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.

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

Patch release v1.1.1 #388

Merged
merged 5 commits into from
Jul 26, 2023
Merged
Show file tree
Hide file tree
Changes from 3 commits
Commits
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
6 changes: 6 additions & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,12 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## v1.1.1 - Abu (Patch) [xxxx-xx-xx]
asp8200 marked this conversation as resolved.
Show resolved Hide resolved
Copy link
Member

Choose a reason for hiding this comment

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

Set date!

Copy link
Collaborator Author

@ramprasadn ramprasadn Jul 26, 2023

Choose a reason for hiding this comment

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

Done! 😄


### `Fixed`

- Avoids errors thrown by bcftools concat due to sample names in input vcf files not being in same order [#388](https://github.com/nf-core/raredisease/pull/388)

## v1.1.0 - Abu [2023-07-21]

### `Added`
Expand Down
4 changes: 2 additions & 2 deletions assets/multiqc_config.yml
Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,9 @@ custom_logo_url: https://github.com/nf-core/raredisease/
custom_logo_title: "nf-core/raredisease"

report_comment: >
This report has been generated by the <a href="https://github.com/nf-core/raredisease/1.1.0" target="_blank">nf-core/raredisease</a>
This report has been generated by the <a href="https://github.com/nf-core/raredisease/1.1.1" target="_blank">nf-core/raredisease</a>
analysis pipeline. For information about how to interpret these results, please see the
<a href="https://nf-co.re/raredisease/1.1.0/output" target="_blank">documentation</a>.
<a href="https://nf-co.re/raredisease/1.1.1/output" target="_blank">documentation</a>.
report_section_order:
"nf-core-raredisease-methods-description":
order: -1000
Expand Down
1 change: 1 addition & 0 deletions conf/modules/merge_annotate_MT.config
Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,7 @@ process {
}

withName: '.*ANALYSE_MT:MERGE_ANNOTATE_MT:BCFTOOLS_MERGE_MT' {
ext.args = '--output-type z'
ext.prefix = { "${meta.id}_merge_mt" }
}

Expand Down
3 changes: 1 addition & 2 deletions conf/modules/raredisease.config
Original file line number Diff line number Diff line change
Expand Up @@ -71,9 +71,8 @@ process {
//

process {
withName: '.*RAREDISEASE:BCFTOOLS_CONCAT' {
withName: '.*RAREDISEASE:GATK4_MERGEVCFS' {
ext.prefix = { "${meta.id}_mito_genome_merged" }
ext.args = " -a "
}
}

Expand Down
19 changes: 19 additions & 0 deletions lib/WorkflowRaredisease.groovy
Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,25 @@ class WorkflowRaredisease {

}

//
// Replace spaces in vcf INFO fields with underscore
//
public static String replaceSpacesInInfoColumn(vcf_file, parent_dir, base_name) {
def outfile = new File(parent_dir + '/' + base_name + '_formatted.vcf')
def writer = outfile.newWriter()
vcf_file.eachLine { line ->
if (line.startsWith("#")) {
writer << line + "\n"
} else {
def split_str = line.tokenize("\t")
split_str[7] = split_str.getAt(7).replaceAll(" ","_")
writer << split_str.join("\t") + "\n"
}
}
writer.close()
return outfile
}

//
// Get workflow summary for MultiQC
//
Expand Down
2 changes: 1 addition & 1 deletion nextflow.config
Original file line number Diff line number Diff line change
Expand Up @@ -271,7 +271,7 @@ manifest {
description = """call and score variants from WGS/WES of rare disease patients"""
mainScript = 'main.nf'
nextflowVersion = '!>=23.04.0'
version = '1.1.0'
version = '1.1.1'
doi = ''
}

Expand Down
6 changes: 5 additions & 1 deletion subworkflows/local/mitochondria/merge_annotate_MT.nf
Original file line number Diff line number Diff line change
Expand Up @@ -143,7 +143,11 @@ workflow MERGE_ANNOTATE_MT {

// HMTNOTE ANNOTATE
HMTNOTE_ANNOTATE(VCFANNO_MT.out.vcf)
ZIP_TABIX_HMTNOTE(HMTNOTE_ANNOTATE.out.vcf)
HMTNOTE_ANNOTATE.out.vcf.map{meta, vcf ->
return [meta, WorkflowRaredisease.replaceSpacesInInfoColumn(vcf, vcf.parent.toString(), vcf.baseName)]
}
.set { ch_hmtnote_reformatted }
ZIP_TABIX_HMTNOTE(ch_hmtnote_reformatted)

// Prepare output
ch_vcf_out = ZIP_TABIX_HMTNOTE.out.gz_tbi.map{meta, vcf, tbi -> return [meta, vcf] }
Expand Down
15 changes: 4 additions & 11 deletions workflows/raredisease.nf
Original file line number Diff line number Diff line change
Expand Up @@ -97,7 +97,7 @@ include { FILTER_VEP as FILTER_VEP_SV } from '../modules/local/filter_
// MODULE: Installed directly from nf-core/modules
//

include { BCFTOOLS_CONCAT } from '../modules/nf-core/bcftools/concat/main'
include { GATK4_MERGEVCFS } from '../modules/nf-core/gatk4/mergevcfs/main'
include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'
include { FASTQC } from '../modules/nf-core/fastqc/main'
include { GATK4_SELECTVARIANTS } from '../modules/nf-core/gatk4/selectvariants/main'
Expand Down Expand Up @@ -483,16 +483,9 @@ workflow RAREDISEASE {
.groupTuple()
.set { ch_merged_vcf }

ANNOTATE_SNVS.out.tbi
.concat(ANALYSE_MT.out.tbi)
.groupTuple()
.set { ch_merged_tbi }

ch_merged_vcf.join(ch_merged_tbi, failOnMismatch:true, failOnDuplicate:true).set {ch_concat_in}

BCFTOOLS_CONCAT (ch_concat_in)
ch_snv_annotate = BCFTOOLS_CONCAT.out.vcf
ch_versions = ch_versions.mix(BCFTOOLS_CONCAT.out.versions)
GATK4_MERGEVCFS (ch_merged_vcf, [[],[]])
asp8200 marked this conversation as resolved.
Show resolved Hide resolved
ch_snv_annotate = GATK4_MERGEVCFS.out.vcf
ch_versions = ch_versions.mix(GATK4_MERGEVCFS.out.versions)
}

ANN_CSQ_PLI_SNV (
Expand Down