Correct -n with -N in samtools fastq to retain paired information in BAM2FASTQ fiels when paired-end mapping

Author: jfy133

CHANGELOG.md

@@ -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 (❤ 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`
 

main.nf

@@ -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
     """ 
 }
 
@@ -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 ){
@@ -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 ) {
@@ -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 ){
@@ -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
         """
     }
 }