controlfreec') {

tabix_in_combined = Channel.empty()

//If no interval/target file is provided, then intervals are generated from FASTA file
if (!params.intervals) {

BUILD_INTERVALS(fasta_fai)
tabix_in_combined = BUILD_INTERVALS.out.bed.map{it -> [[id:it.simpleName], it] }
ch_intervals_combined = BUILD_INTERVALS.out.bed.map{it -> [[id:it.simpleName], it] }

ch_intervals = CREATE_INTERVALS_BED(BUILD_INTERVALS.out.bed)
ch_intervals = CREATE_INTERVALS_BED(ch_intervals_combined)

} else {

tabix_in_combined = Channel.fromPath(file(params.intervals)).map{it -> [[id:it.baseName], it] }
ch_intervals_combined = Channel.fromPath(file(params.intervals)).map{it -> [[id:it.baseName], it] }
ch_intervals = CREATE_INTERVALS_BED(file(params.intervals))

//If interval file is not provided as .bed, but e.g. as .interval_list then convert to BED format
if(!params.intervals.endsWith(".bed")) {
GATK4_INTERVALLISTTOBED(tabix_in_combined)
tabix_in_combined = GATK4_INTERVALLISTTOBED.out.bed
GATK4_INTERVALLISTTOBED(ch_intervals_combined)
ch_intervals_combined = GATK4_INTERVALLISTTOBED.out.bed
ch_versions = ch_versions.mix(GATK4_INTERVALLISTTOBED.out.versions)
}

ch_intervals = CREATE_INTERVALS_BED(file(params.intervals))
}

// Now for the interval.bed the following operations are done:
// 1. Complete intervals file (with all intervals) is indexed
// 2. Interval file is split up into multiple bed files for scatter/gather
// 3. Each bed file from 2. is indexed

// 1. Index complete interval file
TABIX_BGZIPTABIX_INTERVAL_ALL(tabix_in_combined)
ch_intervals_combined_bed_gz_tbi = TABIX_BGZIPTABIX_INTERVAL_ALL.out.gz_tbi.map{ meta, bed, tbi -> [bed, tbi] }
ch_versions = ch_versions.mix(TABIX_BGZIPTABIX_INTERVAL_ALL.out.versions)
// 1. Interval file is split up into multiple bed files for scatter/gather
// 2. Each bed file from 2. is indexed

// 2. Interval file is split up into multiple bed files for scatter/gather & grouping together small intervals
// 1. Interval file is split up into multiple bed files for scatter/gather & grouping together small intervals
ch_intervals = ch_intervals.flatten()
.map{ intervalFile ->
def duration = 0.0
Expand All @@ -95,7 +85,7 @@ workflow PREPARE_INTERVALS {
[it, it.size() ] // Adding number of intervals as elements
}.transpose()

// 3. Create bed.gz and bed.gz.tbi for each interval file. They are split by region (see above)
// 2. Create bed.gz and bed.gz.tbi for each interval file. They are split by region (see above)
tabix_in = ch_intervals.map{ file, num_intervals -> [[id:file.baseName], file] }
TABIX_BGZIPTABIX_INTERVAL_SPLIT(tabix_in)
ch_intervals_bed_gz_tbi = TABIX_BGZIPTABIX_INTERVAL_SPLIT.out.gz_tbi.map{ meta, bed, tbi -> [bed, tbi ]}.toList().map{
Expand All @@ -107,8 +97,8 @@ workflow PREPARE_INTERVALS {
}

emit:
intervals_bed = ch_intervals // path: intervals.bed, num_intervals [intervals split for parallel execution]
intervals_bed_gz_tbi = ch_intervals_bed_gz_tbi // path: target.bed.gz, target.bed.gz.tbi, num_intervals [intervals split for parallel execution]
intervals_combined_bed_gz_tbi = ch_intervals_combined_bed_gz_tbi // path: interval.bed.gz, interval.bed.gz.tbi [all intervals in one file]
versions = ch_versions // channel: [ versions.yml ]
intervals_bed = ch_intervals // path: intervals.bed, num_intervals [intervals split for parallel execution]
intervals_bed_gz_tbi = ch_intervals_bed_gz_tbi // path: target.bed.gz, target.bed.gz.tbi, num_intervals [intervals split for parallel execution]
intervals_bed_combined = ch_intervals_combined.map{meta, bed -> bed } // path: intervals.bed [all intervals in one file]
versions = ch_versions // channel: [ versions.yml ]
}
16 changes: 5 additions & 11 deletions workflows/sarek.nf
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Expand Up @@ -52,7 +52,7 @@ for (param in checkPathParamList) if (param) file(param, checkIfExists: true)
// Set input, can either be from --input or from automatic retrieval in WorkflowSarek.groovy
ch_input_sample = extract_csv(file(params.input, checkIfExists: true))

if (params.wes) {
if (params.wes && !params.step == 'annotate') {
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Ah, so you fixed it already 👍

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yeah since it was a one liner at roughly fit into the theme: fix intervals :D

if (params.intervals && !params.intervals.endsWith("bed")) exit 1, "Target file specified with `--intervals` must be in BED format"
} else {
if (params.intervals && !params.intervals.endsWith("bed") && !params.intervals.endsWith("interval_list")) exit 1, "Interval file must end with .bed or .interval_list"
Expand Down Expand Up @@ -291,17 +291,11 @@ workflow SAREK {
PREPARE_INTERVALS(fasta_fai)

// Intervals for speed up preprocessing/variant calling by spread/gather
// this is not good, we need the combined bed for some tools that don't support scatter/gather. Why would we not use the same intervals for WGS?
// intervals_bed_combined = (params.intervals && params.wes) ? Channel.fromPath(params.intervals).collect() : []
// check if this actually still works if interval_list format
intervals_bed_combined = params.intervals ? Channel.fromPath(params.intervals).collect() : []
//TODO: intervals also with WGS data? Probably need a parameter if WGS for deepvariant tool, that would allow to check here too
intervals_for_preprocessing = (params.wes && params.intervals) ? intervals_bed_combined : []

intervals = PREPARE_INTERVALS.out.intervals_bed // [interval, num_intervals] multiple interval.bed files, divided by useful intervals for scatter/gather
intervals_bed_gz_tbi = PREPARE_INTERVALS.out.intervals_bed_gz_tbi // [interval_bed, tbi, num_intervals] multiple interval.bed.gz/.tbi files, divided by useful intervals for scatter/gather

intervals_bed_combined = params.no_intervals ? [] : PREPARE_INTERVALS.out.intervals_bed_combined // [interval.bed] all intervals in one file
intervals_for_preprocessing = params.wes ? intervals_bed_combined : [] // For QC during preprocessing, we don't need any intervals (MOSDEPTH doesn't take them for WGS)

intervals = PREPARE_INTERVALS.out.intervals_bed // [interval, num_intervals] multiple interval.bed files, divided by useful intervals for scatter/gather
intervals_bed_gz_tbi = PREPARE_INTERVALS.out.intervals_bed_gz_tbi // [interval_bed, tbi, num_intervals] multiple interval.bed.gz/.tbi files, divided by useful intervals for scatter/gather

// Gather used softwares versions
ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions)
Expand Down