From 245a3e2409eca361835101126bbf5b19434efd58 Mon Sep 17 00:00:00 2001
From: mazzalab <t.mazza@css-mendel.it>
Date: Tue, 10 Dec 2024 08:05:46 +0100
Subject: [PATCH] fixed linting fastqgather and reportgather

---
 .../nf-core/wipertools/fastqgather/meta.yml   |  6 ++--
 .../nf-core/wipertools/fastqwiper/meta.yml    |  2 +-
 .../nf-core/wipertools/reportgather/meta.yml  | 32 ++++++++-----------
 3 files changed, 18 insertions(+), 22 deletions(-)

diff --git a/modules/nf-core/wipertools/fastqgather/meta.yml b/modules/nf-core/wipertools/fastqgather/meta.yml
index 7708e69dc1c..4461d631db3 100644
--- a/modules/nf-core/wipertools/fastqgather/meta.yml
+++ b/modules/nf-core/wipertools/fastqgather/meta.yml
@@ -23,9 +23,9 @@ input:
         description: |
           Groovy Map containing sample information
           e.g. [ id:'test', single_end:false ]
-    - fastq_folder_in:
+    - fastq_in:
         type: file
-        description: Directory containing FASTQ chunks to be merged
+        description: List of FASTQ chunk files to be merged
         pattern: "*.{fastq,fastq.gz}"
         ontologies:
           - edam: "http://edamontology.org/format_1930"
@@ -37,7 +37,7 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "*.fastq.gz":
+      - "*_gather.fastq.gz":
           type: file
           description: The resulting FASTQ file
           pattern: "*.fastq.gz"
diff --git a/modules/nf-core/wipertools/fastqwiper/meta.yml b/modules/nf-core/wipertools/fastqwiper/meta.yml
index 11245c45973..2bd03b7e6f6 100644
--- a/modules/nf-core/wipertools/fastqwiper/meta.yml
+++ b/modules/nf-core/wipertools/fastqwiper/meta.yml
@@ -46,7 +46,7 @@ output:
       - "*.report":
           type: file
           description: Summary of the cleaning task
-          pattern: "*.{txt}"
+          pattern: "*.report"
           ontologies:
             - edam: "http://edamontology.org/format_2330"
   - versions:
diff --git a/modules/nf-core/wipertools/reportgather/meta.yml b/modules/nf-core/wipertools/reportgather/meta.yml
index 7708e69dc1c..f713dc86c65 100644
--- a/modules/nf-core/wipertools/reportgather/meta.yml
+++ b/modules/nf-core/wipertools/reportgather/meta.yml
@@ -1,15 +1,13 @@
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
-name: "wipertools_fastqgather"
-description: A tool of the wipertools suite that merges FASTQ chunks produced by wipertools_fastqscatter
+name: "wipertools_reportgather"
+description: A tool of the wipertools suite that merges wiping reports generated by wipertools_fastqwiper
 keywords:
-  - fastq
+  - report
   - merge
   - union
 tools:
-  - "fastqgather":
-      description:
-        "A tool of the wipertools suite that merges FASTQ chunks produced\
-        \ by wipertools_fastqscatter."
+  - "reportgather":
+      description: "A tool of the wipertools suite that merges wiping reports generated by wipertools_fastqwiper."
       homepage: "https://github.com/mazzalab/fastqwiper"
       documentation: "https://github.com/mazzalab/fastqwiper"
       tool_dev_url: "https://github.com/mazzalab/fastqwiper"
@@ -23,27 +21,25 @@ input:
         description: |
           Groovy Map containing sample information
           e.g. [ id:'test', single_end:false ]
-    - fastq_folder_in:
+    - reports:
         type: file
-        description: Directory containing FASTQ chunks to be merged
-        pattern: "*.{fastq,fastq.gz}"
+        description: List of wiping reports to be merged
+        pattern: "*.report"
         ontologies:
-          - edam: "http://edamontology.org/format_1930"
-          - edam: "http://edamontology.org/format_3989"
+          - edam: "http://edamontology.org/format_2330"
 output:
-  - fastq_out:
+  - report_out:
       - meta:
           type: map
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "*.fastq.gz":
+      - "*_gathered.report":
           type: file
-          description: The resulting FASTQ file
-          pattern: "*.fastq.gz"
+          description: The resulting report file
+          pattern: "*.report"
           ontologies:
-            - edam: "http://edamontology.org/format_1930"
-            - edam: "http://edamontology.org/format_3989"
+            - edam: "http://edamontology.org/format_2330"
   - versions:
       - versions.yml:
           type: file