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Fix bwa mem indexing and re-update MQC SeqTools versions after git me… #867

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Merged
jfy133 merged 4 commits into from
Mar 24, 2022
Merged

Fix bwa mem indexing and re-update MQC SeqTools versions after git me… #867

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b58ae39
Fix bwa mem indexing and re-update MQC SeqTools versions after git me…
jfy133 Mar 24, 2022
01655ee
Update changelog and update test
jfy133 Mar 24, 2022
5f85ee6
Add skip collapse flag..
jfy133 Mar 24, 2022
a32bd0b
Merge branch 'dev' into bwamem-fix
jfy133 Mar 24, 2022
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2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
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Expand Up @@ -119,7 +119,7 @@ jobs:
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --mapper 'circularmapper' --circulartarget 'NC_007596.2'
- name: MAPPER_BWAMEM Test running with BWA Mem
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --mapper 'bwamem'
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --mapper 'bwamem' --skip_collapse
- name: MAPPER_BT2 Test running with BowTie2
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --mapper 'bowtie2' --bt2_alignmode 'local' --bt2_sensitivity 'sensitive' --bt2n 1 --bt2l 16 --bt2_trim5 1 --bt2_trim3 1
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -18,6 +18,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
- [#851](https://github.com/nf-core/eager/issues/851) Fixes a file-name clash during additional_library_merge, post-BAM trimming of different UDG treated libraries of a sample
- Renamed a range of MultiQC general stats table headers to improve clarity, documentation has been updated accordingly
- [#857](https://github.com/nf-core/eager/issues/857) Corrected samtools fastq flag to _retain_ read-pair information when converting off-target BAM files to fastq in paired-end mapping (❤ to @alexhbnr for reporting)
- [#858](https://github.com/nf-core/eager/pull/858) Corrected tutorials to reflect updated BAM trimming flags (❤ to @marcel-keller for reporting)
- [#866](https://github.com/nf-core/eager/issues/866) Fixed a typo in the indexing step of BWA mem when not-collapsing (❤ to @alexhbnr for reporting)
- Corrected tutorials to reflect updated BAM trimming flags (❤ to @marcel-keller for reporting and correcting)

### `Dependencies`
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4 changes: 2 additions & 2 deletions environment.yml
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Expand Up @@ -26,12 +26,12 @@ dependencies:
- bioconda::qualimap=2.2.2d
- bioconda::vcf2genome=0.91
- bioconda::damageprofiler=0.4.9 # Don't upgrade - later versions don't allow java 8
- bioconda::multiqc=1.11
- bioconda::multiqc=1.12
- bioconda::pmdtools=0.60
- bioconda::bedtools=2.30.0
- conda-forge::libiconv=1.16
- conda-forge::pigz=2.6
- bioconda::sequencetools=1.4.0.6
- bioconda::sequencetools=1.5.2
- bioconda::preseq=3.1.2
- bioconda::fastp=0.20.1
- bioconda::bamutil=1.0.15
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2 changes: 1 addition & 1 deletion main.nf
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Expand Up @@ -1318,7 +1318,7 @@ process bwamem {
if (!params.single_end && params.skip_collapse){
"""
bwa mem -t ${split_cpus} $fasta $r1 $r2 -R "@RG\\tID:ILLUMINA-${libraryid}\\tSM:${samplename}\\tPL:illumina\\tPU:ILLUMINA-${libraryid}-${seqtype}" | samtools sort -@ ${split_cpus} -O bam - > "${libraryid}"_"${seqtype}".mapped.bam
samtools index ${size} -@ ${task.cpus} "${libraryid}".mapped.bam
samtools index ${size} -@ ${task.cpus} "${libraryid}"_"${seqtype}".mapped.bam
"""
} else {
"""
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