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Added parameter filter_genes_by_aa_length #127
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3114adb
Added parameter filter_genes_by_aa_length
GallVp d694431
Updated snapshots
GallVp 0f7784c
Added test to verify that GFFREAD can filter mRNA by CDS length
GallVp f980772
Updated snapshots
GallVp ab3ae37
Updated README and snapshot
GallVp c65ebaa
Added 1 to filter_genes_by_aa_length to exclude stop codon from filte…
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,38 @@ | ||
nextflow_process { | ||
|
||
name "Test Process GFFREAD" | ||
script "../../../nf-core/gffread/main.nf" | ||
config "./nextflow.config" | ||
process "GFFREAD" | ||
|
||
tag "gffread" | ||
tag "modules_nfcore" | ||
tag "modules" | ||
|
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test("filter by length") { | ||
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when { | ||
process { | ||
""" | ||
input[0] = [ | ||
[id: 'test'], | ||
file("$baseDir" + '/modules/local/tests/gffread/testdata/t.gff', checkIfExists: true) | ||
] | ||
input[1] = [] | ||
""" | ||
} | ||
} | ||
|
||
then { | ||
assertAll ( | ||
{ assert process.success }, | ||
{ assert snapshot(process.out).match() }, | ||
{ assert file(process.out.gffread_gff[0][1]).text.contains('gene19851') }, | ||
{ assert file(process.out.gffread_gff[0][1]).text.contains('gene19851.t1') }, | ||
{ assert ! file(process.out.gffread_gff[0][1]).text.contains('gene19851.t2') } // This is the only transcript which is being knocked out | ||
) | ||
} | ||
|
||
} | ||
|
||
} |
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,47 @@ | ||
{ | ||
"filter by length": { | ||
"content": [ | ||
{ | ||
"0": [ | ||
|
||
], | ||
"1": [ | ||
[ | ||
{ | ||
"id": "test" | ||
}, | ||
"test.gff3:md5,59a7d6ff7123589ef2b90b20043a347c" | ||
] | ||
], | ||
"2": [ | ||
|
||
], | ||
"3": [ | ||
"versions.yml:md5,05f671c6c6e530acedad0af0a5948dbd" | ||
], | ||
"gffread_fasta": [ | ||
|
||
], | ||
"gffread_gff": [ | ||
[ | ||
{ | ||
"id": "test" | ||
}, | ||
"test.gff3:md5,59a7d6ff7123589ef2b90b20043a347c" | ||
] | ||
], | ||
"gtf": [ | ||
|
||
], | ||
"versions": [ | ||
"versions.yml:md5,05f671c6c6e530acedad0af0a5948dbd" | ||
] | ||
} | ||
], | ||
"meta": { | ||
"nf-test": "0.9.2", | ||
"nextflow": "24.04.4" | ||
}, | ||
"timestamp": "2024-12-11T21:11:59.953464" | ||
} | ||
} |
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,5 @@ | ||
process { | ||
withName: GFFREAD { | ||
ext.args = '--no-pseudo --keep-genes -C -l 72' | ||
} | ||
} |
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,47 @@ | ||
##gff-version 3 | ||
### | ||
chr23 AUGUSTUS gene 16515075 16516672 . - . ID=gene19849;description=Protein%20of%20unknown%20function%20%28DUF1635%29 | ||
chr23 AUGUSTUS mRNA 16515075 16516597 1 - . ID=gene19849.t1;Parent=gene19849;description=Protein%20of%20unknown%20function%20%28DUF1635%29 | ||
chr23 AUGUSTUS exon 16515075 16515794 . - . ID=gene19849.t1.exon1;Parent=gene19849.t1 | ||
chr23 AUGUSTUS CDS 16515075 16515794 1 - 0 ID=gene19849.t1.cds1;Parent=gene19849.t1 | ||
chr23 AUGUSTUS exon 16516562 16516597 . - . ID=gene19849.t1.exon2;Parent=gene19849.t1 | ||
chr23 AUGUSTUS CDS 16516562 16516597 1 - 0 ID=gene19849.t1.cds2;Parent=gene19849.t1 | ||
chr23 gmst mRNA 16515075 16516672 . - . ID=gene19849.t2;Parent=gene19849;description=Protein%20of%20unknown%20function%20%28DUF1635%29 | ||
