From 2829d515336a3a96300b11f1ad32020506a9a3ba Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 15:21:26 -0500
Subject: [PATCH 01/40] refactor: Move HAPLINK_VARIANTS module to its own
 folder

---
 main.nf                          | 24 +-----------------------
 modules/haplink/variants/main.nf | 22 ++++++++++++++++++++++
 2 files changed, 23 insertions(+), 23 deletions(-)
 create mode 100644 modules/haplink/variants/main.nf

diff --git a/main.nf b/main.nf
index 58335df..69acadb 100755
--- a/main.nf
+++ b/main.nf
@@ -1,5 +1,6 @@
 #!/usr/bin/env nextflow
 
+include { HAPLINK_VARIANTS } from './modules/haplink/variants'
 include { VIQUAS } from './modules/viquas'
 
 workflow {
@@ -195,29 +196,6 @@ process SHORAH_SHOTGUN {
     """
 }
 
-process HAPLINK_VARIANTS {
-    cpus 2
-    memory '12.GB'
-
-    input:
-    tuple val(prefix), path(bam), path(bai)
-    path reference
-
-    output:
-    tuple val(prefix), path("*.vcf")
-
-    publishDir "results", mode: 'copy'
-
-    script:
-    """
-    export JULIA_NUM_THREADS=${task.cpus}
-    haplink variants \\
-            "${reference}" \\
-            "${bam}" \\
-        > "${prefix}.vcf"
-    """
-}
-
 process HAPLINK_RAW_HAPLOTYPES {
     cpus 2
     memory '12.GB'
diff --git a/modules/haplink/variants/main.nf b/modules/haplink/variants/main.nf
new file mode 100644
index 0000000..8e2c48f
--- /dev/null
+++ b/modules/haplink/variants/main.nf
@@ -0,0 +1,22 @@
+process HAPLINK_VARIANTS {
+    cpus 2
+    memory '12.GB'
+
+    input:
+    tuple val(prefix), path(bam), path(bai)
+    path reference
+
+    output:
+    tuple val(prefix), path("*.vcf")
+
+    publishDir "results", mode: 'copy'
+
+    script:
+    """
+    export JULIA_NUM_THREADS=${task.cpus}
+    haplink variants \\
+            "${reference}" \\
+            "${bam}" \\
+        > "${prefix}.vcf"
+    """
+}

From a223b8746486b3e4e7b8091d17085b478d3780df Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 15:22:13 -0500
Subject: [PATCH 02/40] feat: Add tag directive to HAPLINK_VARIANTS module

---
 modules/haplink/variants/main.nf | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/haplink/variants/main.nf b/modules/haplink/variants/main.nf
index 8e2c48f..4106c78 100644
--- a/modules/haplink/variants/main.nf
+++ b/modules/haplink/variants/main.nf
@@ -1,4 +1,5 @@
 process HAPLINK_VARIANTS {
+    tag "${prefix}"
     cpus 2
     memory '12.GB'
 

From cc433aaffe77e72d6d49bea9b7ce39d935c10f6e Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 15:23:45 -0500
Subject: [PATCH 03/40] feat: Add container directive to HAPLINK_VARIANTS

---
 modules/haplink/variants/main.nf | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/modules/haplink/variants/main.nf b/modules/haplink/variants/main.nf
index 4106c78..324be8f 100644
--- a/modules/haplink/variants/main.nf
+++ b/modules/haplink/variants/main.nf
@@ -3,6 +3,8 @@ process HAPLINK_VARIANTS {
     cpus 2
     memory '12.GB'
 
+    container 'quay.io/biocontainers/haplink:1.0.0--h031d066_0'
+
     input:
     tuple val(prefix), path(bam), path(bai)
     path reference

From 2c755dcd4f88524af2a20c83bd793e37bb1f14e2 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 15:27:05 -0500
Subject: [PATCH 04/40] refactor: Replace hard-coded performance directives
 with process label

---
 modules/haplink/variants/main.nf | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/modules/haplink/variants/main.nf b/modules/haplink/variants/main.nf
index 324be8f..9f036de 100644
--- a/modules/haplink/variants/main.nf
+++ b/modules/haplink/variants/main.nf
@@ -1,7 +1,6 @@
 process HAPLINK_VARIANTS {
     tag "${prefix}"
-    cpus 2
-    memory '12.GB'
+    label 'process_medium'
 
     container 'quay.io/biocontainers/haplink:1.0.0--h031d066_0'
 

From 18875ae1a63de8d09d8ca9db7669a38417ced0f9 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 15:34:27 -0500
Subject: [PATCH 05/40] refactor: Move EFETCH module to its own file

---
 main.nf                | 22 +---------------------
 modules/efetch/main.nf | 20 ++++++++++++++++++++
 2 files changed, 21 insertions(+), 21 deletions(-)
 create mode 100644 modules/efetch/main.nf

diff --git a/main.nf b/main.nf
index 69acadb..3d4bf6a 100755
--- a/main.nf
+++ b/main.nf
@@ -1,5 +1,6 @@
 #!/usr/bin/env nextflow
 
+include { EFETCH } from './modules/efetch'
 include { HAPLINK_VARIANTS } from './modules/haplink/variants'
 include { VIQUAS } from './modules/viquas'
 
@@ -68,27 +69,6 @@ workflow {
     )
 }
 
-process EFETCH {
-    cpus 1
-    memory '256.MB'
-    container 'quay.io/biocontainers/entrez-direct:16.2--he881be0_1'
-
-    publishDir "results", mode: 'copy'
-
-    output:
-    path 'idv4.fasta'
-
-    script:
-    """
-    esearch \\
-            -db nucleotide \\
-            -query "NC_036618.1" \\
-        | efetch \\
-            -format fasta \\
-        > idv4.fasta
-    """
-}
-
 process NANOFILT {
     cpus 1
     memory '8.GB'
diff --git a/modules/efetch/main.nf b/modules/efetch/main.nf
new file mode 100644
index 0000000..00ec585
--- /dev/null
+++ b/modules/efetch/main.nf
@@ -0,0 +1,20 @@
+process EFETCH {
+    cpus 1
+    memory '256.MB'
+    container 'quay.io/biocontainers/entrez-direct:16.2--he881be0_1'
+
+    publishDir "results", mode: 'copy'
+
+    output:
+    path 'idv4.fasta'
+
+    script:
+    """
+    esearch \\
+            -db nucleotide \\
+            -query "NC_036618.1" \\
+        | efetch \\
+            -format fasta \\
+        > idv4.fasta
+    """
+}

From 7a3744a3d36796f7d90833d143ac51935d88ca34 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 15:36:01 -0500
Subject: [PATCH 06/40] refactor: Replace EFETCH performance directives with
 process label

---
 modules/efetch/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/efetch/main.nf b/modules/efetch/main.nf
index 00ec585..2041d45 100644
--- a/modules/efetch/main.nf
+++ b/modules/efetch/main.nf
@@ -1,6 +1,6 @@
 process EFETCH {
-    cpus 1
-    memory '256.MB'
+    label 'process_single'
+
     container 'quay.io/biocontainers/entrez-direct:16.2--he881be0_1'
 
     publishDir "results", mode: 'copy'

From b1ee784daca2f5a722a85f27d15ebd5c2e642ec9 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 15:38:55 -0500
Subject: [PATCH 07/40] refactor: Make reference genome an input for EFETCH

