From e3a5795652ae9838111b33483a80ad733e7501c4 Mon Sep 17 00:00:00 2001
From: Edmund Miller <edmund.a.miller@protonmail.com>
Date: Thu, 24 Mar 2022 21:44:12 -0500
Subject: [PATCH] Homer/findpeaks improvements (#1436)

* fix(homer): Update expected file path to improve caching

* docs(homer): Update findpeaks

* test(homer): Add maketagdirectory dependency

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
---
 modules/homer/findpeaks/main.nf  | 4 ++--
 modules/homer/findpeaks/meta.yml | 6 ++++--
 tests/config/pytest_modules.yml  | 1 +
 3 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/modules/homer/findpeaks/main.nf b/modules/homer/findpeaks/main.nf
index b9947774..4858d6da 100644
--- a/modules/homer/findpeaks/main.nf
+++ b/modules/homer/findpeaks/main.nf
@@ -13,8 +13,8 @@ process HOMER_FINDPEAKS {
     tuple val(meta), path(tagDir)
 
     output:
-    tuple val(meta), path("*peaks.txt"), emit: txt
-    path  "versions.yml"               , emit: versions
+    tuple val(meta), path("*.peaks.txt"), emit: txt
+    path  "versions.yml"                , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/homer/findpeaks/meta.yml b/modules/homer/findpeaks/meta.yml
index e7cef0cd..72eb8d0c 100644
--- a/modules/homer/findpeaks/meta.yml
+++ b/modules/homer/findpeaks/meta.yml
@@ -7,7 +7,9 @@ tools:
   - homer:
       description: |
         HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.
-      documentation: http://homer.ucsd.edu/homer/
+      homepage: "http://homer.ucsd.edu/homer/index.html"
+      documentation: "http://homer.ucsd.edu/homer/"
+      tool_dev_url: "http://homer.ucsd.edu/homer/ngs/peaks.html"
       doi: 10.1016/j.molcel.2010.05.004.
       licence: ["GPL-3.0-or-later"]
 input:
@@ -29,7 +31,7 @@ output:
   - peaks:
       type: file
       description: The found peaks
-      pattern: "*peaks.txt"
+      pattern: "*.peaks.txt"
   - versions:
       type: file
       description: File containing software versions
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 13bcbbd3..a211acbc 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -876,6 +876,7 @@ homer/annotatepeaks:
 
 homer/findpeaks:
   - modules/homer/findpeaks/**
+  - modules/homer/maketagdirectory/**
   - tests/modules/homer/findpeaks/**
 
 homer/maketagdirectory: