NARFMAP segfault (#4895)

* test(narfmap): Add segfault test * fix(narfmap): Clean up log error * test(narfmap): Should segfault * chore(narfmap): Bump to 1.4.2 * test(narfmap): Mark test as passing bioinformaticsorphanage/NARFMAP#10 * style: Add extra tag for nf-core/lint * test: Update all the snapshot declarations * chore: Add a TODO for poddar's test
nf-core · Jul 8, 2024 · ccedf37 · ccedf37
1 parent 1ceaa8b
commit ccedf37
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Showing 10 changed files with 251 additions and 41 deletions.
diff --git a/modules/nf-core/narfmap/align/environment.yml b/modules/nf-core/narfmap/align/environment.yml
@@ -5,7 +5,7 @@ channels:
   - defaults
 dependencies:
   # renovate: datasource=conda depName=bioconda/narfmap
-  - narfmap=1.4.0
+  - narfmap=1.4.2
   # renovate: datasource=conda depName=bioconda/samtools
   - samtools=1.18
   - pigz=2.8
diff --git a/modules/nf-core/narfmap/align/main.nf b/modules/nf-core/narfmap/align/main.nf
@@ -5,8 +5,8 @@ process NARFMAP_ALIGN {
     // TODO Add a singularity image
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'nf-core/modules/narfmap_align:narfmap--8a04bcf8bd9b6242':
-        'nf-core/modules/narfmap_align:narfmap--8a04bcf8bd9b6242' }"
+        'oras://community.wave.seqera.io/library/narfmap_align:8bad41386eab9997':
+        'community.wave.seqera.io/library/narfmap_align:517a1fed8e4e84c1' }"
 
     input:
     tuple val(meta) , path(reads)
@@ -34,7 +34,7 @@ process NARFMAP_ALIGN {
         $args \\
         --num-threads $task.cpus \\
         $reads_command \\
-        2> ${prefix}.narfmap.log \\
+        2> >(tee ${prefix}.narfmap.log >&2) \\
         | samtools $samtools_command $args2 --threads $task.cpus -o ${prefix}.bam -
 
     cat <<-END_VERSIONS > versions.yml

diff --git a/modules/nf-core/narfmap/align/tests/main.nf.test b/modules/nf-core/narfmap/align/tests/main.nf.test
@@ -7,6 +7,7 @@ nextflow_process {
     tag "modules_nfcore"
     tag "narfmap"
     tag "narfmap/align"
+    tag "narfmap/hashtable"
 
     test("sarscov2 - fastq, hashtable, false") {
 
@@ -41,10 +42,12 @@ nextflow_process {
             assertAll (
                 { assert process.success },
                 { assert snapshot(
+                    process.out.bam,
+                    process.out.versions,
                     file(process.out.bam[0][1]).name,
                     file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") },
-                    file(process.out.versions[0]).name
-                ).match() }
+                ).match()
+                }
             )
         }
 
@@ -83,10 +86,12 @@ nextflow_process {
             assertAll (
                 { assert process.success },
                 { assert snapshot(
+                    process.out.bam,
+                    process.out.versions,
                     file(process.out.bam[0][1]).name,
                     file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") },
-                    file(process.out.versions[0]).name
-                ).match() }
+                ).match()
+                }
             )
         }
 
@@ -128,10 +133,12 @@ nextflow_process {
             assertAll (
                 { assert process.success },
                 { assert snapshot(
+                    process.out.bam,
+                    process.out.versions,
                     file(process.out.bam[0][1]).name,
                     file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") },
-                    file(process.out.versions[0]).name
-                ).match() }
+                ).match()
+                }
             )
         }
 
@@ -173,10 +180,12 @@ nextflow_process {
             assertAll (
                 { assert process.success },
                 { assert snapshot(
+                    process.out.bam,
+                    process.out.versions,
                     file(process.out.bam[0][1]).name,
                     file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") },
-                    file(process.out.versions[0]).name
-                ).match() }
+                ).match()
+                }
             )
         }
 
@@ -218,10 +227,12 @@ nextflow_process {
             assertAll (
                 { assert process.success },
                 { assert snapshot(
+                    process.out.bam,
+                    process.out.versions,
                     file(process.out.bam[0][1]).name,
                     file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") },
-                    file(process.out.versions[0]).name
-                ).match() }
+                ).match()
+                }
             )
         }
 
@@ -264,10 +275,12 @@ nextflow_process {
             assertAll (
                 { assert process.success },
                 { assert snapshot(
+                    process.out.bam,
+                    process.out.versions,
                     file(process.out.bam[0][1]).name,
-                    file(process.out.log[0][1]).name,
-                    file(process.out.versions[0]).name
-                ).match() }
+                    file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") },
+                ).match()
+                }
             )
         }
 

