From 2f96ba4e4407ba2b7442cdbe18940d0e31123ed9 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 30 Sep 2023 15:11:52 -0500
Subject: [PATCH] feat!: Remove PREDICTHAPLO module

The developers no longer publish a single-end version of predicthaplo (see
https://github.com/cbg-ethz/PredictHaplo/issues/1). Since this pipeline is
targeting single-end read technologies, drop predicthaplo from the list.
---
 main.nf                      |  6 ------
 modules/predicthaplo/main.nf | 27 ---------------------------
 nextflow.config              |  4 ----
 3 files changed, 37 deletions(-)
 delete mode 100644 modules/predicthaplo/main.nf

diff --git a/main.nf b/main.nf
index af776f3..045da7b 100755
--- a/main.nf
+++ b/main.nf
@@ -6,7 +6,6 @@ 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 } from './modules/nanofilt'
 include { QUASIRECOMB } from './modules/quasirecomb'
@@ -78,11 +77,6 @@ workflow {
         ch_reference
     )
 
-    PREDICTHAPLO(
-        ch_alignments,
-        ch_reference
-    )
-
     QUASIRECOMB( ch_alignments )
 
     SHORAH_AMPLICON(
diff --git a/modules/predicthaplo/main.nf b/modules/predicthaplo/main.nf
deleted file mode 100644
index f403c0e..0000000
--- a/modules/predicthaplo/main.nf
+++ /dev/null
@@ -1,27 +0,0 @@
-process PREDICTHAPLO {
-    tag "${prefix}"
-    label 'process_high'
-    label 'predicthaplo'
-
-    container 'quay.io/biocontainers/predicthaplo:2.1.4--h9b88814_5'
-
-    input:
-    tuple val(prefix), path(bam), path(bai)
-    path(reference)
-
-    output:
-    tuple val(prefix), path("*.fa*")
-
-    publishDir "results/${task.process}", mode: 'copy'
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    """
-    predicthaplo \\
-        --sam "${bam}" \\
-        --reference "${reference}" \\
-        --prefix "${prefix}"
-    """
-}
diff --git a/nextflow.config b/nextflow.config
index 98bf7b1..dab2fc4 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -19,7 +19,6 @@ params {
     // By default, run all haplotypers
     cliquesnv = true
     haplink = true
-    predicthaplo = true
     quasirecomb = true
     shorah = true
     viquas = true
@@ -69,9 +68,6 @@ process {
     withLabel: 'haplink' {
         ext.when = params.haplink
     }
-    withLabel: 'predicthaplo' {
-        ext.when = params.predicthaplo
-    }
     withLabel: 'quasirecomb' {
         ext.when = params.quasirecomb
     }