---
 main.nf                | 2 +-
 modules/efetch/main.nf | 5 ++++-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/main.nf b/main.nf
index 3d4bf6a..54ff5e4 100755
--- a/main.nf
+++ b/main.nf
@@ -11,7 +11,7 @@ workflow {
         .map { file -> tuple(file.simpleName, file) }
         .set { ch_input }
 
-    EFETCH()
+    EFETCH('NC_036618.1')
     EFETCH
         .out
         .set { ch_reference }
diff --git a/modules/efetch/main.nf b/modules/efetch/main.nf
index 2041d45..66272fd 100644
--- a/modules/efetch/main.nf
+++ b/modules/efetch/main.nf
@@ -3,6 +3,9 @@ process EFETCH {
 
     container 'quay.io/biocontainers/entrez-direct:16.2--he881be0_1'
 
+    input:
+    val(genome)
+
     publishDir "results", mode: 'copy'
 
     output:
@@ -12,7 +15,7 @@ process EFETCH {
     """
     esearch \\
             -db nucleotide \\
-            -query "NC_036618.1" \\
+            -query "${genome}" \\
         | efetch \\
             -format fasta \\
         > idv4.fasta

From ec4414184b442c354968e2b11d55d128270a43e1 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 15:39:21 -0500
Subject: [PATCH 08/40] refactor: Change output file name of EFETCH

---
 modules/efetch/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/efetch/main.nf b/modules/efetch/main.nf
index 66272fd..ed38458 100644
--- a/modules/efetch/main.nf
+++ b/modules/efetch/main.nf
@@ -9,7 +9,7 @@ process EFETCH {
     publishDir "results", mode: 'copy'
 
     output:
-    path 'idv4.fasta'
+    path 'reference.fasta'
 
     script:
     """
@@ -18,6 +18,6 @@ process EFETCH {
             -query "${genome}" \\
         | efetch \\
             -format fasta \\
-        > idv4.fasta
+        > reference.fasta
     """
 }

From 0e822c2729434edbd8748f20855c20e413f97c64 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 15:43:10 -0500
Subject: [PATCH 09/40] feat: Add genome tag to EFETCH

---
 modules/efetch/main.nf | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/efetch/main.nf b/modules/efetch/main.nf
index ed38458..f3ce0b3 100644
--- a/modules/efetch/main.nf
+++ b/modules/efetch/main.nf
@@ -1,4 +1,5 @@
 process EFETCH {
+    tag "${genome}"
     label 'process_single'
 
     container 'quay.io/biocontainers/entrez-direct:16.2--he881be0_1'

From f157b0395e888199c2510f3318da1ca73826393c Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 15:44:08 -0500
Subject: [PATCH 10/40] refactor: Move NANOFILT module to its own file

---
 main.nf                  | 29 +----------------------------
 modules/nanofilt/main.nf | 27 +++++++++++++++++++++++++++
 2 files changed, 28 insertions(+), 28 deletions(-)
 create mode 100644 modules/nanofilt/main.nf

diff --git a/main.nf b/main.nf
index 54ff5e4..3d938fa 100755
--- a/main.nf
+++ b/main.nf
@@ -2,6 +2,7 @@
 
 include { EFETCH } from './modules/efetch'
 include { HAPLINK_VARIANTS } from './modules/haplink/variants'
+include { NANOFILT } form './modules/nanofilt'
 include { VIQUAS } from './modules/viquas'
 
 workflow {
@@ -69,34 +70,6 @@ workflow {
     )
 }
 
-process NANOFILT {
-    cpus 1
-    memory '8.GB'
-    container 'quay.io/biocontainers/nanofilt:2.8.0--py_0'
-
-    input:
-    tuple val(prefix), path(reads)
-
-    output:
-    tuple val(prefix), path("*_trimmed.fastq.gz")
-
-    script:
-    """
-    gzip \\
-            -cdf "${reads}" \\
-        | NanoFilt \\
-            --logfile "trimmed/${prefix}.nanofilt.log" \\
-            --length 100 \\
-            --quality 7 \\
-            --headcrop 30 \\
-            --tailcrop 30 \\
-            --minGC 0.1 \\
-            --maxGC 0.9 \\
-        | gzip \\
-        > "${prefix}_trimmed.fastq.gz"
-    """
-}
-
 process MINIMAP2 {
     cpus 4
     memory '8.GB'
diff --git a/modules/nanofilt/main.nf b/modules/nanofilt/main.nf
new file mode 100644
index 0000000..0852f23
--- /dev/null
+++ b/modules/nanofilt/main.nf
@@ -0,0 +1,27 @@
+process NANOFILT {
+    cpus 1
+    memory '8.GB'
+    container 'quay.io/biocontainers/nanofilt:2.8.0--py_0'
+
+    input:
+    tuple val(prefix), path(reads)
+
+    output:
+    tuple val(prefix), path("*_trimmed.fastq.gz")
+
+    script:
+    """
+    gzip \\
+            -cdf "${reads}" \\
+        | NanoFilt \\
+            --logfile "trimmed/${prefix}.nanofilt.log" \\
+            --length 100 \\
+            --quality 7 \\
+            --headcrop 30 \\
+            --tailcrop 30 \\
+            --minGC 0.1 \\
+            --maxGC 0.9 \\
+        | gzip \\
+        > "${prefix}_trimmed.fastq.gz"
+    """
+}

From 461a4b64a34ba79555d192624ed2035a802daf2c Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 15:44:40 -0500
Subject: [PATCH 11/40] feat: Add prefix tag to NANOFILT module

---
 modules/nanofilt/main.nf | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/nanofilt/main.nf b/modules/nanofilt/main.nf
index 0852f23..3343513 100644
--- a/modules/nanofilt/main.nf
+++ b/modules/nanofilt/main.nf
@@ -1,4 +1,5 @@
 process NANOFILT {
+    tag "${prefix}"
     cpus 1
     memory '8.GB'
     container 'quay.io/biocontainers/nanofilt:2.8.0--py_0'

From d12a8b77d83bc038cce8b297bd016a1fbecf59af Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 15:45:34 -0500
Subject: [PATCH 12/40] refactor: Replace NANOFILT performance directives with
 process label

---
 modules/nanofilt/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nanofilt/main.nf b/modules/nanofilt/main.nf
index 3343513..c6ec93f 100644
--- a/modules/nanofilt/main.nf
+++ b/modules/nanofilt/main.nf
@@ -1,7 +1,7 @@
 process NANOFILT {
     tag "${prefix}"
-    cpus 1
-    memory '8.GB'
+    label 'process_low'
+
     container 'quay.io/biocontainers/nanofilt:2.8.0--py_0'
 
     input:

From a9aa590f007574090208bc3b946276c88c94acc8 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 16:05:02 -0500
Subject: [PATCH 13/40] refactor: Move MINIMAP2 module to separate file

---
 main.nf                  | 34 +---------------------------------
 modules/minimap2/main.nf | 32 ++++++++++++++++++++++++++++++++
 2 files changed, 33 insertions(+), 33 deletions(-)
 create mode 100644 modules/minimap2/main.nf

diff --git a/main.nf b/main.nf
index 3d938fa..b80f998 100755
--- a/main.nf
+++ b/main.nf
@@ -2,6 +2,7 @@
 
 include { EFETCH } from './modules/efetch'
 include { HAPLINK_VARIANTS } from './modules/haplink/variants'
+include { MINIMAP2 } from './modules/minimap2'
 include { NANOFILT } form './modules/nanofilt'
 include { VIQUAS } from './modules/viquas'
 
