Skip to content

Add PU tag to Read Groups for all mapping methods #658

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

Merged
jfy133 merged 9 commits into from
Jan 14, 2021
Merged

Add PU tag to Read Groups for all mapping methods #658

Show file tree
Hide file tree
Changes from 8 commits
Commits
Show all changes
9 commits
Select commit Hold shift + click to select a range
85e2e32
Merge pull request #621 from nf-core/dev
jfy133 Dec 9, 2020
0bc87f3
Merge pull request #649 from nf-core/dev
jfy133 Jan 11, 2021
bf95d9f
Add PU tag to Read Groups for all mapping methods
IdoBar Jan 11, 2021
b8073cb
Merge pull request #2 from nf-core/dev
IdoBar Jan 12, 2021
32b4f2b
Added information about fix of issue #655
IdoBar Jan 13, 2021
77003d7
Added contributor info
IdoBar Jan 13, 2021
6ccddad
Fixed lines surrounding the list
IdoBar Jan 13, 2021
270b067
Fix indentation around list item
IdoBar Jan 13, 2021
cb9b7a4
Merge branch 'dev' into patch-2
jfy133 Jan 14, 2021
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
2 changes: 2 additions & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.

### `Fixed`

- [#655](https://github.com/nf-core/eager/issues/655) - Updated read groups for all mappers to allow proper GATK validation

### `Dependencies`

### `Deprecated`
Expand Down
1 change: 1 addition & 0 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -160,6 +160,7 @@ Those who have provided conceptual guidance, suggestions, bug reports etc.

* Arielle Munters
* [Hester van Schalkwyk](https://github.com/hesterjvs)
* [Ido Bar](https://github.com/IdoBar)
* [Irina Velsko](https://github.com/ivelsko)
* [Katerine Eaton](https://github.com/ktmeaton)
* [Luc Venturini](https://github.com/lucventurini)
Expand Down
16 changes: 8 additions & 8 deletions main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1494,14 +1494,14 @@ process bwa {
"""
bwa aln -t ${task.cpus} $fasta ${r1} -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f ${libraryid}.r1.sai
bwa aln -t ${task.cpus} $fasta ${r2} -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f ${libraryid}.r2.sai
bwa sampe -r "@RG\\tID:ILLUMINA-${libraryid}\\tSM:${libraryid}\\tPL:illumina" $fasta ${libraryid}.r1.sai ${libraryid}.r2.sai ${r1} ${r2} | samtools sort -@ ${task.cpus} -O bam - > ${libraryid}_"${seqtype}".mapped.bam
bwa sampe -r "@RG\\tID:ILLUMINA-${libraryid}\\tSM:${libraryid}\\tPL:illumina\\tPU:ILLUMINA-${libraryid}-${seqtype}" $fasta ${libraryid}.r1.sai ${libraryid}.r2.sai ${r1} ${r2} | samtools sort -@ ${task.cpus} -O bam - > ${libraryid}_"${seqtype}".mapped.bam
samtools index "${libraryid}"_"${seqtype}".mapped.bam ${size}
"""
} else {
//PE collapsed, or SE data
"""
bwa aln -t ${task.cpus} ${fasta} ${r1} -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f ${libraryid}.sai
bwa samse -r "@RG\\tID:ILLUMINA-${libraryid}\\tSM:${libraryid}\\tPL:illumina" $fasta ${libraryid}.sai $r1 | samtools sort -@ ${task.cpus} -O bam - > "${libraryid}"_"${seqtype}".mapped.bam
bwa samse -r "@RG\\tID:ILLUMINA-${libraryid}\\tSM:${libraryid}\\tPL:illumina\\tPU:ILLUMINA-${libraryid}-${seqtype}" $fasta ${libraryid}.sai $r1 | samtools sort -@ ${task.cpus} -O bam - > "${libraryid}"_"${seqtype}".mapped.bam
samtools index "${libraryid}"_"${seqtype}".mapped.bam ${size}
"""
}
Expand Down Expand Up @@ -1531,12 +1531,12 @@ process bwamem {

