From a78db057ee409865b358eacbecff5da398134a39 Mon Sep 17 00:00:00 2001
From: subwaystation <simon.heumos@qbic.uni-tuebingen.de>
Date: Thu, 1 Feb 2024 15:57:53 +0100
Subject: [PATCH] now

---
 modules/nf-core/wfmash/environment.yml        |  7 ----
 modules/nf-core/wfmash/meta.yml               |  3 ++
 modules/nf-core/wfmash/tests/main.nf.test     | 39 -------------------
 .../nf-core/wfmash/tests/main.nf.test.snap    | 33 ----------------
 modules/nf-core/wfmash/tests/nextflow.config  | 12 ------
 modules/nf-core/wfmash/tests/tags.yml         |  2 -
 6 files changed, 3 insertions(+), 93 deletions(-)
 delete mode 100644 modules/nf-core/wfmash/environment.yml
 delete mode 100644 modules/nf-core/wfmash/tests/main.nf.test
 delete mode 100644 modules/nf-core/wfmash/tests/main.nf.test.snap
 delete mode 100644 modules/nf-core/wfmash/tests/nextflow.config
 delete mode 100644 modules/nf-core/wfmash/tests/tags.yml

diff --git a/modules/nf-core/wfmash/environment.yml b/modules/nf-core/wfmash/environment.yml
deleted file mode 100644
index 4e7e66c..0000000
--- a/modules/nf-core/wfmash/environment.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-name: wfmash
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
-dependencies:
-  - bioconda::wfmash=0.12.5
diff --git a/modules/nf-core/wfmash/meta.yml b/modules/nf-core/wfmash/meta.yml
index 1063f8b..80e630c 100644
--- a/modules/nf-core/wfmash/meta.yml
+++ b/modules/nf-core/wfmash/meta.yml
@@ -14,6 +14,7 @@ tools:
       tool_dev_url: https://github.com/waveygang/wfmash
       doi: 10.5281/zenodo.6949373
       licence: "['MIT']"
+
 input:
   - meta:
       type: map
@@ -43,6 +44,7 @@ input:
       type: file
       description: Optional inpute file in FASTA format specifying the query sequences as a list.
       pattern: "*.{fa,fna,fasta}"
+
 output:
   - meta:
       type: map
@@ -57,5 +59,6 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
+
 authors:
   - "@subwaystation"
diff --git a/modules/nf-core/wfmash/tests/main.nf.test b/modules/nf-core/wfmash/tests/main.nf.test
deleted file mode 100644
index 41d8c23..0000000
--- a/modules/nf-core/wfmash/tests/main.nf.test
+++ /dev/null
@@ -1,39 +0,0 @@
-nextflow_process {
-
-    name "Test Process WFMASH"
-    script "../main.nf"
-    process "WFMASH"
-    config "./nextflow.config"
-
-    tag "modules"
-    tag "modules_nfcore"
-    tag "wfmash"
-
-    test("homo_sapiens - pangenome - pangenome_fa_bgzip") {
-
-        when {
-            process {
-                """
-                input[0] = [
-                    [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['homo_sapiens']['pangenome']['pangenome_fa_bgzip'], checkIfExists: true),
-                    [], // empty paf input
-                    file(params.test_data['homo_sapiens']['pangenome']['pangenome_fa_bgzip_gzi'], checkIfExists: true), // gzi
-                    file(params.test_data['homo_sapiens']['pangenome']['pangenome_fa_bgzip_fai'], checkIfExists: true) // fai
-                    ]
-                input[1] = true // empty paf input
-                input[2] = []
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-//                 { assert snapshot(process.out).exists() } // if run on more than 1 thread the lines in the resulting PAF will appear in a different order
-            )
-        }
-
-    }
-
-}
diff --git a/modules/nf-core/wfmash/tests/main.nf.test.snap b/modules/nf-core/wfmash/tests/main.nf.test.snap
deleted file mode 100644
index 97a51e4..0000000
--- a/modules/nf-core/wfmash/tests/main.nf.test.snap
+++ /dev/null
@@ -1,33 +0,0 @@
-{
-    "homo_sapiens - pangenome - pangenome_fa_bgzip": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.paf:md5,aa6629548e32b2d036c0767c9086a6dd"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,0da45b7a6424a967e2f39225fb020140"
-                ],
-                "paf": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.paf:md5,aa6629548e32b2d036c0767c9086a6dd"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,0da45b7a6424a967e2f39225fb020140"
-                ]
-            }
-        ],
-        "timestamp": "2024-01-25T15:12:21.284828212"
-    }
-}
\ No newline at end of file
diff --git a/modules/nf-core/wfmash/tests/nextflow.config b/modules/nf-core/wfmash/tests/nextflow.config
deleted file mode 100644
index b7e9c98..0000000
--- a/modules/nf-core/wfmash/tests/nextflow.config
+++ /dev/null
@@ -1,12 +0,0 @@
-process {
-
-    withName: WFMASH {
-        ext.args = {
-            [
-                "-s 500", // necessary because of https://github.com/waveygang/wfmash/issues/218
-                "-X"
-            ].join(" ").trim()
-        }
-    }
-
-}
diff --git a/modules/nf-core/wfmash/tests/tags.yml b/modules/nf-core/wfmash/tests/tags.yml
deleted file mode 100644
index 7001b08..0000000
--- a/modules/nf-core/wfmash/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-wfmash:
-  - "modules/nf-core/wfmash/**"