Add ONT tests

.github/workflows/ci.yml

@@ -25,7 +25,7 @@ jobs:
       matrix:
         parameters:
           - ""
-          - "--input https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/nallo/testdata/samplesheet_multisample_bam.csv --split_fastq 2 --parallel_snv 1 --phaser hiphase_sv"
+          - "--preset ONT_R10 --input https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/nallo/testdata/samplesheet_multisample_bam_ont.csv --split_fastq 2 --parallel_snv 1"
         NXF_VER:
           - "23.04.0"
           - "latest-everything"

CHANGELOG.md

@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Added`
 
 - [#230](https://github.com/genomic-medicine-sweden/nallo/pull/230) - Added nf-test to the short variant calling workflow
+- [#231](https://github.com/genomic-medicine-sweden/nallo/pull/231) - Added initial tests for ONT data
 - [#234](https://github.com/genomic-medicine-sweden/nallo/pull/234) - Added a `--deepvariant_model_type` parameter to override the model type set by `--preset`
 
 ### `Changed`
@@ -19,6 +20,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- [#231](https://github.com/genomic-medicine-sweden/nallo/pull/231) - Fixed certain tags in input BAM files being transfered over to (re)aligned BAM
+
 ### Parameters
 
 | Old parameter | New parameter              |

conf/modules/bam_to_fastq.config

@@ -26,10 +26,12 @@ process {
 
     withName: '.*:BAM_TO_FASTQ:SAMTOOLS_FASTQ' {
 
-        // Maybe should only allow unmapped data
-        // Unsure why SA tag is still there after reset
-        ext.args = '-x SA'   // samtools reset
-        ext.args2 = '-T \\*' // samtools fastq
+        // Strip tags with -x, and keep the rest
+        ext.args = { [
+            '-x HP,PS', // phasing
+            '-x AS,CC,CG,CP,H1,H2,HI,H0,IH,MC,MD,MQ,NM,SA,TS'
+        ].join(' ') }
+        ext.args2 = '-T \\*'
 
         ext.prefix = { "${input}" }
     }