if (!params.single_end && params.skip_collapse){
"""
bwa mem -t ${task.cpus} $fasta $r1 $r2 -R "@RG\\tID:ILLUMINA-${libraryid}\\tSM:${libraryid}\\tPL:illumina" | samtools sort -@ ${task.cpus} -O bam - > "${libraryid}"_"${seqtype}".mapped.bam
bwa mem -t ${task.cpus} $fasta $r1 $r2 -R "@RG\\tID:ILLUMINA-${libraryid}\\tSM:${libraryid}\\tPL:illumina\\tPU:ILLUMINA-${libraryid}-${seqtype}" | samtools sort -@ ${task.cpus} -O bam - > "${libraryid}"_"${seqtype}".mapped.bam
samtools index ${size} -@ ${task.cpus} "${libraryid}".mapped.bam
"""
} else {
"""
bwa mem -t ${task.cpus} $fasta $r1 -R "@RG\\tID:ILLUMINA-${libraryid}\\tSM:${libraryid}\\tPL:illumina" | samtools sort -@ ${task.cpus} -O bam - > "${libraryid}"_"${seqtype}".mapped.bam
bwa mem -t ${task.cpus} $fasta $r1 -R "@RG\\tID:ILLUMINA-${libraryid}\\tSM:${libraryid}\\tPL:illumina\\tPU:ILLUMINA-${libraryid}-${seqtype}" | samtools sort -@ ${task.cpus} -O bam - > "${libraryid}"_"${seqtype}".mapped.bam
samtools index -@ ${task.cpus} "${libraryid}"_"${seqtype}".mapped.bam ${size}
"""
}
Expand Down Expand Up @@ -1600,15 +1600,15 @@ process circularmapper{
"""
bwa aln -t ${task.cpus} $elongated_root $r1 -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f ${libraryid}.r1.sai
bwa aln -t ${task.cpus} $elongated_root $r2 -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f ${libraryid}.r2.sai
bwa sampe -r "@RG\\tID:ILLUMINA-${libraryid}\\tSM:${libraryid}\\tPL:illumina" $elongated_root ${libraryid}.r1.sai ${libraryid}.r2.sai $r1 $r2 > tmp.out
bwa sampe -r "@RG\\tID:ILLUMINA-${libraryid}\\tSM:${libraryid}\\tPL:illumina\\tPU:ILLUMINA-${libraryid}-${seqtype}" $elongated_root ${libraryid}.r1.sai ${libraryid}.r2.sai $r1 $r2 > tmp.out
realignsamfile -e ${params.circularextension} -i tmp.out -r $fasta $filter
samtools sort -@ ${task.cpus} -O bam tmp_realigned.bam > ${libraryid}_"${seqtype}".mapped.bam
samtools index "${libraryid}"_"${seqtype}".mapped.bam ${size}
"""
} else {
"""
bwa aln -t ${task.cpus} $elongated_root $r1 -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f ${libraryid}.sai
bwa samse -r "@RG\\tID:ILLUMINA-${libraryid}\\tSM:${libraryid}\\tPL:illumina" $elongated_root ${libraryid}.sai $r1 > tmp.out
bwa samse -r "@RG\\tID:ILLUMINA-${libraryid}\\tSM:${libraryid}\\tPL:illumina\\tPU:ILLUMINA-${libraryid}-${seqtype}" $elongated_root ${libraryid}.sai $r1 > tmp.out
realignsamfile -e ${params.circularextension} -i tmp.out -r $fasta $filter
samtools sort -@ ${task.cpus} -O bam tmp_realigned.bam > "${libraryid}"_"${seqtype}".mapped.bam
samtools index "${libraryid}"_"${seqtype}".mapped.bam ${size}
Expand Down Expand Up @@ -1677,13 +1677,13 @@ process bowtie2 {
//PE data without merging, PE data without any AR applied
if ( seqtype == 'PE' && ( params.skip_collapse || params.skip_adapterremoval ) ){
"""
bowtie2 -x ${fasta} -1 ${r1} -2 ${r2} -p ${task.cpus} ${sensitivity} ${bt2n} ${bt2l} ${trim5} ${trim3} 2> "${libraryid}"_bt2.log | samtools sort -@ ${task.cpus} -O bam > "${libraryid}"_"${seqtype}".mapped.bam
bowtie2 -x ${fasta} -1 ${r1} -2 ${r2} -p ${task.cpus} ${sensitivity} ${bt2n} ${bt2l} ${trim5} ${trim3} --rg-id ILLUMINA-${libraryid} --rg SM:${libraryid} --rg PL:illumina --rg PU:ILLUMINA-${libraryid}-${seqtype} 2> "${libraryid}"_bt2.log | samtools sort -@ ${task.cpus} -O bam > "${libraryid}"_"${seqtype}".mapped.bam
samtools index "${libraryid}"_"${seqtype}".mapped.bam ${size}
"""
} else {
//PE collapsed, or SE data
"""
bowtie2 -x ${fasta} -U ${r1} -p ${task.cpus} ${sensitivity} ${bt2n} ${bt2l} ${trim5} ${trim3} 2> "${libraryid}"_bt2.log | samtools sort -@ ${task.cpus} -O bam > "${libraryid}"_"${seqtype}".mapped.bam
bowtie2 -x ${fasta} -U ${r1} -p ${task.cpus} ${sensitivity} ${bt2n} ${bt2l} ${trim5} ${trim3} --rg-id ILLUMINA-${libraryid} --rg SM:${libraryid} --rg PL:illumina --rg PU:ILLUMINA-${libraryid}-${seqtype} 2> "${libraryid}"_bt2.log | samtools sort -@ ${task.cpus} -O bam > "${libraryid}"_"${seqtype}".mapped.bam
samtools index "${libraryid}"_"${seqtype}".mapped.bam ${size}
"""
}
Expand Down
⚡