Update isoseq modules and migrate to nf-test

modules/nf-core/isoseq3/cluster/environment.yml

@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::isoseq3=3.8.1
+  - bioconda::isoseq3=4.0.0

modules/nf-core/isoseq3/cluster/main.nf

@@ -4,8 +4,8 @@ process ISOSEQ3_CLUSTER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/isoseq3:3.8.1--h9ee0642_0' :
-        'biocontainers/isoseq3:3.8.1--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/isoseq3:4.0.0--h9ee0642_0' :
+        'biocontainers/isoseq3:4.0.0--h9ee0642_0' }"
 
     input:
     tuple val(meta), path(bam)
@@ -31,15 +31,15 @@ process ISOSEQ3_CLUSTER {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    isoseq3 \\
+    isoseq \\
         cluster \\
         $bam \\
         ${prefix}.transcripts.bam \\
         $args
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        isoseq3: \$( isoseq3 cluster --version | head -n 1 | sed 's/isoseq cluster //g' | sed 's/ (.*//g' )
+        isoseq3: \$( isoseq cluster --version | head -n 1 | sed 's/isoseq cluster //g' | sed 's/ (.*//g' )
     END_VERSIONS
     """
 }

modules/nf-core/isoseq3/cluster/meta.yml

@@ -2,6 +2,9 @@ name: isoseq3_cluster
 description: IsoSeq3 - Cluster - Cluster trimmed consensus sequences
 keywords:
   - cluster
+  - HiFi
+  - isoseq
+  - Pacbio
 tools:
   - isoseq3:
       description: IsoSeq3 - Cluster - Cluster trimmed consensus sequences
@@ -25,7 +28,7 @@ output:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - version:
+  - versions:
       type: file
       description: File containing software version
       pattern: "versions.yml"

modules/nf-core/isoseq3/cluster/tests/main.nf.test

@@ -0,0 +1,46 @@
+nextflow_process {
+
+    name "Test Process ISOSEQ3_CLUSTER"
+    script "../main.nf"
+    config "./nextflow.config"
+    process "ISOSEQ3_CLUSTER"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "isoseq3"
+    tag "isoseq3/cluster"
+
+    test("Main test") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.test_data['homo_sapiens']['pacbio']['refine'], checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll {
+                assert process.success
+                assert snapshot(process.out.bam).match("bam")
+                assert snapshot(process.out.pbi).match("pbi")
+                assert snapshot(process.out.cluster).match("cluster")
+                assert snapshot(process.out.cluster_report).match("cluster_report")
+                assert snapshot(process.out.hq_bam).match("hq_bam")
+                assert snapshot(process.out.hq_pbi).match("hq_pbi")
+                assert snapshot(process.out.lq_bam).match("lq_bam")
+                assert snapshot(process.out.lq_pbi).match("lq_pbi")
+                assert snapshot(process.out.singletons_bam).match("singletons_bam")
+                assert snapshot(process.out.singletons_pbi).match("singletons_pbi")
+                assert snapshot(process.out.versions).match("versions")
+            }
+
+        }
+
+    }
+
+}

modules/nf-core/isoseq3/cluster/tests/main.nf.test.snap

@@ -0,0 +1,140 @@
+{
+    "cluster": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.transcripts.cluster:md5,e25f5e4179bc8b6accec024008001c52"
+                ]
+            ]
+        ],
+        "timestamp": "2024-01-16T17:51:37.025827"
+    },
+    "singletons_bam": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.transcripts.singletons.bam:md5,f8bcaa7d071be24c199d4243e77a65a6"
+                ]
+            ]
+        ],
+        "timestamp": "2024-01-17T08:55:36.093361"
+    },
+    "lq_bam": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.transcripts.lq.bam:md5,f4948859ae09db09221ef7c08b9dc1ea"
+                ]
+            ]
+        ],
+        "timestamp": "2024-01-17T08:55:36.011969"
+    },
+    "hq_bam": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.transcripts.hq.bam:md5,0ad13a6f56aa1800cc553ee3e8f52e59"
+                ]
+            ]
+        ],
+        "timestamp": "2024-01-17T08:55:35.949396"
+    },
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,a10cb8125ff5dc181f08493e68900b4d"
+            ]
+        ],
+        "timestamp": "2024-01-16T17:51:37.300931"
+    },
+    "pbi": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.transcripts.bam.pbi:md5,0f9569d3132bc58a3b6827364215d2a8"
+                ]
+            ]
+        ],
+        "timestamp": "2024-01-17T08:55:35.917491"
+    },
+    "singletons_pbi": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.transcripts.singletons.bam.pbi:md5,f63eed07e30bc66a72c6ebd24d0116e0"
+                ]
+            ]
+        ],
+        "timestamp": "2024-01-17T08:55:36.151147"
+    },
+    "cluster_report": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.transcripts.cluster_report.csv:md5,5437fc2d59122b28d81c3f1215f6ff17"
+                ]
+            ]
+        ],
+        "timestamp": "2024-01-16T17:51:37.069648"
+    },
+    "hq_pbi": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.transcripts.hq.bam.pbi:md5,4eecd253bb8cb0dbdc039ec80bb88ba0"
+                ]
+            ]
+        ],
+        "timestamp": "2024-01-17T08:55:35.977037"
+    },
+    "lq_pbi": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.transcripts.lq.bam.pbi:md5,d1f96a5748c71d9eb1b69c620412c863"
+                ]
+            ]
+        ],
+        "timestamp": "2024-01-17T08:55:36.032895"
+    },
+    "bam": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.transcripts.bam:md5,540c126bca7bd75f7a9084d3e2e642f7"
+                ]
+            ]
+        ],
+        "timestamp": "2024-01-17T08:55:35.880903"
+    }
+}

