Merge pull request #131 from Plant-Food-Research-Open/fix/short_intron

Fixed a crash due to short introns
Plant-Food-Research-Open · Dec 20, 2024 · d069633 · d069633
2 parents 2a0c7a2 + 3459b40
commit d069633
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v0.6.0 - [16-Dec-2024]
+## v0.6.0 - [20-Dec-2024]
 
 ### 'Added'
 
@@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 3. Fixed an issue in `genepal_report.Rmd` which caused the pangene matrix plot to fail when the number of clusters exceeded 65536 [#124](https://github.com/Plant-Food-Research-Open/genepal/issues/124)
 4. Fixed an issue where `GENEPALREPORT` process failed due to OOM kill signal from SLURM [#123](https://github.com/Plant-Food-Research-Open/genepal/issues/123)
 5. Fixed an issue where Gff merge after liftoff failed when one of the Gff files did not contain any genes
+6. Fixed an issue where `gxf_fasta_agat_spaddintrons_spextractsequences` crashed due to short introns [#89](https://github.com/Plant-Food-Research-Open/genepal/issues/89)
 
 ### `Dependencies`
 

diff --git a/modules.json b/modules.json
@@ -111,7 +111,7 @@
                     },
                     "gxf_fasta_agat_spaddintrons_spextractsequences": {
                         "branch": "main",
-                        "git_sha": "7bf6fbca23edc94490ffa6709f52b2f71c6fb130",
+                        "git_sha": "ed4146008dbdcfd4823252b456de32059e2d07f4",
                         "installed_by": ["subworkflows"]
                     }
                 }

diff --git a/subworkflows/gallvp/gxf_fasta_agat_spaddintrons_spextractsequences/main.nf b/subworkflows/gallvp/gxf_fasta_agat_spaddintrons_spextractsequences/main.nf
@@ -30,9 +30,9 @@ workflow GXF_FASTA_AGAT_SPADDINTRONS_SPEXTRACTSEQUENCES {
                                         | collectFile
                                         | map { gxf -> [ gxf.baseName.replace('.nointrons', ''), gxf ] }
                                         | join(
-                                            ch_gxf.map { meta, gxf -> [ meta.id, meta ] }
+                                            ch_gxf.map { meta, _gxf -> [ meta.id, meta ] }
                                         )
-                                        | map { id, gxf, meta -> [ meta, gxf ] }
+                                        | map { _id, gxf, meta -> [ meta, gxf ] }
 
     // MODULE: AGAT_SPADDINTRONS
     AGAT_SPADDINTRONS ( ch_gxf_purged, [] )
@@ -46,11 +46,11 @@ workflow GXF_FASTA_AGAT_SPADDINTRONS_SPEXTRACTSEQUENCES {
                                         | join(
                                             ch_fasta.map { meta2, fasta -> [ meta2.id, fasta ] }
                                         )
-                                        | map { id, meta, gff3, fasta -> [ meta, gff3, fasta ] }
+                                        | map { _id, meta, gff3, fasta -> [ meta, gff3, fasta ] }
 
     AGAT_SPEXTRACTSEQUENCES(
-        ch_gxf_fasta.map { meta, gff3, fasta -> [ meta, gff3 ] },
-        ch_gxf_fasta.map { meta, gff3, fasta -> fasta },
+        ch_gxf_fasta.map { meta , gff3  , _fasta    -> [ meta, gff3 ] },
+        ch_gxf_fasta.map { _meta, _gff3 , fasta     -> fasta },
         [] // config
     )
 
@@ -61,16 +61,20 @@ workflow GXF_FASTA_AGAT_SPADDINTRONS_SPEXTRACTSEQUENCES {
     ch_splice_motifs                    = ch_intron_sequences
                                         | map { meta, fasta ->
                                             def splice_motifs = fasta.splitFasta ( record: [id: true, seqString: true] )
-                                                .collect { el -> [ el.id, "${el.seqString[0..1]}${el.seqString[-2..-1]}" ].join('\t') }
+                                                .collect { el ->
+                                                    el.seqString.size() < 4
+                                                    ? [ el.id, '-' ].join('\t')
+                                                    : [ el.id, "${el.seqString[0..1]}${el.seqString[-2..-1]}" ].join('\t')
+                                                }
 
                                             [ "${meta.id}.motifs.tsv", splice_motifs.join('\n') ]
                                         }
                                         | collectFile
                                         | map { tsv -> [ tsv.baseName.replace('.motifs', ''), tsv ] }
                                         | join(
-                                            ch_gxf_purged.map { meta, gxf -> [ meta.id, meta ] }
+                                            ch_gxf_purged.map { meta, _gxf -> [ meta.id, meta ] }
                                         )
-                                        | map { id, tsv, meta -> [ meta, tsv ] }
+                                        | map { _id, tsv, meta -> [ meta, tsv ] }
 