@@ -70,39 +71,6 @@ workflow {
     )
 }
 
-process MINIMAP2 {
-    cpus 4
-    memory '8.GB'
-    container 'quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0'
-
-    input:
-    tuple val(prefix), path(reads)
-    path reference
-
-    publishDir "results", mode: 'copy'
-
-    output:
-    tuple val(prefix), path("*.bam"), path("*.bam.bai")
-    script:
-    """
-    minimap2 \\
-            -x map-ont \\
-            --MD \\
-            --eqx \\
-            -t ${task.cpus} \\
-            -a \\
-            "${reference}" \\
-            "${reads}" \\
-    | samtools sort \\
-    | samtools view \\
-            -@ ${task.cpus} \\
-            -b \\
-            -h \\
-            -o "${prefix}.bam"
-    samtools index "${prefix}.bam"
-    """
-}
-
 process SHORAH_AMPLICON {
     label 'process_high'
     container 'quay.io/biocontainers/shorah:1.99.2--py38h73782ee_8'
diff --git a/modules/minimap2/main.nf b/modules/minimap2/main.nf
new file mode 100644
index 0000000..610028b
--- /dev/null
+++ b/modules/minimap2/main.nf
@@ -0,0 +1,32 @@
+process MINIMAP2 {
+    cpus 4
+    memory '8.GB'
+    container 'quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0'
+
+    input:
+    tuple val(prefix), path(reads)
+    path reference
+
+    publishDir "results", mode: 'copy'
+
+    output:
+    tuple val(prefix), path("*.bam"), path("*.bam.bai")
+    script:
+    """
+    minimap2 \\
+            -x map-ont \\
+            --MD \\
+            --eqx \\
+            -t ${task.cpus} \\
+            -a \\
+            "${reference}" \\
+            "${reads}" \\
+    | samtools sort \\
+    | samtools view \\
+            -@ ${task.cpus} \\
+            -b \\
+            -h \\
+            -o "${prefix}.bam"
+    samtools index "${prefix}.bam"
+    """
+}

From b08d9df6a94150410c2c91708bee98d4e0749dd2 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 16:05:29 -0500
Subject: [PATCH 14/40] feat: Add prefix tag to MINIMAP2

---
 modules/minimap2/main.nf | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/minimap2/main.nf b/modules/minimap2/main.nf
index 610028b..d0d82dc 100644
--- a/modules/minimap2/main.nf
+++ b/modules/minimap2/main.nf
@@ -1,4 +1,5 @@
 process MINIMAP2 {
+    tag "${prefix}"
     cpus 4
     memory '8.GB'
     container 'quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0'

From 89323bf2c656f48713f16ccaf34fd64dbdc5c3cb Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 16:06:12 -0500
Subject: [PATCH 15/40] refactor: Replace MINIMAP2 performance directives with
 process label

---
 modules/minimap2/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/minimap2/main.nf b/modules/minimap2/main.nf
index d0d82dc..7d3c2aa 100644
--- a/modules/minimap2/main.nf
+++ b/modules/minimap2/main.nf
@@ -1,7 +1,7 @@
 process MINIMAP2 {
     tag "${prefix}"
-    cpus 4
-    memory '8.GB'
+    label 'process_medium'
+
     container 'quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0'
 
     input:

From dbea6fb30a105b134a75874606b7a2cb4247cc5e Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 16:09:21 -0500
Subject: [PATCH 16/40] refactor: Move SHORAH_AMPLICON to its own file

---
 main.nf                         | 24 +-----------------------
 modules/shorah/amplicon/main.nf | 22 ++++++++++++++++++++++
 2 files changed, 23 insertions(+), 23 deletions(-)
 create mode 100644 modules/shorah/amplicon/main.nf

diff --git a/main.nf b/main.nf
index b80f998..82a0fbf 100755
--- a/main.nf
+++ b/main.nf
@@ -4,6 +4,7 @@ include { EFETCH } from './modules/efetch'
 include { HAPLINK_VARIANTS } from './modules/haplink/variants'
 include { MINIMAP2 } from './modules/minimap2'
 include { NANOFILT } form './modules/nanofilt'
+include { SHORAH_AMPLICON } from './modules/shorah/amplicon'
 include { VIQUAS } from './modules/viquas'
 
 workflow {
@@ -71,29 +72,6 @@ workflow {
     )
 }
 
-process SHORAH_AMPLICON {
-    label 'process_high'
-    container 'quay.io/biocontainers/shorah:1.99.2--py38h73782ee_8'
-
-    input:
-    tuple val(prefix), path(bam)
-    path(reference)
-
-    output:
-    tuple val(prefix), path("*.vcf")
-    tuple val(prefix), path("*support.fas")
-
-    publishDir "results/shorah-amplicon", mode: 'copy'
-
-    script:
-    """
-    shorah amplicon \\
-        -t ${task.cpus} \\
-        -f ${reference} \\
-        -b ${bam} \\
-    """
-}
-
 process SHORAH_SHOTGUN {
     label 'process_high'
     container 'quay.io/biocontainers/shorah:1.99.2--py38h73782ee_8'
diff --git a/modules/shorah/amplicon/main.nf b/modules/shorah/amplicon/main.nf
new file mode 100644
index 0000000..c15cd43
--- /dev/null
+++ b/modules/shorah/amplicon/main.nf
@@ -0,0 +1,22 @@
+process SHORAH_AMPLICON {
+    label 'process_high'
+    container 'quay.io/biocontainers/shorah:1.99.2--py38h73782ee_8'
+
+    input:
+    tuple val(prefix), path(bam)
+    path(reference)
+
+    output:
+    tuple val(prefix), path("*.vcf")
+    tuple val(prefix), path("*support.fas")
+
+    publishDir "results/shorah-amplicon", mode: 'copy'
+
+    script:
+    """
+    shorah amplicon \\
+        -t ${task.cpus} \\
+        -f ${reference} \\
+        -b ${bam} \\
+    """
+}

From f6111f27c20f66f7801d77ec778489617441a3c2 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 16:09:47 -0500
Subject: [PATCH 17/40] feat: Add prefix tag to SHORAH_AMPLICON

---
 modules/shorah/amplicon/main.nf | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/modules/shorah/amplicon/main.nf b/modules/shorah/amplicon/main.nf
index c15cd43..5c68ca1 100644
--- a/modules/shorah/amplicon/main.nf
+++ b/modules/shorah/amplicon/main.nf
@@ -1,5 +1,7 @@
 process SHORAH_AMPLICON {
+    tag "${prefix}"
     label 'process_high'
+
     container 'quay.io/biocontainers/shorah:1.99.2--py38h73782ee_8'
 
     input:

From db0255c54ac7070c66c6836dc13c440bdf43a7ea Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 16:12:40 -0500
Subject: [PATCH 18/40] refactor: Move SHORAH_SHOTGUN to its own file