diff --git a/modules/nf-core/narfmap/align/tests/main.nf.test.snap b/modules/nf-core/narfmap/align/tests/main.nf.test.snap
@@ -1,6 +1,18 @@
 {
     "homo_sapiens - [fastq1, fastq2], hashtable, true": {
         "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.bam:md5,5c407c8e621fc931af17a585526598bf"
+                ]
+            ],
+            [
+                "versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7"
+            ],
             "test.bam",
             [
                 "decompHashTableCtxInit...",
@@ -9,21 +21,53 @@
                 "decompHashTableExtIndex...",
                 "decompHashTableAutoHits...",
                 "decompHashTableSetFlags..."
-            ],
-            "versions.yml"
+            ]
         ],
-        "timestamp": "2023-11-23T10:12:03.844836279"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-08T11:45:10.095839411"
     },
     "sarscov2 - [fastq1, fastq2], hashtable, true - stub": {
         "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                "versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7"
+            ],
             "test.bam",
-            "test.log",
-            "versions.yml"
+            [
+
+            ]
         ],
-        "timestamp": "2023-11-22T13:41:18.016853266"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-08T11:45:22.364107512"
     },
     "sarscov2 - fastq, hashtable, false": {
         "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.bam:md5,ea3a6f419b6c8f91e99603058c608124"
+                ]
+            ],
+            [
+                "versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7"
+            ],
             "test.bam",
             [
                 "decompHashTableCtxInit...",
@@ -32,13 +76,28 @@
                 "decompHashTableExtIndex...",
                 "decompHashTableAutoHits...",
                 "decompHashTableSetFlags..."
-            ],
-            "versions.yml"
+            ]
         ],
-        "timestamp": "2023-11-23T10:11:33.956661024"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-08T11:43:57.96792573"
     },
     "sarscov2 - fastq, hashtable, true": {
         "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.bam:md5,e2632fce5442e05210edd516715489c4"
+                ]
+            ],
+            [
+                "versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7"
+            ],
             "test.bam",
             [
                 "decompHashTableCtxInit...",
@@ -47,13 +106,28 @@
                 "decompHashTableExtIndex...",
                 "decompHashTableAutoHits...",
                 "decompHashTableSetFlags..."
-            ],
-            "versions.yml"
+            ]
         ],
-        "timestamp": "2023-11-23T10:11:40.270598375"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-08T11:44:17.486586239"
     },
     "sarscov2 - [fastq1, fastq2], hashtable, false": {
         "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.bam:md5,ef0c12ae27778b906fd4f822ef7ce074"
+                ]
+            ],
+            [
+                "versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7"
+            ],
             "test.bam",
             [
                 "decompHashTableCtxInit...",
@@ -62,13 +136,28 @@
                 "decompHashTableExtIndex...",
                 "decompHashTableAutoHits...",
                 "decompHashTableSetFlags..."
-            ],
-            "versions.yml"
+            ]
         ],
-        "timestamp": "2023-11-23T10:11:46.928978876"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-08T11:44:48.178604348"
     },
     "sarscov2 - [fastq1, fastq2], hashtable, true": {
         "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.bam:md5,54965e6a11a9c31b1ae3c7e896c96c32"
+                ]
+            ],
+            [
+                "versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7"
+            ],
             "test.bam",
             [
                 "decompHashTableCtxInit...",
@@ -77,9 +166,12 @@
                 "decompHashTableExtIndex...",
                 "decompHashTableAutoHits...",
                 "decompHashTableSetFlags..."
-            ],
-            "versions.yml"
+            ]
         ],
-        "timestamp": "2023-11-23T10:11:53.506727278"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-08T11:44:55.858525101"
     }
 }
diff --git a/modules/nf-core/narfmap/align/tests/segfault.nf.test b/modules/nf-core/narfmap/align/tests/segfault.nf.test
@@ -0,0 +1,67 @@
+nextflow_process {
+
+    name "Test Process NARFMAP_ALIGN"
+    script "../main.nf"
+    process "NARFMAP_ALIGN"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "narfmap"
+    tag "narfmap/align"
+    tag "narfmap/hashtable"
+    tag "bug"
+
+    test("This should segfault") {
+
+        setup {
+            run("NARFMAP_HASHTABLE") {
+                script "../../hashtable/main.nf"
+                process {
+                    """
+                    input[0] = [
+                        [id:'test'],
+                        file('https://raw.githubusercontent.com/nf-core/test-datasets/nascent/reference/GRCh38_chr21.fa', checkIfExists: true)
+                    ]
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true ], // meta map
+                    file('https://raw.githubusercontent.com/nf-core/test-datasets/nascent/testdata/SRX882903_T2.fastq.gz', checkIfExists: true)
+                ]
+                input[1] = NARFMAP_HASHTABLE.out.hashmap
+                input[2] = false //sort
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(
+                    process.out.bam,
+                    process.out.versions,
+                    file(process.out.bam[0][1]).name,
+                    file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") },
+                ).match()
+                }
+            )
+        }
+
+    }
+
+    // TODO
+    // https://nfcore.slack.com/archives/CGFUX04HZ/p1718268624579699?thread_ts=1718108323.285709&cid=CGFUX04HZ
+    // https://ftp.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/NIST_HiSeq_HG002_Homogeneity-10953946/HG002_HiSeq300x_fastq/140528_D00360_0018_AH8VC6ADXX/Project_RM8391_RM8392/Sample_2A1/2A1_CGATGT_L001_R1_001.fastq.gz
+    // https://ftp.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/NIST_HiSeq_HG002_Homogeneity-10953946/HG002_HiSeq300x_fastq/140528_D00360_0018_AH8VC6ADXX/Project_RM8391_RM8392/Sample_2A1/2A1_CGATGT_L001_R2_001.fastq.gz
+    // {{dragen}} \
+    //     -r /home/tigem/h.poddar/short_reads_pipelines/ref_genome/GRCh37/hash/ \
+    //     -1 /home/tigem/h.poddar/DRAGMAP/2A1_CGATGT_L001_R1_001.fastq.gz \
+    //     -2 /home/tigem/h.poddar/DRAGMAP/2A1_CGATGT_L001_R2_001.fastq.gz \
+    //     | samtools view -h -O BAM - > aligned.bam
+
+}