From 3faea8aac574cd42ad3dd85f64f264521a274e18 Mon Sep 17 00:00:00 2001
From: Sofia Stamouli <sofia.stamouli@scilifelab.se>
Date: Tue, 1 Nov 2022 17:34:37 +0100
Subject: [PATCH 1/2] Fix porechop conflict

---
 modules.json                                   |  4 ++--
 .../nf-core/porechop/{ => porechop}/main.nf    |  3 +--
 .../nf-core/porechop/{ => porechop}/meta.yml   |  2 +-
 subworkflows/local/longread_preprocessing.nf   | 18 +++++++++---------
 4 files changed, 13 insertions(+), 14 deletions(-)
 rename modules/nf-core/porechop/{ => porechop}/main.nf (97%)
 rename modules/nf-core/porechop/{ => porechop}/meta.yml (98%)

diff --git a/modules.json b/modules.json
index be3d193..c0e0a3a 100644
--- a/modules.json
+++ b/modules.json
@@ -141,9 +141,9 @@
                         "branch": "master",
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
-                    "porechop": {
+                    "porechop/porechop": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "2a4e85eb81875a572bb58133e37f84ba3cc484d7"
                     },
                     "prinseqplusplus": {
                         "branch": "master",
diff --git a/modules/nf-core/porechop/main.nf b/modules/nf-core/porechop/porechop/main.nf
similarity index 97%
rename from modules/nf-core/porechop/main.nf
rename to modules/nf-core/porechop/porechop/main.nf
index 77050bc..f946417 100644
--- a/modules/nf-core/porechop/main.nf
+++ b/modules/nf-core/porechop/porechop/main.nf
@@ -1,4 +1,4 @@
-process PORECHOP {
+process PORECHOP_PORECHOP {
     tag "$meta.id"
     label 'process_medium'
 
@@ -28,7 +28,6 @@ process PORECHOP {
         $args \\
         -o ${prefix}.fastq.gz \\
         > ${prefix}.log
-
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         porechop: \$( porechop --version )
diff --git a/modules/nf-core/porechop/meta.yml b/modules/nf-core/porechop/porechop/meta.yml
similarity index 98%
rename from modules/nf-core/porechop/meta.yml
rename to modules/nf-core/porechop/porechop/meta.yml
index e526317..98b838f 100644
--- a/modules/nf-core/porechop/meta.yml
+++ b/modules/nf-core/porechop/porechop/meta.yml
@@ -1,4 +1,4 @@
-name: porechop
+name: "porechop_porechop"
 description: Adapter removal and demultiplexing of Oxford Nanopore reads
 keywords:
   - adapter
diff --git a/subworkflows/local/longread_preprocessing.nf b/subworkflows/local/longread_preprocessing.nf
index 3da49ce..961417d 100644
--- a/subworkflows/local/longread_preprocessing.nf
+++ b/subworkflows/local/longread_preprocessing.nf
@@ -5,7 +5,7 @@
 include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/fastqc/main'
 include { FALCO as FALCO_PROCESSED   } from '../../modules/nf-core/falco/main'
 
-include { PORECHOP                   } from '../../modules/nf-core/porechop/main'
+include { PORECHOP_PORECHOP          } from '../../modules/nf-core/porechop/porechop/main'
 include { FILTLONG                   } from '../../modules/nf-core/filtlong/main'
 
 workflow LONGREAD_PREPROCESSING {
@@ -17,9 +17,9 @@ workflow LONGREAD_PREPROCESSING {
     ch_multiqc_files = Channel.empty()
 
     if ( !params.longread_qc_skipadaptertrim && params.longread_qc_skipqualityfilter) {
-        PORECHOP ( reads )
+        PORECHOP_PORECHOP ( reads )
 
-        ch_processed_reads = PORECHOP.out.reads
+        ch_processed_reads = PORECHOP_PORECHOP.out.reads
                                         .map {
                                                 meta, reads ->
                                                 def meta_new = meta.clone()
@@ -27,8 +27,8 @@ workflow LONGREAD_PREPROCESSING {
                                                 [ meta_new, reads ]
                                         }
 
-        ch_versions = ch_versions.mix(PORECHOP.out.versions.first())
-        ch_multiqc_files = ch_multiqc_files.mix( PORECHOP.out.log )
+        ch_versions = ch_versions.mix(PORECHOP_PORECHOP.out.versions.first())
+        ch_multiqc_files = ch_multiqc_files.mix( PORECHOP_PORECHOP.out.log )
 
     } else if ( params.longread_qc_skipadaptertrim && !params.longread_qc_skipqualityfilter) {
 
@@ -37,8 +37,8 @@ workflow LONGREAD_PREPROCESSING {
         ch_multiqc_files = ch_multiqc_files.mix( FILTLONG.out.log )
 
     } else {
-        PORECHOP ( reads )
-        ch_clipped_reads = PORECHOP.out.reads
+        PORECHOP_PORECHOP ( reads )
+        ch_clipped_reads = PORECHOP_PORECHOP.out.reads
                                         .map {
                                                 meta, reads ->
                                                 def meta_new = meta.clone()
@@ -48,9 +48,9 @@ workflow LONGREAD_PREPROCESSING {
 
         ch_processed_reads = FILTLONG ( ch_clipped_reads.map{ meta, reads -> [meta, [], reads ]} ).reads
 
-        ch_versions = ch_versions.mix(PORECHOP.out.versions.first())
+        ch_versions = ch_versions.mix(PORECHOP_PORECHOP.out.versions.first())
         ch_versions = ch_versions.mix(FILTLONG.out.versions.first())
-        ch_multiqc_files = ch_multiqc_files.mix( PORECHOP.out.log )
+        ch_multiqc_files = ch_multiqc_files.mix( PORECHOP_PORECHOP.out.log )
         ch_multiqc_files = ch_multiqc_files.mix( FILTLONG.out.log )
     }
 

From e4307ad8abfa123d749cd70ce37cff486e804590 Mon Sep 17 00:00:00 2001
From: Sofia Stamouli <sofia.stamouli@scilifelab.se>
Date: Tue, 1 Nov 2022 20:50:42 +0100
Subject: [PATCH 2/2] Change modules.config to include porechop_porechop

---
 conf/modules.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/modules.config b/conf/modules.config
index 397e0c2..dad18a2 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -134,7 +134,7 @@ process {
         ]
     }
 
-    withName: PORECHOP {
+    withName: PORECHOP_PORECHOP {
         ext.prefix = { "${meta.id}_${meta.run_accession}" }
         publishDir = [
             path: { "${params.outdir}/porechop" },