---
 main.nf                        | 24 +-----------------------
 modules/shorah/shotgun/main.nf | 22 ++++++++++++++++++++++
 2 files changed, 23 insertions(+), 23 deletions(-)
 create mode 100644 modules/shorah/shotgun/main.nf

diff --git a/main.nf b/main.nf
index 82a0fbf..d6449ed 100755
--- a/main.nf
+++ b/main.nf
@@ -5,6 +5,7 @@ include { HAPLINK_VARIANTS } from './modules/haplink/variants'
 include { MINIMAP2 } from './modules/minimap2'
 include { NANOFILT } form './modules/nanofilt'
 include { SHORAH_AMPLICON } from './modules/shorah/amplicon'
+include { SHORAH_SHOTGUN } from './modules/shorah/shotgun'
 include { VIQUAS } from './modules/viquas'
 
 workflow {
@@ -72,29 +73,6 @@ workflow {
     )
 }
 
-process SHORAH_SHOTGUN {
-    label 'process_high'
-    container 'quay.io/biocontainers/shorah:1.99.2--py38h73782ee_8'
-
-    input:
-    tuple val(prefix), path(bam)
-    path(reference)
-
-    output:
-    tuple val(prefix), path("*.vcf")
-    tuple val(prefix), path("*support.fas")
-
-    publishDir "results/shorah-shotgun", mode: 'copy'
-
-    script:
-    """
-    shorah shotgun \\
-        -t ${task.cpus} \\
-        -f ${reference} \\
-        -b ${bam} \\
-    """
-}
-
 process HAPLINK_RAW_HAPLOTYPES {
     cpus 2
     memory '12.GB'
diff --git a/modules/shorah/shotgun/main.nf b/modules/shorah/shotgun/main.nf
new file mode 100644
index 0000000..467e4ea
--- /dev/null
+++ b/modules/shorah/shotgun/main.nf
@@ -0,0 +1,22 @@
+process SHORAH_SHOTGUN {
+    label 'process_high'
+    container 'quay.io/biocontainers/shorah:1.99.2--py38h73782ee_8'
+
+    input:
+    tuple val(prefix), path(bam)
+    path(reference)
+
+    output:
+    tuple val(prefix), path("*.vcf")
+    tuple val(prefix), path("*support.fas")
+
+    publishDir "results/shorah-shotgun", mode: 'copy'
+
+    script:
+    """
+    shorah shotgun \\
+        -t ${task.cpus} \\
+        -f ${reference} \\
+        -b ${bam} \\
+    """
+}

From abfed449f6613a4f724a0351a37fbc4705b0e0fa Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 16:13:06 -0500
Subject: [PATCH 19/40] feat: Add prefix tag to SHORAH_SHOTGUN

---
 modules/shorah/shotgun/main.nf | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/modules/shorah/shotgun/main.nf b/modules/shorah/shotgun/main.nf
index 467e4ea..89b8ef7 100644
--- a/modules/shorah/shotgun/main.nf
+++ b/modules/shorah/shotgun/main.nf
@@ -1,5 +1,7 @@
 process SHORAH_SHOTGUN {
+    tag "${prefix}"
     label 'process_high'
+
     container 'quay.io/biocontainers/shorah:1.99.2--py38h73782ee_8'
 
     input:

From 47500bc9867d93d3b67f5358621da90552baf905 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 16:20:44 -0500
Subject: [PATCH 20/40] feat: Add new HAPLINK_HAPLOTYPES module

---
 modules/haplink/haplotypes/main.nf | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 modules/haplink/haplotypes/main.nf

diff --git a/modules/haplink/haplotypes/main.nf b/modules/haplink/haplotypes/main.nf
new file mode 100644
index 0000000..e4b96e8
--- /dev/null
+++ b/modules/haplink/haplotypes/main.nf
@@ -0,0 +1,28 @@
+process HAPLINK_HAPLOTYPES {
+    tag "${prefix}"
+    label 'process_high'
+
+    container 'quay.io/biocontainers/haplink:1.0.0--h031d066_0'
+
+    input:
+    tuple val(prefix), path(bam), path(bai)
+    path reference
+
+    output:
+    tuple val(prefix), path("*.yaml")
+
+    publishDir "results/${task.process}", mode: 'copy'
+
+    script:
+    def ml_args = task.ext.ml_args ?: ''
+    """
+    export JULIA_NUM_THREADS=${task.cpus}
+    haplink haplotypes \\
+            "${reference}" \\
+            "${vcf}" \\
+            "${bam}" \\
+        --frequency 0.01 \\
+        ${ml_args} \\
+        > "${prefix}.yaml"
+    """
+}

From 52ca8f152836904803c499cdcd6d0726cfc0d28b Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 16:24:57 -0500
Subject: [PATCH 21/40] refactor: Replace in-workflow HAPLINK processes with
 imported modules

---
 main.nf         | 55 ++-----------------------------------------------
 nextflow.config |  8 +++++++
 2 files changed, 10 insertions(+), 53 deletions(-)

diff --git a/main.nf b/main.nf
index d6449ed..f6fbf59 100755
--- a/main.nf
+++ b/main.nf
@@ -1,6 +1,8 @@
 #!/usr/bin/env nextflow
 
 include { EFETCH } from './modules/efetch'
+include { HAPLINK_HAPLOTYPES as HAPLINK_ML_HAPLOTYPES } from './modules/haplink/haplotypes'
+include { HAPLINK_HAPLOTYPES as HAPLINK_RAW_HAPLOTYPES } from './modules/haplink/haplotypes'
 include { HAPLINK_VARIANTS } from './modules/haplink/variants'
 include { MINIMAP2 } from './modules/minimap2'
 include { NANOFILT } form './modules/nanofilt'
@@ -73,59 +75,6 @@ workflow {
     )
 }
 
-process HAPLINK_RAW_HAPLOTYPES {
-    cpus 2
-    memory '12.GB'
-
-    input:
-    tuple val(prefix), path(bam), path(bai), path(vcf)
-    path reference
-
-    output:
-    tuple val(prefix), path("*.yaml")
-
-    publishDir "results/raw-haplotypes", mode: 'copy'
-
-    script:
-    """
-    export JULIA_NUM_THREADS=${task.cpus}
-    haplink haplotypes \\
-            "${reference}" \\
-            "${vcf}" \\
-            "${bam}" \\
-        --frequency 0.01 \\
-        > "${prefix}.yaml"
-    """
-}
-
-process HAPLINK_ML_HAPLOTYPES {
-    cpus 8
-    memory '12.GB'
-
-    input:
-    tuple val(prefix), path(bam), path(bai), path(vcf)
-    path reference
-
-    output:
-    tuple val(prefix), path("*.yaml")
-
-    publishDir "results/ml-haplotypes", mode: 'copy'
-
-    script:
-    """
-    export JULIA_NUM_THREADS=${task.cpus}
-    haplink haplotypes \\
-            "${reference}" \\
-            "${vcf}" \\
-            "${bam}" \\
-        --simulated-reads \\
-        --overlap-min 20 \\
-        --overlap-max 8000 \\
-        --frequency 0.01 \\
-        > "${prefix}.yaml"
-    """
-}
-
 process HAPLINK_SEQUENCES {
     cpus 1
     memory '6.GB'
diff --git a/nextflow.config b/nextflow.config
index 84597cb..fce47a2 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -1,6 +1,14 @@
 process {
     errorStrategy = 'finish'
     time = '7d'
+
+    withName: 'HAPLINK_ML_HAPLOTYPES' {
+        ext.ml_args = """
+        --simulated-reads \\
+        --overlap-min 20 \\
+        --overlap-max 8000 \\
+        """
+    }
 }
 
 singularity.enabled = true

From 5162f649d876d61dc18132feb16e9fb89184839f Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 16:26:25 -0500
Subject: [PATCH 22/40] refactor: Move HAPLINK_SEQUENCES module to its own file