chr23 gmst exon 16515075 16515794 50.2 - 0 ID=gene19849.t2.exon1;Parent=gene19849.t2 | ||
chr23 gmst CDS 16515075 16515794 50.2 - 0 ID=gene19849.t2.cds1;Parent=gene19849.t2 | ||
chr23 gmst exon 16516562 16516672 50.2 - 0 ID=gene19849.t2.exon2;Parent=gene19849.t2 | ||
chr23 gmst CDS 16516562 16516672 50.2 - 0 ID=gene19849.t2.cds2;Parent=gene19849.t2 | ||
### | ||
chr23 gmst gene 16530414 16531453 . - . ID=gene19850;description=Myb-like%20DNA-binding%20domain | ||
chr23 gmst mRNA 16530414 16531453 . - . ID=gene19850.t1;Parent=gene19850;description=Myb-like%20DNA-binding%20domain | ||
chr23 gmst exon 16530414 16531041 42.7 - 1 ID=gene19850.t1.exon1;Parent=gene19850.t1 | ||
chr23 gmst CDS 16530414 16531041 42.7 - 1 ID=gene19850.t1.cds1;Parent=gene19850.t1 | ||
chr23 gmst exon 16531197 16531453 42.7 - 0 ID=gene19850.t1.exon2;Parent=gene19850.t1 | ||
chr23 gmst CDS 16531197 16531453 42.7 - 0 ID=gene19850.t1.cds2;Parent=gene19850.t1 | ||
### | ||
chr23 AUGUSTUS gene 16530414 16531542 . - . ID=gene19851;description=Differing%20isoform%20descriptions | ||
chr23 AUGUSTUS mRNA 16530414 16531542 1 - . ID=gene19851.t1;Parent=gene19851;description=Myb-like%20DNA-binding%20domain | ||
chr23 AUGUSTUS exon 16530414 16530721 . - . ID=gene19851.t1.exon1;Parent=gene19851.t1 | ||
chr23 AUGUSTUS CDS 16530414 16530721 1 - 2 ID=gene19851.t1.cds1;Parent=gene19851.t1 | ||
chr23 AUGUSTUS exon 16530824 16531041 . - . ID=gene19851.t1.exon2;Parent=gene19851.t1 | ||
chr23 AUGUSTUS CDS 16530824 16531041 1 - 1 ID=gene19851.t1.cds2;Parent=gene19851.t1 | ||
chr23 AUGUSTUS exon 16531197 16531326 . - . ID=gene19851.t1.exon3;Parent=gene19851.t1 | ||
chr23 AUGUSTUS CDS 16531197 16531326 1 - 2 ID=gene19851.t1.cds3;Parent=gene19851.t1 | ||
chr23 AUGUSTUS exon 16531428 16531542 . - . ID=gene19851.t1.exon4;Parent=gene19851.t1 | ||
chr23 AUGUSTUS CDS 16531428 16531542 1 - 0 ID=gene19851.t1.cds4;Parent=gene19851.t1 | ||
chr23 GeneMark.hmm3 mRNA 16531514 16531542 . - . ID=gene19851.t2;Parent=gene19851;description=Hypothetical%20protein%20%7C%20no%20eggnog%20hit | ||
chr23 GeneMark.hmm3 exon 16531514 16531542 . - 0 ID=gene19851.t2.exon1;Parent=gene19851.t2 | ||
chr23 GeneMark.hmm3 CDS 16531514 16531542 . - 0 ID=gene19851.t2.cds1;Parent=gene19851.t2 | ||
### | ||
chr23 AUGUSTUS gene 16539401 16545431 . + . ID=gene19852;description=nuclease%20HARBI1 | ||
chr23 AUGUSTUS mRNA 16539401 16545431 1 + . ID=gene19852.t1;Parent=gene19852;description=nuclease%20HARBI1 | ||
chr23 AUGUSTUS exon 16539401 16539509 . + . ID=gene19852.t1.exon1;Parent=gene19852.t1 | ||
chr23 AUGUSTUS CDS 16539401 16539509 1 + 0 ID=gene19852.t1.cds1;Parent=gene19852.t1 | ||
chr23 AUGUSTUS exon 16544386 16545431 . + . ID=gene19852.t1.exon2;Parent=gene19852.t1 | ||
chr23 AUGUSTUS CDS 16544386 16545431 1 + 2 ID=gene19852.t1.cds2;Parent=gene19852.t1 | ||
### | ||
chr23 AUGUSTUS gene 16556338 16556796 . + . ID=gene19853;description=Zinc%20finger%20protein | ||
chr23 AUGUSTUS mRNA 16556338 16556796 1 + . ID=gene19853.t1;Parent=gene19853;description=Zinc%20finger%20protein | ||
chr23 AUGUSTUS exon 16556338 16556796 . + . ID=gene19853.t1.exon1;Parent=gene19853.t1 | ||
chr23 AUGUSTUS CDS 16556338 16556796 1 + 0 ID=gene19853.t1.cds1;Parent=gene19853.t1 | ||
### |
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@rosscrowhurst
params.filter_genes_by_aa_length is multiplied by 3 to get the CDS length for the
-l
parameter.