tests/modules/nf-core/pbccs/nextflow.config → modules/nf-core/isoseq3/cluster/tests/nextflow.config

@@ -1,9 +1,6 @@
 process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-    withName: PBCCS {
-        ext.args = '--min-rq 0.9'
-    }
+    ext.args = '--singletons --use-qvs --verbose'
 
 }

modules/nf-core/isoseq3/cluster/tests/tags.yml

@@ -0,0 +1,2 @@
+isoseq3/cluster:
+  - modules/nf-core/isoseq3/cluster/**

modules/nf-core/isoseq3/refine/environment.yml

@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::isoseq3=3.8.2
+  - bioconda::isoseq3=4.0.0

modules/nf-core/isoseq3/refine/main.nf

@@ -4,20 +4,20 @@ process ISOSEQ3_REFINE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/isoseq3:3.8.2--h9ee0642_0' :
-        'biocontainers/isoseq3:3.8.2--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/isoseq3:4.0.0--h9ee0642_0' :
+        'biocontainers/isoseq3:4.0.0--h9ee0642_0' }"
 
     input:
     tuple val(meta), path(bam)
     path primers
 
     output:
-    tuple val(meta), path("*.bam")                        , emit: bam
-    tuple val(meta), path("*.bam.pbi")                    , emit: pbi
-    tuple val(meta), path("*.consensusreadset.xml")       , emit: consensusreadset
-    tuple val(meta), path("*.filter_summary.report.json") , emit: summary
-    tuple val(meta), path("*.report.csv")                 , emit: report
-    path  "versions.yml"                                  , emit: versions
+    tuple val(meta), path("*.bam")                       , emit: bam
+    tuple val(meta), path("*.bam.pbi")                   , emit: pbi
+    tuple val(meta), path("*.consensusreadset.xml")      , emit: consensusreadset
+    tuple val(meta), path("*.filter_summary.report.json"), emit: summary
+    tuple val(meta), path("*.report.csv")                , emit: report
+    path  "versions.yml"                                 , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -26,7 +26,7 @@ process ISOSEQ3_REFINE {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    isoseq3 \\
+    isoseq \\
         refine \\
         -j $task.cpus \\
         $args \\
@@ -36,7 +36,7 @@ process ISOSEQ3_REFINE {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        isoseq3: \$( isoseq3 refine --version | head -n 1 | sed 's/isoseq refine //' | sed 's/ (commit.\\+//' )
+        isoseq3: \$( isoseq refine --version | head -n 1 | sed 's/isoseq refine //' | sed 's/ (commit.\\+//' )
     END_VERSIONS
     """
 }

modules/nf-core/isoseq3/refine/tests/main.nf.test

@@ -0,0 +1,37 @@
+nextflow_process {
+
+    name "Test Process ISOSEQ3_REFINE"
+    script "../main.nf"
+    config "./nextflow.config"
+    process "ISOSEQ3_REFINE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "isoseq3"
+    tag "isoseq3/refine"
+
+    test("Main test") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.test_data['homo_sapiens']['pacbio']['lima'], checkIfExists: true),
+                ]
+                input[1] = file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out.bam).match("bam")
+            assert snapshot(process.out.pbi).match("pbi")
+            assert snapshot(process.out.report).match("report")
+            assert snapshot(process.out.versions).match("versions")
+        }
+
+    }
+
+}

modules/nf-core/isoseq3/refine/tests/main.nf.test.snap

@@ -0,0 +1,49 @@
+{
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,6cc3190a74e747de318b9b1227379bee"
+            ]
+        ],
+        "timestamp": "2024-01-17T10:06:26.844337"
+    },
+    "pbi": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.refine.bam.pbi:md5,fcd3c9b9c7efea71732591ff1271a3b5"
+                ]
+            ]
+        ],
+        "timestamp": "2024-01-17T10:06:26.482922"
+    },
+    "report": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.refine.report.csv:md5,d42a139e5d9b08396bdb087c01243ea9"
+                ]
+            ]
+        ],
+        "timestamp": "2024-01-17T10:06:26.665805"
+    },
+    "bam": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.refine.bam:md5,4a666931c2c8843d8a8f0d901e1ba15f"
+                ]
+            ]
+        ],
+        "timestamp": "2024-01-17T10:06:26.286284"
+    }
+}