---
 main.nf                           | 25 +------------------------
 modules/haplink/sequences/main.nf | 23 +++++++++++++++++++++++
 2 files changed, 24 insertions(+), 24 deletions(-)
 create mode 100644 modules/haplink/sequences/main.nf

diff --git a/main.nf b/main.nf
index f6fbf59..8bc7a7f 100755
--- a/main.nf
+++ b/main.nf
@@ -3,6 +3,7 @@
 include { EFETCH } from './modules/efetch'
 include { HAPLINK_HAPLOTYPES as HAPLINK_ML_HAPLOTYPES } from './modules/haplink/haplotypes'
 include { HAPLINK_HAPLOTYPES as HAPLINK_RAW_HAPLOTYPES } from './modules/haplink/haplotypes'
+include { HAPLINK_SEQUENCES } from './modules/haplink/sequences'
 include { HAPLINK_VARIANTS } from './modules/haplink/variants'
 include { MINIMAP2 } from './modules/minimap2'
 include { NANOFILT } form './modules/nanofilt'
@@ -74,27 +75,3 @@ workflow {
         ch_reference
     )
 }
-
-process HAPLINK_SEQUENCES {
-    cpus 1
-    memory '6.GB'
-
-    input:
-    tuple val(prefix), val(method), path(yaml)
-    path reference
-
-    output:
-    tuple val(prefix), val(method), path("*.fasta")
-
-    publishDir "results/${method}-haplotypes", mode: 'copy'
-
-    script:
-    """
-    export JULIA_NUM_THREADS=${task.cpus}
-    haplink sequences \\
-            "${reference}" \\
-            "${yaml}" \\
-            --prefix "${prefix}" \\
-        > "${prefix}.fasta"
-    """
-}
diff --git a/modules/haplink/sequences/main.nf b/modules/haplink/sequences/main.nf
new file mode 100644
index 0000000..46610e8
--- /dev/null
+++ b/modules/haplink/sequences/main.nf
@@ -0,0 +1,23 @@
+process HAPLINK_SEQUENCES {
+    cpus 1
+    memory '6.GB'
+
+    input:
+    tuple val(prefix), val(method), path(yaml)
+    path reference
+
+    output:
+    tuple val(prefix), val(method), path("*.fasta")
+
+    publishDir "results/${method}-haplotypes", mode: 'copy'
+
+    script:
+    """
+    export JULIA_NUM_THREADS=${task.cpus}
+    haplink sequences \\
+            "${reference}" \\
+            "${yaml}" \\
+            --prefix "${prefix}" \\
+        > "${prefix}.fasta"
+    """
+}

From 517b8eb66bc7d9715eced41719ac6cc3b6856aa4 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 16:27:17 -0500
Subject: [PATCH 23/40] feat: Add method/prefix tag to HAPLINK_SEQUENCES

---
 modules/haplink/sequences/main.nf | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/haplink/sequences/main.nf b/modules/haplink/sequences/main.nf
index 46610e8..f47e9a6 100644
--- a/modules/haplink/sequences/main.nf
+++ b/modules/haplink/sequences/main.nf
@@ -1,4 +1,5 @@
 process HAPLINK_SEQUENCES {
+    tag "${method}: ${prefix}"
     cpus 1
     memory '6.GB'
 

From 095aff629d2926bffd32a1d604a2fc6e3dfda6b1 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 16:28:12 -0500
Subject: [PATCH 24/40] refactor: Replace performance directives with process
 label

---
 modules/haplink/sequences/main.nf | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/modules/haplink/sequences/main.nf b/modules/haplink/sequences/main.nf
index f47e9a6..257b969 100644
--- a/modules/haplink/sequences/main.nf
+++ b/modules/haplink/sequences/main.nf
@@ -1,7 +1,6 @@
 process HAPLINK_SEQUENCES {
     tag "${method}: ${prefix}"
-    cpus 1
-    memory '6.GB'
+    label 'process_single'
 
     input:
     tuple val(prefix), val(method), path(yaml)

From 475120357972bcc7e3a9a6e3ca1849bd42919c16 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 16:28:57 -0500
Subject: [PATCH 25/40] feat: Add container directive to HAPLINK_SEQUENCES

---
 modules/haplink/sequences/main.nf | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/modules/haplink/sequences/main.nf b/modules/haplink/sequences/main.nf
index 257b969..bd09d66 100644
--- a/modules/haplink/sequences/main.nf
+++ b/modules/haplink/sequences/main.nf
@@ -2,6 +2,8 @@ process HAPLINK_SEQUENCES {
     tag "${method}: ${prefix}"
     label 'process_single'
 
+    container 'quay.io/biocontainers/haplink:1.0.0--h031d066_0'
+
     input:
     tuple val(prefix), val(method), path(yaml)
     path reference

From 002bd44975c21d508ef6124b69e85164c3826a2a Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 16:30:24 -0500
Subject: [PATCH 26/40] refactor: Change output directory to match haplotypes

---
 main.nf                           | 4 ++--
 modules/haplink/sequences/main.nf | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/main.nf b/main.nf
index 8bc7a7f..e623fa6 100755
--- a/main.nf
+++ b/main.nf
@@ -49,7 +49,7 @@ workflow {
     )
     HAPLINK_RAW_HAPLOTYPES
         .out
-    .map{ [ it[0], 'raw', it[1] ] }
+    .map{ [ it[0], 'HAPLINK_RAW_HAPLOTYPES', it[1] ] }
     .set{ ch_raw_haplotypes }
 
     HAPLINK_ML_HAPLOTYPES(
@@ -58,7 +58,7 @@ workflow {
     )
     HAPLINK_ML_HAPLOTYPES
         .out
-        .map{ [ it[0], 'ml', it[1] ] }
+        .map{ [ it[0], 'HAPLINK_ML_HAPLOTYPES', it[1] ] }
         .set{ ch_ml_haplotypes }
 
     ch_raw_haplotypes
diff --git a/modules/haplink/sequences/main.nf b/modules/haplink/sequences/main.nf
index bd09d66..109b92f 100644
--- a/modules/haplink/sequences/main.nf
+++ b/modules/haplink/sequences/main.nf
@@ -11,7 +11,7 @@ process HAPLINK_SEQUENCES {
     output:
     tuple val(prefix), val(method), path("*.fasta")
 
-    publishDir "results/${method}-haplotypes", mode: 'copy'
+    publishDir "results/${method}", mode: 'copy'
 
     script:
     """

From 5c4d02263be3cfd927d594d365702d5c162808ab Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 16:32:29 -0500
Subject: [PATCH 27/40] refactor: Replace custom publish dirs with reference to
 task.process

---
 modules/haplink/variants/main.nf | 2 +-
 modules/shorah/amplicon/main.nf  | 2 +-
 modules/shorah/shotgun/main.nf   | 2 +-
 modules/viquas/main.nf           | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/haplink/variants/main.nf b/modules/haplink/variants/main.nf
index 9f036de..b4f7149 100644
--- a/modules/haplink/variants/main.nf
+++ b/modules/haplink/variants/main.nf
@@ -11,7 +11,7 @@ process HAPLINK_VARIANTS {
     output:
     tuple val(prefix), path("*.vcf")
 
-    publishDir "results", mode: 'copy'
+    publishDir "results/${task.process}", mode: 'copy'
 
     script:
     """
diff --git a/modules/shorah/amplicon/main.nf b/modules/shorah/amplicon/main.nf
index 5c68ca1..d35961a 100644
--- a/modules/shorah/amplicon/main.nf
+++ b/modules/shorah/amplicon/main.nf
@@ -12,7 +12,7 @@ process SHORAH_AMPLICON {
     tuple val(prefix), path("*.vcf")
     tuple val(prefix), path("*support.fas")
 
