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Samtools fastq fix #859

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Merged
jfy133 merged 2 commits into from
Mar 23, 2022
Merged

Samtools fastq fix #859

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26a0503
Correct `-n` with `-N` in samtools fastq to retain paired information…
jfy133 Mar 23, 2022
61f6559
Update Changelog
jfy133 Mar 23, 2022
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5 changes: 3 additions & 2 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -11,13 +11,14 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.

- [#828](https://github.com/nf-core/eager/issues/828) Improved error message if required metagenomic screening parameters not set correctly
- [#836](https://github.com/nf-core/eager/issues/836) Remove deprecated parameters from test profiles
- [#838](https://github.com/nf-core/eager/issues/836) Fix --snpcapture_bed files not being picked up by Nextflow (thanks to @meganemichel for reporting)
- [#838](https://github.com/nf-core/eager/issues/836) Fix --snpcapture_bed files not being picked up by Nextflow (❤ to @meganemichel for reporting)
- [#843](https://github.com/nf-core/eager/issues/843) Re-add direct piping of AdapterRemovalFixPrefix to pigz
- [#844](https://github.com/nf-core/eager/issues/844) Fixed reference masking prior to pmdtools
- [#845](https://github.com/nf-core/eager/issues/845) Updates parameter documention to specify `-s` preseq parameter also applies to lc_extrap
- [#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
- [#858](https://github.com/nf-core/eager/pull/858) Corrected tutorials to reflect updated BAM trimming flags (thanks to @marcel-keller for reporting)
- [#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)

### `Dependencies`

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10 changes: 5 additions & 5 deletions main.nf
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Expand Up @@ -638,7 +638,7 @@ process convertBam {
script:
base = "${bam.baseName}"
"""
samtools fastq -tn ${bam} | pigz -p ${task.cpus} > ${base}.converted.fastq.gz
samtools fastq -t ${bam} | pigz -p ${task.cpus} > ${base}.converted.fastq.gz
"""
}

Expand Down Expand Up @@ -1683,7 +1683,7 @@ process samtools_filter {
samtools index ${libraryid}.filtered.bam ${size}

## FASTQ
samtools fastq -tn ${libraryid}.unmapped.bam | pigz -p ${task.cpus - 1} > ${libraryid}.unmapped.fastq.gz
samtools fastq -tN ${libraryid}.unmapped.bam | pigz -p ${task.cpus - 1} > ${libraryid}.unmapped.fastq.gz
rm ${libraryid}.unmapped.bam
"""
} else if ( "${params.bam_unmapped_type}" == "both" && params.bam_filter_minreadlength == 0 ){
Expand All @@ -1693,7 +1693,7 @@ process samtools_filter {
samtools index ${libraryid}.filtered.bam ${size}

## FASTQ
samtools fastq -tn ${libraryid}.unmapped.bam | pigz -p ${task.cpus -1} > ${libraryid}.unmapped.fastq.gz
samtools fastq -tN ${libraryid}.unmapped.bam | pigz -p ${task.cpus -1} > ${libraryid}.unmapped.fastq.gz
"""
// Unmapped/MAPQ Filtering WITH min-length filtering
} else if ( "${params.bam_unmapped_type}" == "keep" && params.bam_filter_minreadlength != 0 ) {
Expand Down Expand Up @@ -1723,7 +1723,7 @@ process samtools_filter {
samtools index ${libraryid}.filtered.bam ${size}

## FASTQ
samtools fastq -tn ${libraryid}.unmapped.bam | pigz -p ${task.cpus - 1} > ${libraryid}.unmapped.fastq.gz
samtools fastq -tN ${libraryid}.unmapped.bam | pigz -p ${task.cpus - 1} > ${libraryid}.unmapped.fastq.gz
rm ${libraryid}.unmapped.bam
"""
} else if ( "${params.bam_unmapped_type}" == "both" && params.bam_filter_minreadlength != 0 ){
Expand All @@ -1734,7 +1734,7 @@ process samtools_filter {
samtools index ${libraryid}.filtered.bam ${size}

## FASTQ
samtools fastq -tn ${libraryid}.unmapped.bam | pigz -p ${task.cpus} > ${libraryid}.unmapped.fastq.gz
samtools fastq -tN ${libraryid}.unmapped.bam | pigz -p ${task.cpus} > ${libraryid}.unmapped.fastq.gz
"""
}
}
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