feat: Add control flow for choosing haplotypers

modules/cliquesnv/main.nf

@@ -1,6 +1,7 @@
 process CLIQUESNV {
     tag "${prefix}"
     label 'process_high'
+    label 'cliquesnv'
 
     container 'quay.io/biocontainers/cliquesnv:2.0.3--hdfd78af_0'
 
@@ -14,6 +15,9 @@ process CLIQUESNV {
 
     publishDir "results/${task.process}", mode: 'copy'
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def jmemstring = task.memory.toMega() + 'M'
     """

modules/haplink/haplotypes/main.nf

@@ -1,6 +1,7 @@
 process HAPLINK_HAPLOTYPES {
     tag "${prefix}"
     label 'process_high'
+    label 'haplink'
 
     container 'quay.io/biocontainers/haplink:1.0.0--h031d066_0'
 
@@ -13,6 +14,9 @@ process HAPLINK_HAPLOTYPES {
 
     publishDir "results/${task.process}", mode: 'copy'
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def ml_args = task.ext.ml_args ?: ''
     """

modules/haplink/sequences/main.nf

@@ -1,6 +1,7 @@
 process HAPLINK_SEQUENCES {
     tag "${method}: ${prefix}"
     label 'process_single'
+    label 'haplink'
 
     container 'quay.io/biocontainers/haplink:1.0.0--h031d066_0'
 
@@ -13,6 +14,9 @@ process HAPLINK_SEQUENCES {
 
     publishDir "results/${method}", mode: 'copy'
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     """
     export JULIA_NUM_THREADS=${task.cpus}

modules/haplink/variants/main.nf

@@ -1,6 +1,7 @@
 process HAPLINK_VARIANTS {
     tag "${prefix}"
     label 'process_medium'
+    label 'haplink'
 
     container 'quay.io/biocontainers/haplink:1.0.0--h031d066_0'
 
@@ -13,6 +14,9 @@ process HAPLINK_VARIANTS {
 
     publishDir "results/${task.process}", mode: 'copy'
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     """
     export JULIA_NUM_THREADS=${task.cpus}

modules/predicthaplo/main.nf

@@ -1,6 +1,7 @@
 process PREDICTHAPLO {
     tag "${prefix}"
     label 'process_high'
+    label 'predicthaplo'
 
     container 'quay.io/biocontainers/predicthaplo:2.1.4--h9b88814_5'
 
@@ -13,6 +14,9 @@ process PREDICTHAPLO {
 
     publishDir "results/${task.process}", mode: 'copy'
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     """
     predicthaplo \\

modules/quasirecomb/main.nf

@@ -1,6 +1,7 @@
 process QUASIRECOMB {
     tag "${prefix}"
     label 'process_high'
+    label 'quasirecomb'
 
     container 'quay.io/biocontainers/quasirecomb:1.2--hdfd78af_1'
 
@@ -12,6 +13,9 @@ process QUASIRECOMB {
 
     publishDir "results/${task.process}", mode: 'copy'
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def jmemstring = task.memory.toMega() + 'M'
     """

modules/shorah/amplicon/main.nf

@@ -1,6 +1,7 @@
 process SHORAH_AMPLICON {
     tag "${prefix}"
     label 'process_high'
+    label 'shorah'
 
     container 'quay.io/biocontainers/shorah:1.99.2--py38h73782ee_8'
 
@@ -14,6 +15,9 @@ process SHORAH_AMPLICON {
 
     publishDir "results/${task.process}", mode: 'copy'
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     """
     shorah amplicon \\

modules/shorah/shotgun/main.nf

@@ -1,6 +1,7 @@
 process SHORAH_SHOTGUN {
     tag "${prefix}"
     label 'process_high'
+    label 'shorah'
 
     container 'quay.io/biocontainers/shorah:1.99.2--py38h73782ee_8'
 
@@ -14,6 +15,9 @@ process SHORAH_SHOTGUN {
 
     publishDir "results/${task.process}", mode: 'copy'
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     """
     shorah shotgun \\

modules/viquas/main.nf

@@ -1,6 +1,7 @@
 process VIQUAS {
     tag "${prefix}"
     label 'process_high'
+    label 'viquas'
 
     container 'code.millironx.com/millironx/haplotyper-battle-royale:viquas'
 
@@ -13,6 +14,9 @@ process VIQUAS {
 
     publishDir "results/${task.process}", mode: 'copy'
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     """
     viquas \\

nextflow.config

@@ -14,6 +14,15 @@ params {
     max_memory = '128.GB'
     max_cpus = 16
     max_time = '240.h'
+
+    // Haplotyper options
+    // By default, run all haplotypers
+    cliquesnv = true
+    haplink = true
+    predicthaplo = true
+    quasirecomb = true
+    shorah = true
+    viquas = true
 }
 
 process {
@@ -53,6 +62,25 @@ process {
         --overlap-max 8000 \\
         """
     }
+
+    withLabel: 'cliquesnv' {
+        ext.when = params.cliquesnv
+    }
+    withLabel: 'haplink' {
+        ext.when = params.haplink
+    }
+    withLabel: 'predicthaplo' {
+        ext.when = params.predicthaplo
+    }
+    withLabel: 'quasirecomb' {
+        ext.when = params.quasirecomb
+    }
+    withLabel: 'shorah' {
+        ext.when = params.shorah
+    }
+    withLabel: 'viquas' {
+        ext.when = params.viquas
+    }
 }
 
 try {