Skip to content

output all cram files #275

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

Open
wants to merge 4 commits into
base: dev
Choose a base branch
from
Open

output all cram files #275

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
524364e
output all cram files
matthdsm Jun 2, 2025
0800d4a
disable cram output (#277)
matthdsm Jun 2, 2025
1c1eb82
add filter to stand alone wes config (#276)
matthdsm Jun 2, 2025
f88f934
typo
matthdsm Jun 2, 2025
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
11 changes: 6 additions & 5 deletions conf/copgt.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,9 +5,10 @@
*/

params {
callers = "haplotypecaller"
only_call = true
roi = "${params.genomes_base}/Hsapiens/GRCh38/regions/coPGT-M/coPGT-M_v1.bed"
scatter_count = 8
filter = true
callers = "haplotypecaller"
only_call = true
roi = "${params.genomes_base}/Hsapiens/GRCh38/regions/coPGT-M/coPGT-M_v1.bed"
scatter_count = 8
filter = true
skip_merged_cram_output = true
}
1 change: 1 addition & 0 deletions conf/copgt_joint.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,4 +11,5 @@ params {
roi = "${params.genomes_base}/Hsapiens/GRCh38/regions/coPGT-M/coPGT-M_v1.bed"
scatter_count = 8
filter = true
skip_merged_cram_output = true
}
2 changes: 2 additions & 0 deletions conf/seqplorer.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -20,4 +20,6 @@ params {

vcfanno_config = "https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-configs/main/conf/Hsapiens/vcfanno/cmgg_vcfanno.toml"
vcfanno_resources = "${params.genomes_base}/Hsapiens/GRCh38/variation/dbscSNV-1.1/dbscSNV.txt.gz;${params.genomes_base}/Hsapiens/GRCh38/variation/dbscSNV-1.1/dbscSNV.txt.gz.tbi;${params.genomes_base}/Hsapiens/GRCh38/variation/gnomAD/exomes/r2.2.1/gnomad_exomes.vcf.gz;${params.genomes_base}/Hsapiens/GRCh38/variation/gnomAD/exomes/r2.2.1/gnomad_exomes.vcf.gz.csi;${params.genomes_base}/Hsapiens/GRCh38/variation/clinvar/clinvar_20221119.vcf.gz;${params.genomes_base}/Hsapiens/GRCh38/variation/clinvar/clinvar_20221119.vcf.gz.tbi;${params.genomes_base}/Hsapiens/GRCh38/variation/gnomAD/genomes/r3.1.2/gnomad_genomes.vcf.gz;${params.genomes_base}/Hsapiens/GRCh38/variation/gnomAD/genomes/r3.1.2/gnomad_genomes.vcf.gz.csi;${params.genomes_base}/Hsapiens/GRCh38/variation/dbNSFP-4.3/dbNSFP4.3a_grch38.gz;${params.genomes_base}/Hsapiens/GRCh38/variation/dbNSFP-4.3/dbNSFP4.3a_grch38.gz.tbi"

skip_merged_cram_output = true
}
12 changes: 7 additions & 5 deletions conf/wes.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,9 +5,11 @@
*/

params {
callers = "haplotypecaller"
scatter_count = 8
roi = "${params.genomes_base}/Hsapiens/GRCh38/regions/CMGG_WES_analysis_ROI_v6.bed"
updio = true
automap = true
callers = "haplotypecaller"
scatter_count = 8
roi = "${params.genomes_base}/Hsapiens/GRCh38/regions/CMGG_WES_analysis_ROI_v6.bed"
updio = true
automap = true
filter = true
skip_merged_cram_output = true
}
4 changes: 2 additions & 2 deletions main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -209,7 +209,7 @@ workflow {
)

publish:
merged_crams = SMALLVARIANTS.out.merged_crams
crams = SMALLVARIANTS.out.crams
mosdepth_reports = SMALLVARIANTS.out.mosdepth_reports
gvcfs = SMALLVARIANTS.out.gvcfs.filter { _meta, gvcf, _tbi -> gvcf.startsWith(workflow.workDir) } // Filtering out input GVCFs from the output publishing fixes an issue in the current implementation of the workflow output definitions: https://github.com/nextflow-io/nextflow/issues/5480
single_beds = SMALLVARIANTS.out.single_beds
Expand All @@ -229,7 +229,7 @@ workflow {
}

output {
merged_crams {
crams {
path { meta, cram, crai ->
cram >> "${meta.family}/${meta.id}_${params.unique_out}/${meta.id}.cram"
crai >> "${meta.family}/${meta.id}_${params.unique_out}/${meta.id}.cram.crai"
Expand Down
1 change: 0 additions & 1 deletion subworkflows/local/cram_prepare_samtools_bedtools/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -176,7 +176,6 @@ workflow CRAM_PREPARE_SAMTOOLS_BEDTOOLS {

emit:
ready_crams = ch_ready_crams // [ val(meta), path(cram), path(crai) ]
merged_crams = ch_merged_crams // [ val(meta), path(cram), path(crai) ]
ready_bams = ch_ready_bams // [ val(meta), path(bam), path(bai) ]
ready_beds = ch_ready_beds // [ val(meta), path(bed) ]
perbase_beds = ch_perbase_beds // [ val(meta), path(bed), path(csi) ]
Expand Down
4 changes: 2 additions & 2 deletions workflows/smallvariants.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -416,7 +416,7 @@ workflow SMALLVARIANTS {
ch_reports = ch_reports.mix(CRAM_PREPARE_SAMTOOLS_BEDTOOLS.out.reports)
def ch_single_beds = CRAM_PREPARE_SAMTOOLS_BEDTOOLS.out.ready_beds
def ch_perbase_beds = CRAM_PREPARE_SAMTOOLS_BEDTOOLS.out.perbase_beds
def ch_merged_crams = CRAM_PREPARE_SAMTOOLS_BEDTOOLS.out.merged_crams
def ch_ready_crams = CRAM_PREPARE_SAMTOOLS_BEDTOOLS.out.ready_crams
def ch_mosdepth_reports = CRAM_PREPARE_SAMTOOLS_BEDTOOLS.out.mosdepth_reports

//
Expand Down Expand Up @@ -868,7 +868,7 @@ workflow SMALLVARIANTS {
)

emit:
merged_crams = ch_merged_crams // channel: [ val(meta), path(cram), path(crai) ]
crams = ch_ready_crams // channel: [ val(meta), path(cram), path(crai) ]
mosdepth_reports = ch_mosdepth_reports // channel: [ val(meta), path(mosdepth_report) ]
gvcfs = ch_gvcfs_ready // channel: [ val(meta), path(gvcf), path(tbi) ]
genomicsdb = ch_final_genomicsdb // channel: [ val(meta), path(genomicsdb) ]
Expand Down
Loading