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Add flag to only output BAM files #213

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Add flag to only output BAM files #213

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9ded9c8
Add alignment_only flag
alkc Jul 29, 2024
0814e0f
Don't process bam when alignment_only run
alkc Jul 29, 2024
b20aa59
Add alignment_only to a few more processes
alkc Jul 29, 2024
a30e13d
Add alignment_only condition to mtBAM processes
alkc Jul 29, 2024
0955ad4
Don't generate yaml for align-only
alkc Jul 29, 2024
b97ca07
BAM only changenotes
alkc Jul 29, 2024
4ced2ae
Update docs
alkc Jul 30, 2024
1de61dc
Merge branch 'master' into add-align-only-flag
alkc Aug 13, 2024
085c08f
Drop QC data output from align only runs
alkc Aug 13, 2024
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5 changes: 5 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -1,6 +1,11 @@
# CHANGELOG

### TBA

* add flag `--alignment_only` to only output genomic and mito `.bam` and QC data

### 3.9.4

* Use -K flag in bwa-mem for consistent results

### 3.9.3
Expand Down
2 changes: 2 additions & 0 deletions configs/nextflow.hopper.config
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Original file line number Diff line number Diff line change
Expand Up @@ -94,6 +94,8 @@ params {

run_chanjo2 = true
reanalyze = false

alignment_only = false
}

process {
Expand Down
4 changes: 4 additions & 0 deletions docs/running_the_pipeline.md
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Expand Up @@ -103,3 +103,7 @@ Assuming it is named `jobfile.run`, then it can be queued by running:
sbatch jobfile.run
```

## BAM and Sequencing QC-only run

For an alignment and QC-only run, where the pipeline only outputs genomic and mitochondrial BAM files and associated QC data, pass the `--alignment_only` to `nextflow run`

46 changes: 29 additions & 17 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -449,6 +449,9 @@ process bqsr {
set group, id, file("${id}.bqsr.table") into dnascope_bqsr
set group, file("*versions.yml") into ch_bqsr_versions

when:
!params.alignment_only

script:
"""
sentieon driver -t ${task.cpus} \\
Expand Down Expand Up @@ -485,6 +488,9 @@ process sentieon_qc {
// stageOutMode 'copy'
container = "${params.container_sentieon}"

when:
!params.alignment_only

input:
set id, group, file(bam), file(bai) from qc_bam.mix(bam_qc_choice)

Expand Down Expand Up @@ -590,7 +596,7 @@ process d4_coverage {
container = "${params.container_d4tools}"

when:
params.run_chanjo2
params.run_chanjo2 && !params.alignment_only

input:
set group, id, file(bam), file(bai) from d4_bam
Expand Down Expand Up @@ -642,7 +648,7 @@ process depth_onco {
// stageOutMode 'copy'

when:
params.assay == "swea"
params.assay == "swea" && !params.alignment_only

input:
set group, id, file(bam), file(bai) from depth_onco
Expand Down Expand Up @@ -670,7 +676,7 @@ process SMNCopyNumberCaller {
tag "$id"

when:
params.antype == "wgs"
params.antype == "wgs" && !params.alignment_only

input:
set group, id, file(bam), file(bai) from smncnc_bam.mix(bam_SMN_choice)
Expand Down Expand Up @@ -751,7 +757,7 @@ process expansionhunter {
// stageOutMode 'copy'

when:
params.str
params.str && !params.alignment_only

input:
set group, id, file(bam), file(bai), sex, type \
Expand Down Expand Up @@ -1019,7 +1025,7 @@ process melt {
set id, group, file(bam), file(bai), val(INS_SIZE), val(MEAN_DEPTH), val(COV_DEV) from bam_melt.mix(bam_melt_choice).join(qc_melt_val)

when:
params.run_melt
params.run_melt && !params.alignment_only

output:
set group, id, file("${id}.melt.merged.vcf") into melt_vcf_nonfiltered