-    publishDir "results/shorah-amplicon", mode: 'copy'
+    publishDir "results/${task.process}", mode: 'copy'
 
     script:
     """
diff --git a/modules/shorah/shotgun/main.nf b/modules/shorah/shotgun/main.nf
index 89b8ef7..224dca9 100644
--- a/modules/shorah/shotgun/main.nf
+++ b/modules/shorah/shotgun/main.nf
@@ -12,7 +12,7 @@ process SHORAH_SHOTGUN {
     tuple val(prefix), path("*.vcf")
     tuple val(prefix), path("*support.fas")
 
-    publishDir "results/shorah-shotgun", mode: 'copy'
+    publishDir "results/${task.process}", mode: 'copy'
 
     script:
     """
diff --git a/modules/viquas/main.nf b/modules/viquas/main.nf
index 16bb7b5..ab467a3 100644
--- a/modules/viquas/main.nf
+++ b/modules/viquas/main.nf
@@ -11,7 +11,7 @@ process VIQUAS {
     output:
     tuple val(prefix), path("*.fa")
 
-    publishDir "results/viquas", mode: 'copy'
+    publishDir "results/${task.process}", mode: 'copy'
 
     script:
     """

From de853c2d229106ddcf99ef877ecb35cc012f35e8 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 16:40:04 -0500
Subject: [PATCH 28/40] feat: Add CliqueSNV module

---
 modules/cliquesnv/main.nf | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 modules/cliquesnv/main.nf

diff --git a/modules/cliquesnv/main.nf b/modules/cliquesnv/main.nf
new file mode 100644
index 0000000..f22ffa1
--- /dev/null
+++ b/modules/cliquesnv/main.nf
@@ -0,0 +1,27 @@
+process CLIQUESNV {
+    tag "${prefix}"
+    label 'process_high'
+
+    container 'quay.io/biocontainers/cliquesnv:2.0.3--hdfd78af_0'
+
+    input:
+    tuple val(prefix), path(bam)
+    val(method)
+
+    output:
+    tuple val(prefix), path("*.json")
+    tuple val(prefix), path("*.fasta")
+
+    publishDir "results/${task.process}", mode: 'copy'
+
+    script:
+    def jmemstring = task.memory.toMega() + 'M'
+    """
+    cliquesnv \\
+        -Xmx${jmemstring} \\
+        -threads ${task.cpus} \\
+        -m '${method}' \\
+        -in "${bam}" \\
+        -outDir .
+    """
+}

From 5ab64a8feab2c283eb881a6714e3ac88521ccf2b Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 16:43:02 -0500
Subject: [PATCH 29/40] feat: Add CliqueSNV haplotype calling to pipeline

---
 main.nf | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/main.nf b/main.nf
index e623fa6..65b1fd1 100755
--- a/main.nf
+++ b/main.nf
@@ -1,5 +1,6 @@
 #!/usr/bin/env nextflow
 
+include { CLIQUESNV } from './modules/cliquesnv'
 include { EFETCH } from './modules/efetch'
 include { HAPLINK_HAPLOTYPES as HAPLINK_ML_HAPLOTYPES } from './modules/haplink/haplotypes'
 include { HAPLINK_HAPLOTYPES as HAPLINK_RAW_HAPLOTYPES } from './modules/haplink/haplotypes'
@@ -74,4 +75,9 @@ workflow {
         ch_alignments,
         ch_reference
     )
+
+    CLIQUESNV(
+        ch_alignments,
+        'snv-pacbio'
+    )
 }

From 3e6a0ca5df0caab7d99b32448d398e739dfbec63 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 16:54:49 -0500
Subject: [PATCH 30/40] feat: Add QuasiRecomb module

---
 modules/quasirecomb/main.nf | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 modules/quasirecomb/main.nf

diff --git a/modules/quasirecomb/main.nf b/modules/quasirecomb/main.nf
new file mode 100644
index 0000000..e2896c0
--- /dev/null
+++ b/modules/quasirecomb/main.nf
@@ -0,0 +1,27 @@
+process QUASIRECOMB {
+    tag "${prefix}"
+    label 'process_high'
+
+    container 'quay.io/biocontainers/quasirecomb:1.2--hdfd78af_1'
+
+    input:
+    tuple val(prefix), path(bam)
+
+    output:
+    tuple val(prefix), path("*.fasta")
+
+    publishDir "results/${task.process}", mode: 'copy'
+
+    script:
+    def jmemstring = task.memory.toMega() + 'M'
+    """
+    quasirecomb \\
+        -XX:+UseParallelGC \\
+        -Xms2g \\
+        -Xmx${jmemstring} \\
+        -XX:+UseNUMA \\
+        -XX:NewRatio=9 \\
+        -i "${bam}"
+    mv quasispecies.fasta "${prefix}.fasta"
+    """
+}

From 137804518f421d9e0769bba96b2c4a458497483f Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Mon, 25 Sep 2023 17:59:14 -0500
Subject: [PATCH 31/40] feat: Add nf-core config parameters

---
 nextflow.config | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/nextflow.config b/nextflow.config
index fce47a2..3585de1 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -1,3 +1,21 @@
+params {
+    reference = null
+
+    // Config options
+    config_profile_name = null
+    config_profile_description = null
+    custom_config_version = 'master'
+    custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
+    config_profile_contact = null
+    config_profile_url = null
+
+    // Max resource options
+    // Defaults only, expecting to be overwritten
+    max_memory = '128.GB'
+    max_cpus = 16
+    max_time = '240.h'
+}
+
 process {
     errorStrategy = 'finish'
     time = '7d'
@@ -11,6 +29,12 @@ process {
     }
 }
 
+try {
+    includeConfig "${params.custom_config_base}/nfcore_custom.config"
+} catch (Exception e) {
+    System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
+}
+
 singularity.enabled = true
 
 env {

From 7f43f0282fd4a4ca3c6bf3cb3cf734cb2a9b9f5d Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Mon, 25 Sep 2023 18:05:10 -0500
Subject: [PATCH 32/40] feat: Add nf-core resource allocation parameters

---
 nextflow.config | 61 +++++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 59 insertions(+), 2 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index 3585de1..de600ab 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -17,8 +17,34 @@ params {
 }
 
 process {
-    errorStrategy = 'finish'
-    time = '7d'
+    cpus = { check_max(1 * task.attempt, 'cpus') }
+    memory = { check_max(6.GB * task.attempt, 'memory') }
+    time = { check_max(4.h * task.attempt, 'time') }
+
+    errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
+    maxRetries = 1
+    maxErrors = '-1'
+
+    withLabel:process_single {
+        cpus = { check_max(1, 'cpus') }
+        memory = { check_max( 6.GB * task.attempt, 'memory') }
+        time = { check_max( 4.h * task.attempt, 'time') }
+    }
+    withLabel:process_low {
+        cpus = { check_max( 2 * task.attempt, 'cpus') }
+        memory = { check_max( 12.GB * task.attempt, 'memory') }
+        time = { check_max( 4.h * task.attempt, 'time') }
+    }
+    withLabel:process_medium {
+        cpus = { check_max( 6 * task.attempt, 'cpus') }
+        memory = { check_max( 36.GB * task.attempt, 'memory') }
+        time = { check_max( 8.h * task.attempt, 'time') }
+    }
+    withLabel:process_high {
+        cpus = { check_max( 12 * task.attempt, 'cpus') }
+        memory = { check_max( 72.GB * task.attempt, 'memory') }
+        time = { check_max( 16.h  * task.attempt, 'time') }
+    }
 
     withName: 'HAPLINK_ML_HAPLOTYPES' {
         ext.ml_args = """
@@ -41,3 +67,34 @@ env {
     R_PROFILE_USER   = "/.Rprofile"
     R_ENVIRON_USER   = "/.Renviron"
 }
+
+def check_max(obj, type) {
+    if (type == 'memory') {
+        try {
+            if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
+                return params.max_memory as nextflow.util.MemoryUnit
+            else
+                return obj
+        } catch (all) {
+            println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
+            return obj
+        }
+    } else if (type == 'time') {
+        try {
+            if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
+                return params.max_time as nextflow.util.Duration
+            else
+                return obj
+        } catch (all) {
+            println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
+            return obj
+        }
+    } else if (type == 'cpus') {
+        try {
+            return Math.min( obj, params.max_cpus as int )
+        } catch (all) {
+            println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
+            return obj
+        }
+    }
+}

