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

Chromograph viz #507

Merged
merged 5 commits into from
Feb 2, 2024
Merged

Chromograph viz #507

Show file tree
Hide file tree
Changes from 4 commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
a51428a
chromograph viz
ramprasadn Jan 31, 2024
ff858d7
update chromograph
ramprasadn Feb 1, 2024
0b18299
Merge branch 'dev' into chromograph_viz
ramprasadn Feb 1, 2024
1f4368d
update changelog
ramprasadn Feb 2, 2024
b1f0c84
update output docs
ramprasadn Feb 2, 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
1 change: 1 addition & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Add FOUND_IN tag, which mentions the variant caller that found the mutation, in the INFO column of the vcf files [#471](https://github.com/nf-core/raredisease/pull/471)
- A new parameter `vep_plugin_files` to supply files required by vep plugins [#482](https://github.com/nf-core/raredisease/pull/482)
- New workflow for annotating mobile elements [#483](https://github.com/nf-core/raredisease/pull/483)
- Chromograph to plot coverage across chromosomes [#507](https://github.com/nf-core/raredisease/pull/507)

### `Changed`

Expand Down
5 changes: 5 additions & 0 deletions conf/modules/qc_bam.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -50,6 +50,11 @@ process {
ext.args = '-clip'
}

withName: '.*QC_BAM:CHROMOGRAPH_COV' {
ext.args = '--euploid --step 500'
ext.prefix = { "${meta2.id}_chromographcov" }
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

We want to publish this directory as it contains the plots. We should also describe the outfiles

Copy link
Collaborator Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

All outputs from the qc bam subworkflow are published by default. I will update the documentation now.

Copy link
Collaborator Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I have updated the document now.

}

withName: '.*QC_BAM:MOSDEPTH' {
ext.args = '--d4'
ext.prefix = { "${meta.id}_mosdepth" }
Expand Down
2 changes: 1 addition & 1 deletion modules.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -82,7 +82,7 @@
},
"chromograph": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"git_sha": "f05512229a501df5d67273bb7358c5f69667f40d",
"installed_by": ["modules"]
},
"cnvnator/cnvnator": {
Expand Down
4 changes: 2 additions & 2 deletions modules/nf-core/chromograph/main.nf
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

2 changes: 1 addition & 1 deletion modules/nf-core/chromograph/meta.yml
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

38 changes: 38 additions & 0 deletions modules/nf-core/chromograph/tests/main.nf.test
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

2 changes: 2 additions & 0 deletions modules/nf-core/chromograph/tests/tags.yml
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

5 changes: 4 additions & 1 deletion subworkflows/local/qc_bam.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,13 +4,14 @@

include { PICARD_COLLECTMULTIPLEMETRICS } from '../../modules/nf-core/picard/collectmultiplemetrics/main'
include { PICARD_COLLECTHSMETRICS } from '../../modules/nf-core/picard/collecthsmetrics/main'
include { CHROMOGRAPH as CHROMOGRAPH_COV } from '../../modules/nf-core/chromograph/main'
include { QUALIMAP_BAMQC } from '../../modules/nf-core/qualimap/bamqc/main'
include { TIDDIT_COV } from '../../modules/nf-core/tiddit/cov/main'
include { MOSDEPTH } from '../../modules/nf-core/mosdepth/main'
include { UCSC_WIGTOBIGWIG } from '../../modules/nf-core/ucsc/wigtobigwig/main'
include { PICARD_COLLECTWGSMETRICS as PICARD_COLLECTWGSMETRICS } from '../../modules/nf-core/picard/collectwgsmetrics/main'
include { PICARD_COLLECTWGSMETRICS as PICARD_COLLECTWGSMETRICS_Y } from '../../modules/nf-core/picard/collectwgsmetrics/main'
include { SENTIEON_WGSMETRICS } from '../../modules/nf-core/sentieon/wgsmetrics/main'
include { SENTIEON_WGSMETRICS } from '../../modules/nf-core/sentieon/wgsmetrics/main'
include { SENTIEON_WGSMETRICS as SENTIEON_WGSMETRICS_Y } from '../../modules/nf-core/sentieon/wgsmetrics/main'
include { NGSBITS_SAMPLEGENDER } from '../../modules/nf-core/ngsbits/samplegender/main'

Expand Down Expand Up @@ -51,6 +52,8 @@ workflow QC_BAM {

UCSC_WIGTOBIGWIG (TIDDIT_COV.out.wig, ch_chrom_sizes)

CHROMOGRAPH_COV([[:],[]], TIDDIT_COV.out.wig, [[:],[]], [[:],[]], [[:],[]], [[:],[]], [[:],[]])

ch_bam_bai.map{ meta, bam, bai -> [meta, bam, bai, []]}.set{ch_mosdepth_in}
MOSDEPTH (ch_mosdepth_in, ch_genome_fasta)

Expand Down
Loading