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Plant-Food-Research-Open · Dec 11, 2024 · f980772 · f980772
1 parent 0f7784c
commit f980772
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Showing 10 changed files with 17 additions and 318 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -240,8 +240,8 @@ process { // SUBWORKFLOW: GFF_MERGE_CLEANUP
         ext.prefix = { "${meta.id}.liftoff.braker" }
     }
 
-    withName: '.*:GFF_MERGE_CLEANUP:AGAT_SPFILTERBYORFSIZE' {
-        ext.args = params.filter_genes_by_aa_length ? "-s ${params.filter_genes_by_aa_length}" : ''
+    withName: '.*:GFF_MERGE_CLEANUP:FILTER_BY_ORF_SIZE' {
+        ext.args = params.filter_genes_by_aa_length ? "--no-pseudo --keep-genes -C -l ${params.filter_genes_by_aa_length * 3}" : ''
     }
 
     withName: '.*:GFF_MERGE_CLEANUP:GT_GFF3' {

diff --git a/modules.json b/modules.json
@@ -15,11 +15,6 @@
                         "git_sha": "a8939d36280e7d9037c7cf164eeede19e46546a4",
                         "installed_by": ["gxf_fasta_agat_spaddintrons_spextractsequences"]
                     },
-                    "agat/spfilterbyorfsize": {
-                        "branch": "main",
-                        "git_sha": "a0054cdffbd84f002fb6582b28575b699e01098e",
-                        "installed_by": ["modules"]
-                    },
                     "agat/spflagshortintrons": {
                         "branch": "main",
                         "git_sha": "d8f08700c82a3bd14811a3dfe7e7d63838130693",

diff --git a/modules/gallvp/agat/spfilterbyorfsize/environment.yml b/modules/gallvp/agat/spfilterbyorfsize/environment.yml
diff --git a/modules/gallvp/agat/spfilterbyorfsize/main.nf b/modules/gallvp/agat/spfilterbyorfsize/main.nf
diff --git a/modules/gallvp/agat/spfilterbyorfsize/meta.yml b/modules/gallvp/agat/spfilterbyorfsize/meta.yml
diff --git a/modules/gallvp/agat/spfilterbyorfsize/tests/main.nf.test b/modules/gallvp/agat/spfilterbyorfsize/tests/main.nf.test
diff --git a/modules/gallvp/agat/spfilterbyorfsize/tests/main.nf.test.snap b/modules/gallvp/agat/spfilterbyorfsize/tests/main.nf.test.snap
diff --git a/subworkflows/local/gff_merge_cleanup.nf b/subworkflows/local/gff_merge_cleanup.nf
@@ -1,6 +1,6 @@
 include { AGAT_SPMERGEANNOTATIONS               } from '../../modules/nf-core/agat/spmergeannotations/main'
 include { GT_GFF3                               } from '../../modules/nf-core/gt/gff3/main'
-include { AGAT_SPFILTERBYORFSIZE                } from '../../modules/gallvp/agat/spfilterbyorfsize/main'
+include { GFFREAD as FILTER_BY_ORF_SIZE         } from '../../modules/nf-core/gffread/main'
 include { AGAT_CONVERTSPGXF2GXF                 } from '../../modules/nf-core/agat/convertspgxf2gxf/main'
 
 workflow GFF_MERGE_CLEANUP {
@@ -31,18 +31,18 @@ workflow GFF_MERGE_CLEANUP {
                                 | mix ( ch_gff_branch.braker_only.map { meta, braker_gff, _liftoff_gff -> [ meta, braker_gff ] } )
     ch_versions                 = ch_versions.mix(AGAT_SPMERGEANNOTATIONS.out.versions.first())
 
-    // MODULE: AGAT_SPFILTERBYORFSIZE
+    // MODULE: GFFREAD as FILTER_BY_ORF_SIZE
     ch_filter_input             = ch_merged_gff
                                 | branch {
                                     filter: val_filter_by_aa_length != null
                                     pass: val_filter_by_aa_length == null
                                 }
 
-    AGAT_SPFILTERBYORFSIZE ( ch_filter_input.filter, [] )
+    FILTER_BY_ORF_SIZE ( ch_filter_input.filter, [] )
 
-    ch_filtered_gff             = AGAT_SPFILTERBYORFSIZE.out.passed_gff
+    ch_filtered_gff             = FILTER_BY_ORF_SIZE.out.gffread_gff
                                 | mix ( ch_filter_input.pass )
-    ch_versions                 = ch_versions.mix(AGAT_SPFILTERBYORFSIZE.out.versions.first())
+    ch_versions                 = ch_versions.mix(FILTER_BY_ORF_SIZE.out.versions.first())
 
     // MODULE: GT_GFF3
     GT_GFF3 ( ch_filtered_gff )

diff --git a/tests/minimal/main.nf.test.snap b/tests/minimal/main.nf.test.snap
@@ -16,9 +16,6 @@
                     "AGAT_SPEXTRACTSEQUENCES": {
                         "agat": "v1.4.0"
                     },
-                    "AGAT_SPFILTERBYORFSIZE": {
-                        "agat": "v1.4.1"
-                    },
                     "BRAKER3": {
                         "braker3": "3.0.8",
                         "augustus": "3.5.0",
@@ -40,6 +37,9 @@
                     "FASTAVALIDATOR": {
                         "py_fasta_validator": 0.6
                     },
+                    "FILTER_BY_ORF_SIZE": {
+                        "gffread": "0.12.7"
+                    },
                     "FINAL_GFF_CHECK": {
                         "genometools": "1.6.5"
                     },
@@ -70,9 +70,9 @@
                 "stable paths": [
                     "a_thaliana.cdna.fasta:md5,12b9bef973e488640aec8c04ba3882fe",
                     "a_thaliana.cds.fasta:md5,b81060419355a590560f92aec8536281",
-                    "a_thaliana.gt.gff3:md5,8ab16549095f605ff8715ac4a3de58ed",
+                    "a_thaliana.gt.gff3:md5,528459cf9596523bf66de99d24c37e20",
                     "a_thaliana.pep.fasta:md5,4994c0393ca0245a1c57966d846d101e",
-                    "a_thaliana.gff3:md5,d23d16cd86499d48a30ffb981ed27891",
+                    "a_thaliana.gff3:md5,30adac1b21d7aaed6ca7fb71ab33f32d",
                     "summary_stats.json:md5,007ba5cf2b7a2fd395a27d9458ca2d2e"
                 ],
                 "stable names": [
@@ -97,6 +97,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-12-11T06:36:01.956188"
+        "timestamp": "2024-12-11T21:49:09.751422"
     }
 }