From 96471746b9ff1bcc5e8479dd79e279002476f751 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Mon, 25 Sep 2023 18:16:50 -0500
Subject: [PATCH 33/40] feat: Replace hard-coded singularity with profile-based
 containers

---
 nextflow.config | 60 ++++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 59 insertions(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index de600ab..4e4c25c 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -61,7 +61,65 @@ try {
     System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
 }
 
-singularity.enabled = true
+profiles {
+    docker {
+        docker.enabled = true
+        docker.userEmulation = true
+        conda.enabled = false
+        singularity.enabled = false
+        podman.enabled = false
+        shifter.enabled = false
+        charliecloud.enabled = false
+        apptainer.enabled = false
+    }
+    singularity {
+        singularity.enabled = true
+        singularity.autoMounts = true
+        conda.enabled = false
+        docker.enabled = false
+        podman.enabled = false
+        shifter.enabled = false
+        charliecloud.enabled = false
+        apptainer.enabled = false
+    }
+    podman {
+        podman.enabled = true
+        conda.enabled = false
+        docker.enabled = false
+        singularity.enabled = false
+        shifter.enabled = false
+        charliecloud.enabled = false
+        apptainer.enabled = false
+    }
+    shifter {
+        shifter.enabled = true
+        conda.enabled = false
+        docker.enabled = false
+        singularity.enabled = false
+        podman.enabled = false
+        charliecloud.enabled = false
+        apptainer.enabled = false
+    }
+    charliecloud {
+        charliecloud.enabled = true
+        conda.enabled = false
+        docker.enabled = false
+        singularity.enabled = false
+        podman.enabled = false
+        shifter.enabled = false
+        apptainer.enabled = false
+    }
+    apptainer {
+        apptainer.enabled = true
+        apptainer.autoMounts = true
+        conda.enabled = false
+        docker.enabled = false
+        singularity.enabled = false
+        podman.enabled = false
+        shifter.enabled = false
+        charliecloud.enabled = false
+    }
+}
 
 env {
     R_PROFILE_USER   = "/.Rprofile"

From d8fee48c28e8e6b63b9fc7361e8100a4637b56f8 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Mon, 25 Sep 2023 18:44:50 -0500
Subject: [PATCH 34/40] feat: Add CliqueSNV to pipeline

---
 main.nf | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/main.nf b/main.nf
index 65b1fd1..c73f49c 100755
--- a/main.nf
+++ b/main.nf
@@ -34,6 +34,11 @@ workflow {
         .out
         .set { ch_alignments }
 
+    CLIQUESNV(
+        ch_alignments,
+        'snv-pacbio'
+    )
+
     HAPLINK_VARIANTS( ch_alignments, ch_reference )
     HAPLINK_VARIANTS
         .out
@@ -75,9 +80,4 @@ workflow {
         ch_alignments,
         ch_reference
     )
-
-    CLIQUESNV(
-        ch_alignments,
-        'snv-pacbio'
-    )
 }

From 029f3a512691a7e8ea0027705083768047b13c9f Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Mon, 25 Sep 2023 18:46:38 -0500
Subject: [PATCH 35/40] feat: Add PREDICTHAPLO module

---
 modules/predicthaplo/main.nf | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 modules/predicthaplo/main.nf

diff --git a/modules/predicthaplo/main.nf b/modules/predicthaplo/main.nf
new file mode 100644
index 0000000..71d2fc1
--- /dev/null
+++ b/modules/predicthaplo/main.nf
@@ -0,0 +1,23 @@
+process PREDICTHAPLO {
+    tag "${prefix}"
+    label 'process_high'
+
+    container 'quay.io/biocontainers/predicthaplo:2.1.4--h9b88814_5'
+
+    input:
+    tuple val(prefix), path(bam)
+    path(reference)
+
+    output:
+    tuple val(prefix), path("*.fa*")
+
+    publishDir "results/${task.process}", mode: 'copy'
+
+    script:
+    """
+    predicthaplo \\
+        --sam "${bam}" \\
+        --reference "${reference}" \\
+        --prefix "${prefix}"
+    """
+}

From 5cc886779964f8479e909793e72fa3760fff085b Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Mon, 25 Sep 2023 18:47:48 -0500
Subject: [PATCH 36/40] feat: Add PREDICTHAPLO to pipeline

---
 main.nf | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/main.nf b/main.nf
index c73f49c..8cf7dd2 100755
--- a/main.nf
+++ b/main.nf
@@ -6,6 +6,7 @@ include { HAPLINK_HAPLOTYPES as HAPLINK_ML_HAPLOTYPES } from './modules/haplink/
 include { HAPLINK_HAPLOTYPES as HAPLINK_RAW_HAPLOTYPES } from './modules/haplink/haplotypes'
 include { HAPLINK_SEQUENCES } from './modules/haplink/sequences'
 include { HAPLINK_VARIANTS } from './modules/haplink/variants'
+include { PREDICTHAPLO } from './modules/predicthaplo'
 include { MINIMAP2 } from './modules/minimap2'
 include { NANOFILT } form './modules/nanofilt'
 include { SHORAH_AMPLICON } from './modules/shorah/amplicon'
@@ -76,6 +77,11 @@ workflow {
         ch_reference
     )
 
+    PREDICTHAPLO(
+        ch_alignments,
+        ch_reference
+    )
+
     VIQUAS(
         ch_alignments,
         ch_reference

From 444001b49931911958695cd201752b4971922f33 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Mon, 25 Sep 2023 18:50:37 -0500
Subject: [PATCH 37/40] feat: Add QUASIRECOMB to pipeline

---
 main.nf | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index 8cf7dd2..4042eeb 100755
--- a/main.nf
+++ b/main.nf
@@ -8,7 +8,8 @@ include { HAPLINK_SEQUENCES } from './modules/haplink/sequences'
 include { HAPLINK_VARIANTS } from './modules/haplink/variants'
 include { PREDICTHAPLO } from './modules/predicthaplo'
 include { MINIMAP2 } from './modules/minimap2'
-include { NANOFILT } form './modules/nanofilt'
+include { NANOFILT } from './modules/nanofilt'
+include { QUASIRECOMB } from './modules/quasirecomb'
 include { SHORAH_AMPLICON } from './modules/shorah/amplicon'
 include { SHORAH_SHOTGUN } from './modules/shorah/shotgun'
 include { VIQUAS } from './modules/viquas'
@@ -82,6 +83,8 @@ workflow {
         ch_reference
     )
 
+    QUASIRECOMB( ch_alignments )
+
     VIQUAS(
         ch_alignments,
         ch_reference

From 355ce9a00a04722173b398a77d0286b5ee57b63f Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Mon, 25 Sep 2023 18:51:58 -0500
Subject: [PATCH 38/40] feat: Add SHORAH processes to pipeline

---
 main.nf | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/main.nf b/main.nf
index 4042eeb..af776f3 100755
--- a/main.nf
+++ b/main.nf
@@ -85,6 +85,16 @@ workflow {
 