Expand Down Expand Up @@ -1107,7 +1113,7 @@ process dnascope {
container = "${params.container_sentieon}"

when:
params.varcall
params.varcall && !params.alignment_only

input:
set group, id, bam, bai, bqsr from complete_bam.mix(dnascope_bam_choice).join(dnascope_bqsr, by: [0,1])
Expand Down Expand Up @@ -1317,7 +1323,7 @@ process freebayes {
// stageOutMode 'copy'

when:
params.antype == "panel"
params.antype == "panel" && !params.alignment_only

input:
set group, id, file(bam), file(bai) from bam_freebayes.mix(bam_freebayes_choice)
Expand Down Expand Up @@ -1434,8 +1440,8 @@ process sentieon_mitochondrial_qc {
container = "${params.container_sentieon}"

when:
params.antype == "wgs"
params.antype == "wgs" && !params.alignment_only

input:
set group, id, file(bam), file(bai) from qc_mito_bam

Expand Down Expand Up @@ -1505,7 +1511,7 @@ process run_mutect2 {
publishDir "${OUTDIR}/vcf", mode: 'copy', overwrite: 'true', pattern: '*.vcf'

when:
!params.onco
!params.onco && !params.alignment_only

input:
set group, id, file(bam), file(bai) from mutserve_bam.groupTuple()
Expand Down Expand Up @@ -1702,6 +1708,9 @@ process run_eklipse {
set group, file("${id}_eklipse.INFO") into eklipse_INFO
set group, file("*versions.yml") into ch_run_eklipse_versions

when:
!params.alignment_only

script:
"""
source activate htslib10
Expand Down Expand Up @@ -2558,7 +2567,7 @@ process gatkcov {
set group, file("*versions.yml") into ch_gatkcov_versions

when:
params.gatkcov
params.gatkcov && !params.alignment_only

script:
"""
Expand Down Expand Up @@ -2690,7 +2699,7 @@ process gatk_coverage {
tag "$id"

when:
params.sv && params.gatkcnv
params.sv && params.gatkcnv && !params.alignment_only

input:
set group, id, file(bam), file(bai) from bam_gatk.mix(bam_gatk_choice)
Expand Down Expand Up @@ -2969,7 +2978,7 @@ process manta {
// stageOutMode 'copy'

when:
params.sv && params.antype == "wgs"
params.sv && params.antype == "wgs" && !params.alignment_only

input:
set group, id, file(bam), file(bai) from bam_manta.mix(bam_manta_choice)
Expand Down Expand Up @@ -3016,7 +3025,7 @@ process manta_panel {
// stageOutMode 'copy'

when:
params.sv && params.antype == "panel"
params.sv && params.antype == "panel" && !params.alignment_only

input:
set group, id, file(bam), file(bai) from bam_manta_panel.mix(bam_mantapanel_choice)
Expand Down Expand Up @@ -3062,7 +3071,7 @@ process delly_panel {
cache 'deep'

when:
params.sv && params.antype == "panel" && params.delly
params.sv && params.antype == "panel" && params.delly && !params.alignment_only

input:
set group, id, file(bam), file(bai) from bam_delly_panel.mix(bam_dellypanel_choice)
Expand Down Expand Up @@ -3109,7 +3118,7 @@ process cnvkit_panel {
// stageOutMode 'copy'

when:
params.sv && params.antype == "panel"
params.sv && params.antype == "panel" && !params.alignment_only

input:
set group, id, file(bam), file(bai), file(vcf), file(multi), val(INS_SIZE), val(MEAN_DEPTH), val(COV_DEV) from bam_cnvkit_panel.mix(bam_cnvkitpanel_choice).join(vcf_cnvkit, by:[0,1]).join(qc_cnvkit_val, by:[0,1]).view()
Expand Down Expand Up @@ -3248,7 +3257,7 @@ process tiddit {
// stageOutMode 'copy'

when:
params.sv && params.antype == "wgs"
params.sv && params.antype == "wgs" && !params.alignment_only


input:
Expand Down Expand Up @@ -3844,6 +3853,9 @@ process create_yaml {
time '5m'
memory '1 GB'

when:
!params.alignment_only

input:
set group, id, sex, mother, father, phenotype, diagnosis, type, assay, clarity_sample_id, ffpe, analysis, type, file(ped), file(INFO) from yml_diag.join(ped_scout).join(yaml_INFO)

Expand Down