From bcc1e37cb99cc33835736f563b54410a36aa0288 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jo=C3=A3o=20Cavalcante?= <jvfecav@gmail.com>
Date: Tue, 3 Dec 2024 14:29:56 -0300
Subject: [PATCH] fix: Fix host removal flag (#42)

* fix: Add host removal

* ci: Update setup nf version

* ci: Update checkout step

* ci: Use specific nf version

* chore: Bump version
---
 .github/workflows/ci.yml |  6 +++---
 nextflow.config          |  2 +-
 workflows/euryale.nf     | 20 +++++++++++---------
 3 files changed, 15 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 364ec65..438e2cc 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -40,13 +40,13 @@ jobs:
       matrix:
         profile: ["docker", "singularity"]
         NXF_VER:
-          - "latest-everything"
+          - "23.10.0"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v2
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
         with:
           version: "${{ matrix.NXF_VER }}"
 
diff --git a/nextflow.config b/nextflow.config
index d80d1bd..139a466 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -211,7 +211,7 @@ manifest {
     description     = """A pipeline for taxonomic classification and functional annotation of metagenomics reads. Based on MEDUSA."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version         = '1.0.3'
+    version         = '1.0.4'
     doi             = ''
 }
 
diff --git a/workflows/euryale.nf b/workflows/euryale.nf
index 11a5414..279893e 100644
--- a/workflows/euryale.nf
+++ b/workflows/euryale.nf
@@ -109,15 +109,17 @@ workflow EURYALE {
         ch_multiqc_files = ch_multiqc_files.mix(PREPROCESS.out.multiqc_files.collect())
     }
 
-    if (ch_host_reference || ch_bowtie2_db) {
-        HOST_REMOVAL (
-            clean_reads,
-            ch_host_reference,
-            ch_bowtie2_db
-        )
-
-        HOST_REMOVAL.out.unaligned_reads
-            .set { clean_reads }
+    if (!params.skip_host_removal) {
+        if (ch_host_reference || ch_bowtie2_db) {
+            HOST_REMOVAL (
+                    clean_reads,
+                    ch_host_reference,
+                    ch_bowtie2_db
+                    )
+
+                HOST_REMOVAL.out.unaligned_reads
+                .set { clean_reads }
+        }
     }
     if (params.assembly_based) {
         ASSEMBLY (