Update tasmanian-mismatch to 2.0.4

README.md

@@ -106,7 +106,7 @@ Modify the conf/references.config file to specify your genome files
 ## Reference Genomes
 Pre-built reference genomes with methylation spike-in controls + CpG Island Annotation files:
 - **T2T CHM13**: [T2T_chm13v2.0+  meth_controls](https://neb-em-seq-sra.s3.us-east-1.amazonaws.com/T2T_chm13v2.0%2Bmeth_controls.fa.gz) [CpG Islands](https://neb-em-seq-sra.s3.us-east-1.amazonaws.com/human_t2t_cpg_islands.gtf)
-- **GRCh38**: [GRCh39 + meth controls](https://neb-em-seq-sra.s3.us-east-1.amazonaws.com/grch38_core%2Bmeth_controls.fa.gz) [CpG Islands](https://neb-em-seq-sra.s3.us-east-1.amazonaws.com/human_grch38_cpg_islands.gtf)
+- **GRCh38**: [GRCh38 + meth controls](https://neb-em-seq-sra.s3.us-east-1.amazonaws.com/grch38_core%2Bmeth_controls.fa.gz) [CpG Islands](https://neb-em-seq-sra.s3.us-east-1.amazonaws.com/human_grch38_cpg_islands.gtf)
 - **GRCm39**: [GRCm39 + meth_controls](https://neb-em-seq-sra.s3.us-east-1.amazonaws.com/grcm39%2Bmeth_controls.fa.gz) [CpG Islands](https://neb-em-seq-sra.s3.us-east-1.amazonaws.com/grcm39_cpg_islands.gtf)
 - Create your own reference by appending the [control sequences](assets/methylation_controls.fa) to your preferred genome fasta (e.g. `cat genome.fa methylation_controls.fa > genome+methylation_controls.fa`)
    | Sequence | Methylation State                                | Purpose |

main.nf

@@ -1,3 +1,4 @@
+// Nextflow v24 or older only: uncomment the line below (see README's Upgrade section)
 // nextflow.preview.topic = true
 
 include { registerEmailNotifications }                        from './lib/notifications.nf'

modules/tasmanian.nf

@@ -2,7 +2,7 @@ process tasmanian {
     label 'medium_cpu'
     tag { library }
     publishDir "${params.outputDir}/stats/tasmanian"
-    conda "bioconda::samtools=1.22 bioconda::tasmanian-mismatch=1.0.9"
+    conda "bioconda::tasmanian-mismatch=2.0.5"
 
     errorStrategy { task.attempt <= 1 ? 'retry' : 'terminate' }
     maxRetries 1
@@ -15,14 +15,18 @@ process tasmanian {
 
     output:
         tuple val(library), path("${library}.tasmanian.csv"), emit: for_agg
-        tuple val("${task.process}"), val('samtools'), eval('samtools --version | head -n 1 | sed \'s/^samtools //\''), topic: versions
-        tuple val("${task.process}"), val('tasmanian'), val('*should be* 1.0.9'), topic: versions
+        tuple val("${task.process}"), val('tasmanian-mismatch'), val('2.0.5'), topic: versions
 
     script:
     """
     set +e
     set +o pipefail
-    samtools view -q 30 -F 3840 ${bam} | head -n 2000000 | run_tasmanian -r ${genome_fa} > ${library}.tasmanian.csv
+    tasmanian-mismatch ${bam} ${genome_fa} \
+        --position-mode read \
+        --min-base-quality 20 \
+        --min-map-quality 30 \
+        -F 3840 \
+        -o ${library}.tasmanian.csv
     """
 
 }