     QUASIRECOMB( ch_alignments )
 
+    SHORAH_AMPLICON(
+        ch_alignments,
+        ch_reference
+    )
+
+    SHORAH_SHOTGUN(
+        ch_alignments,
+        ch_reference
+    )
+
     VIQUAS(
         ch_alignments,
         ch_reference

From 9364225e74a4e6f9773ac559f776d523adf7f100 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Tue, 26 Sep 2023 08:06:43 -0500
Subject: [PATCH 39/40] fix: Change input cardinality on haplotyping modules

---
 modules/cliquesnv/main.nf          | 2 +-
 modules/haplink/haplotypes/main.nf | 2 +-
 modules/predicthaplo/main.nf       | 2 +-
 modules/quasirecomb/main.nf        | 2 +-
 modules/shorah/amplicon/main.nf    | 2 +-
 modules/shorah/shotgun/main.nf     | 2 +-
 6 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/modules/cliquesnv/main.nf b/modules/cliquesnv/main.nf
index f22ffa1..f00d979 100644
--- a/modules/cliquesnv/main.nf
+++ b/modules/cliquesnv/main.nf
@@ -5,7 +5,7 @@ process CLIQUESNV {
     container 'quay.io/biocontainers/cliquesnv:2.0.3--hdfd78af_0'
 
     input:
-    tuple val(prefix), path(bam)
+    tuple val(prefix), path(bam), path(bai)
     val(method)
 
     output:
diff --git a/modules/haplink/haplotypes/main.nf b/modules/haplink/haplotypes/main.nf
index e4b96e8..e178112 100644
--- a/modules/haplink/haplotypes/main.nf
+++ b/modules/haplink/haplotypes/main.nf
@@ -5,7 +5,7 @@ process HAPLINK_HAPLOTYPES {
     container 'quay.io/biocontainers/haplink:1.0.0--h031d066_0'
 
     input:
-    tuple val(prefix), path(bam), path(bai)
+    tuple val(prefix), path(bam), path(bai), path(vcf)
     path reference
 
     output:
diff --git a/modules/predicthaplo/main.nf b/modules/predicthaplo/main.nf
index 71d2fc1..2c14476 100644
--- a/modules/predicthaplo/main.nf
+++ b/modules/predicthaplo/main.nf
@@ -5,7 +5,7 @@ process PREDICTHAPLO {
     container 'quay.io/biocontainers/predicthaplo:2.1.4--h9b88814_5'
 
     input:
-    tuple val(prefix), path(bam)
+    tuple val(prefix), path(bam), path(bai)
     path(reference)
 
     output:
diff --git a/modules/quasirecomb/main.nf b/modules/quasirecomb/main.nf
index e2896c0..085122e 100644
--- a/modules/quasirecomb/main.nf
+++ b/modules/quasirecomb/main.nf
@@ -5,7 +5,7 @@ process QUASIRECOMB {
     container 'quay.io/biocontainers/quasirecomb:1.2--hdfd78af_1'
 
     input:
-    tuple val(prefix), path(bam)
+    tuple val(prefix), path(bam), path(bai)
 
     output:
     tuple val(prefix), path("*.fasta")
diff --git a/modules/shorah/amplicon/main.nf b/modules/shorah/amplicon/main.nf
index d35961a..171cf6b 100644
--- a/modules/shorah/amplicon/main.nf
+++ b/modules/shorah/amplicon/main.nf
@@ -5,7 +5,7 @@ process SHORAH_AMPLICON {
     container 'quay.io/biocontainers/shorah:1.99.2--py38h73782ee_8'
 
     input:
-    tuple val(prefix), path(bam)
+    tuple val(prefix), path(bam), path(bai)
     path(reference)
 
     output:
diff --git a/modules/shorah/shotgun/main.nf b/modules/shorah/shotgun/main.nf
index 224dca9..9f2ece9 100644
--- a/modules/shorah/shotgun/main.nf
+++ b/modules/shorah/shotgun/main.nf
@@ -5,7 +5,7 @@ process SHORAH_SHOTGUN {
     container 'quay.io/biocontainers/shorah:1.99.2--py38h73782ee_8'
 
     input:
-    tuple val(prefix), path(bam)
+    tuple val(prefix), path(bam), path(bai)
     path(reference)
 
     output:

From b98a7977013b4e15934bc459abca325872aeb3f9 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Tue, 26 Sep 2023 08:27:22 -0500
Subject: [PATCH 40/40] feat: Add control flow for choosing haplotypers

---
 modules/cliquesnv/main.nf          |  4 ++++
 modules/haplink/haplotypes/main.nf |  4 ++++
 modules/haplink/sequences/main.nf  |  4 ++++
 modules/haplink/variants/main.nf   |  4 ++++
 modules/predicthaplo/main.nf       |  4 ++++
 modules/quasirecomb/main.nf        |  4 ++++
 modules/shorah/amplicon/main.nf    |  4 ++++
 modules/shorah/shotgun/main.nf     |  4 ++++
 modules/viquas/main.nf             |  4 ++++
 nextflow.config                    | 28 ++++++++++++++++++++++++++++
 10 files changed, 64 insertions(+)

diff --git a/modules/cliquesnv/main.nf b/modules/cliquesnv/main.nf
index f00d979..da197e7 100644
--- a/modules/cliquesnv/main.nf
+++ b/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'
     """
diff --git a/modules/haplink/haplotypes/main.nf b/modules/haplink/haplotypes/main.nf
index e178112..5673af4 100644
--- a/modules/haplink/haplotypes/main.nf
+++ b/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 ?: ''
     """
diff --git a/modules/haplink/sequences/main.nf b/modules/haplink/sequences/main.nf
index 109b92f..fa1c76e 100644
--- a/modules/haplink/sequences/main.nf
+++ b/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=${task.cpus}
diff --git a/modules/haplink/variants/main.nf b/modules/haplink/variants/main.nf
index b4f7149..ec6e9c8 100644
--- a/modules/haplink/variants/main.nf
+++ b/modules/haplink/variants/main.nf
@@ -1,6 +1,7 @@
 process HAPLINK_VARIANTS {
     tag "${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=${task.cpus}
diff --git a/modules/predicthaplo/main.nf b/modules/predicthaplo/main.nf
index 2c14476..f403c0e 100644
--- a/modules/predicthaplo/main.nf
+++ b/modules/predicthaplo/main.nf
@@ -1,6 +1,7 @@
 process PREDICTHAPLO {
     tag "${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 \\
diff --git a/modules/quasirecomb/main.nf b/modules/quasirecomb/main.nf
index 085122e..8e054cf 100644
--- a/modules/quasirecomb/main.nf
+++ b/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'
     """
diff --git a/modules/shorah/amplicon/main.nf b/modules/shorah/amplicon/main.nf
index 171cf6b..c8ccf38 100644
--- a/modules/shorah/amplicon/main.nf
+++ b/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 \\
diff --git a/modules/shorah/shotgun/main.nf b/modules/shorah/shotgun/main.nf
index 9f2ece9..2b7aa86 100644
--- a/modules/shorah/shotgun/main.nf
+++ b/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 \\
diff --git a/modules/viquas/main.nf b/modules/viquas/main.nf
index ab467a3..ad19953 100644
--- a/modules/viquas/main.nf
+++ b/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 \\
diff --git a/nextflow.config b/nextflow.config
index 4e4c25c..98bf7b1 100644
--- a/nextflow.config
+++ b/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 {