     // collectFile: Mark gff3
     ch_marked_gff3                      = ch_introns_gff
@@ -106,9 +110,9 @@ workflow GXF_FASTA_AGAT_SPADDINTRONS_SPEXTRACTSEQUENCES {
                                         | collectFile
                                         | map { gff3 -> [ gff3.baseName.replace('.marked', ''), gff3 ] }
                                         | join(
-                                            ch_gxf_purged.map { meta, gxf -> [ meta.id, meta ] }
+                                            ch_gxf_purged.map { meta, _gxf -> [ meta.id, meta ] }
                                         )
-                                        | map { id, gff3, meta -> [ meta, gff3 ] }
+                                        | map { _id, gff3, meta -> [ meta, gff3 ] }
 
     emit:
     motifs_tsv                          = ch_splice_motifs  // channel: [ val(meta), tsv ]

diff --git a/subworkflows/local/tests/gxf_fasta_agat_spaddintrons_spextractsequences/main.nf.test b/subworkflows/local/tests/gxf_fasta_agat_spaddintrons_spextractsequences/main.nf.test
@@ -0,0 +1,39 @@
+nextflow_workflow {
+
+    name "Test Subworkflow GXF_FASTA_AGAT_SPADDINTRONS_SPEXTRACTSEQUENCES"
+    script "../../../gallvp/gxf_fasta_agat_spaddintrons_spextractsequences/main.nf"
+    workflow "GXF_FASTA_AGAT_SPADDINTRONS_SPEXTRACTSEQUENCES"
+    config './nextflow.config'
+
+    tag "subworkflows"
+    tag "subworkflows_gallvp"
+    tag "subworkflows/gxf_fasta_agat_spaddintrons_spextractsequences"
+    tag "modules/nf-core/gunzip"
+    tag "agat/spextractsequences"
+    tag "agat/spaddintrons"
+
+    test("scaffold_4 - fasta - gff3") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of ( [
+                    [ id:'test' ],
+                    file("$baseDir" + '/subworkflows/local/tests/gxf_fasta_agat_spaddintrons_spextractsequences/testdata/scaffold_4.gff', checkIfExists: true)
+                ] )
+                input[1] = Channel.of ( [
+                    [ id:'test' ],
+                    file("$baseDir" + '/subworkflows/local/tests/gxf_fasta_agat_spaddintrons_spextractsequences/testdata/scaffold_4.fasta', checkIfExists: true)
+                ] )
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(workflow.out).match()}
+            )
+        }
+    }
+}
diff --git a/subworkflows/local/tests/gxf_fasta_agat_spaddintrons_spextractsequences/main.nf.test.snap b/subworkflows/local/tests/gxf_fasta_agat_spaddintrons_spextractsequences/main.nf.test.snap
@@ -0,0 +1,53 @@
+{
+    "scaffold_4 - fasta - gff3": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.motifs.tsv:md5,b0a99a7a7bf598bbf1e25ca3690567c6"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.marked.gff3:md5,f464b2e0dc24238e69c3e9e1419c1b3b"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,1befbe41bc7abbf49767b8dc68877bc7",
+                    "versions.yml:md5,65042e008b2466984150cb219a05291c"
+                ],
+                "marked_gff3": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.marked.gff3:md5,f464b2e0dc24238e69c3e9e1419c1b3b"
+                    ]
+                ],
+                "motifs_tsv": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.motifs.tsv:md5,b0a99a7a7bf598bbf1e25ca3690567c6"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,1befbe41bc7abbf49767b8dc68877bc7",
+                    "versions.yml:md5,65042e008b2466984150cb219a05291c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2024-12-20T12:00:17.861955"
+    }
+}
diff --git a/subworkflows/local/tests/gxf_fasta_agat_spaddintrons_spextractsequences/nextflow.config b/subworkflows/local/tests/gxf_fasta_agat_spaddintrons_spextractsequences/nextflow.config
@@ -0,0 +1,6 @@
+process {
+
+    withName: AGAT_SPEXTRACTSEQUENCES {
+        ext.args = '-t intron'
+    }
+}
diff --git a/...s/local/tests/gxf_fasta_agat_spaddintrons_spextractsequences/testdata/README.md b/...s/local/tests/gxf_fasta_agat_spaddintrons_spextractsequences/testdata/README.md
@@ -0,0 +1 @@
+This test data is from an _Actinidia_ genome. To minify the data, the gene coordinates have been shifted back by 630000. The Gff file has a single bp intron which is not flagged by `agat_sp_flag_short_introns.pl` from version `quay.io/biocontainers/agat:1.4.1--pl5321hdfd78af_0`. See issue <https://github.com/NBISweden/AGAT/issues/516> for further details.
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		This test data is from an _Actinidia_ genome. To minify the data, the gene coordinates have been shifted back by 630000. The Gff file has a single bp intron which is not flagged by `agat_sp_flag_short_introns.pl` from version `quay.io/biocontainers/agat:1.4.1--pl5321hdfd78af_0`. See issue <https://github.com/NBISweden/AGAT/issues/516> for further details.