yahs release update (nf-core#6695)

* update yahs version and output options * update yahs version and output options * add correct datatype in nf-test, new version yahs would attempt scaffolding based on alignment file * add samtools tag
herpov · Oct 2, 2024 · 01baaa9 · 01baaa9
1 parent f59304f
commit 01baaa9
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Showing 4 changed files with 41 additions and 52 deletions.
diff --git a/modules/nf-core/yahs/main.nf b/modules/nf-core/yahs/main.nf
@@ -4,17 +4,17 @@ process YAHS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/yahs:1.2a.2--h7132678_0':
-        'biocontainers/yahs:1.2a.2--h7132678_0' }"
+        'https://depot.galaxyproject.org/singularity/yahs:1.2--he4a0461_1':
+        'biocontainers/yahs:1.2--he4a0461_1' }"
 
     input:
     tuple val(meta), path(hic_map)
     path fasta
     path fai
 
     output:
-    tuple val(meta), path("*scaffolds_final.fa") , emit: scaffolds_fasta
-    tuple val(meta), path("*scaffolds_final.agp"), emit: scaffolds_agp
+    tuple val(meta), path("*scaffolds_final.fa") , emit: scaffolds_fasta,  optional: true
+    tuple val(meta), path("*scaffolds_final.agp"), emit: scaffolds_agp,    optional: true
     tuple val(meta), path("*bin")                , emit: binary
     path "versions.yml"                          , emit: versions
 

diff --git a/modules/nf-core/yahs/meta.yml b/modules/nf-core/yahs/meta.yml
@@ -75,3 +75,4 @@ authors:
   - "@ksenia-krasheninnikova"
 maintainers:
   - "@ksenia-krasheninnikova"
+  - "@yy5"
diff --git a/modules/nf-core/yahs/tests/main.nf.test b/modules/nf-core/yahs/tests/main.nf.test
@@ -9,18 +9,36 @@ nextflow_process {
     tag "modules"
     tag "modules_nfcore"
     tag "yahs"
+    tag "samtools/view"
 
-    test("sarscov2-bed-fasta-fai") {
+    setup {
+            run("SAMTOOLS_VIEW") {
+            script "../../samtools/view"
+            process {
+                 """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
+                    []
+                ])
+                input[1] = Channel.of([
+                    [ id:'genome' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[2] = []
+                """
+            }
+            }
+        }
+
+    test("homo_sapiens-bam-fasta-fai") {
 
         when {
             process {
                 """
-                input[0] = [ [ id:'test' ],
-				file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
-				]
-				input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
-				input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
-
+                input[0] = SAMTOOLS_VIEW.out.bam
+				input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+				input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
                 """
             }
         }

diff --git a/modules/nf-core/yahs/tests/main.nf.test.snap b/modules/nf-core/yahs/tests/main.nf.test.snap
@@ -1,67 +1,37 @@
 {
-    "test-yahs": {
+    "homo_sapiens-bam-fasta-fai": {
         "content": [
             {
                 "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test_scaffolds_final.fa:md5,a7673a43fb4e3f0a87d2ca2fe48bd442"
-                    ]
+
                 ],
                 "1": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test_scaffolds_final.agp:md5,7134a33534816100a84a6d32351c2168"
-                    ]
+
                 ],
                 "2": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bin:md5,c60503a616a0f7726176febdad3ae186"
-                    ]
+
                 ],
                 "3": [
-                    "versions.yml:md5,007c44dd06fe8686b6f8068314601462"
+
                 ],
                 "binary": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bin:md5,c60503a616a0f7726176febdad3ae186"
-                    ]
+
                 ],
                 "scaffolds_agp": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test_scaffolds_final.agp:md5,7134a33534816100a84a6d32351c2168"
-                    ]
+
                 ],
                 "scaffolds_fasta": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test_scaffolds_final.fa:md5,a7673a43fb4e3f0a87d2ca2fe48bd442"
-                    ]
+
                 ],
                 "versions": [
-                    "versions.yml:md5,007c44dd06fe8686b6f8068314601462"
+
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-08-23T08:47:14.869961"
+        "timestamp": "2024-09-26T22:35:24.103271222"
     }
 }