From 847bebc0abfdf6b9ebff8fe2dfd6abda51d7c04e Mon Sep 17 00:00:00 2001
From: Daniel Lundin <erik.rikard.daniel@gmail.com>
Date: Thu, 15 Sep 2022 14:06:18 +0200
Subject: [PATCH] Make hmmer/hmmalign output files with correct prefix (#2067)

---
 modules/hmmer/hmmalign/main.nf               |  2 +-
 tests/modules/hmmer/hmmalign/main.nf         | 15 ++++++++++++++-
 tests/modules/hmmer/hmmalign/nextflow.config |  3 +++
 tests/modules/hmmer/hmmalign/test.yml        |  8 ++++++++
 4 files changed, 26 insertions(+), 2 deletions(-)

diff --git a/modules/hmmer/hmmalign/main.nf b/modules/hmmer/hmmalign/main.nf
index f8156e04..b15740aa 100644
--- a/modules/hmmer/hmmalign/main.nf
+++ b/modules/hmmer/hmmalign/main.nf
@@ -25,7 +25,7 @@ process HMMER_HMMALIGN {
     hmmalign \\
         $args \\
         $hmm \\
-        $fasta | gzip -c > ${meta.id}.sthlm.gz
+        $fasta | gzip -c > ${prefix}.sthlm.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/tests/modules/hmmer/hmmalign/main.nf b/tests/modules/hmmer/hmmalign/main.nf
index 0a462a7a..7e48d00a 100644
--- a/tests/modules/hmmer/hmmalign/main.nf
+++ b/tests/modules/hmmer/hmmalign/main.nf
@@ -2,7 +2,8 @@
 
 nextflow.enable.dsl = 2
 
-include { HMMER_HMMALIGN } from '../../../../modules/hmmer/hmmalign/main.nf'
+include { HMMER_HMMALIGN as HMMER_HMMALIGN        } from '../../../../modules/hmmer/hmmalign/main.nf'
+include { HMMER_HMMALIGN as HMMER_HMMALIGN_PREFIX } from '../../../../modules/hmmer/hmmalign/main.nf'
 
 workflow test_hmmer_hmmalign {
 
@@ -15,3 +16,15 @@ workflow test_hmmer_hmmalign {
 
     HMMER_HMMALIGN ( input, hmm )
 }
+
+workflow test_hmmer_hmmalign_prefix {
+
+    input = [
+        [ id:'test' ], // meta map
+        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/e_coli_k12_16s.fna.gz')      // Change to params.test_data syntax after the data is included in tests/config/test_data.config
+    ]
+
+    hmm   = file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/bac.16S_rRNA.hmm.gz')
+
+    HMMER_HMMALIGN_PREFIX ( input, hmm )
+}
diff --git a/tests/modules/hmmer/hmmalign/nextflow.config b/tests/modules/hmmer/hmmalign/nextflow.config
index 8730f1c4..b2115af5 100644
--- a/tests/modules/hmmer/hmmalign/nextflow.config
+++ b/tests/modules/hmmer/hmmalign/nextflow.config
@@ -2,4 +2,7 @@ process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
+    withName: HMMER_HMMALIGN_PREFIX {
+        ext.prefix = { "${meta.id}.prefix" }
+    }
 }
diff --git a/tests/modules/hmmer/hmmalign/test.yml b/tests/modules/hmmer/hmmalign/test.yml
index 2e5ccfaf..becf51dd 100644
--- a/tests/modules/hmmer/hmmalign/test.yml
+++ b/tests/modules/hmmer/hmmalign/test.yml
@@ -6,3 +6,11 @@
   files:
     - path: output/hmmer/test.sthlm.gz
       md5sum: ddaa8b96291edf4e1a929a224329161b
+- name: hmmer hmmalign test_hmmer_hmmalign_prefix
+  command: nextflow run ./tests/modules/hmmer/hmmalign -entry test_hmmer_hmmalign_prefix -c ./tests/config/nextflow.config -c ./tests/modules/hmmer/hmmalign/nextflow.config
+  tags:
+    - hmmer
+    - hmmer/hmmalign
+  files:
+    - path: output/hmmer/test.prefix.sthlm.gz
+      md5sum: ddaa8b96291edf4e1a929a224329161b