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Fix test_build
1 parent eac2b9b commit eaa140d

3 files changed

Lines changed: 21 additions & 52 deletions

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‎tests/.nftignore‎

Lines changed: 19 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -13,25 +13,25 @@ references/salmon/salmon/pre_indexing.log
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references/salmon/salmon/ref_indexing.log
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references/salmon/salmon/seq.bin
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references/star/Log.out
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references/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/
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references/starfusion/ctat_genome_lib_build_dir/PFAM.domtblout.dat.gz
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references/starfusion/ctat_genome_lib_build_dir/blast_pairs.dat.gz
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references/starfusion/ctat_genome_lib_build_dir/blast_pairs.idx
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references/starfusion/ctat_genome_lib_build_dir/fusion_annot_lib.idx
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references/starfusion/ctat_genome_lib_build_dir/pfam_domains.dbm
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references/starfusion/ctat_genome_lib_build_dir/ref_annot.cdna.fa
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references/starfusion/ctat_genome_lib_build_dir/ref_annot.cdna.fa.idx
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references/starfusion/ctat_genome_lib_build_dir/ref_annot.cds
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references/starfusion/ctat_genome_lib_build_dir/ref_annot.cdsplus.fa
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references/starfusion/ctat_genome_lib_build_dir/ref_annot.cdsplus.fa.idx
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references/starfusion/ctat_genome_lib_build_dir/ref_annot.gtf.gene_spans
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references/starfusion/ctat_genome_lib_build_dir/ref_annot.pep
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references/starfusion/ctat_genome_lib_build_dir/ref_annot.prot_info.dbm
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references/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.nin
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references/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.njs
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references/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/Log.out
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references/starfusion/ctat_genome_lib_build_dir/trans.blast.align_coords.align_coords.dbm
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references/starfusion/*_genome_lib_build_dir/ref_genome.fa.star.idx/
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references/starfusion/*_genome_lib_build_dir/PFAM.domtblout.dat.gz
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references/starfusion/*_genome_lib_build_dir/blast_pairs.dat.gz
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references/starfusion/*_genome_lib_build_dir/blast_pairs.idx
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references/starfusion/*_genome_lib_build_dir/fusion_annot_lib.idx
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references/starfusion/*_genome_lib_build_dir/pfam_domains.dbm
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references/starfusion/*_genome_lib_build_dir/ref_annot.cdna.fa
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references/starfusion/*_genome_lib_build_dir/ref_annot.cdna.fa.idx
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references/starfusion/*_genome_lib_build_dir/ref_annot.cds
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references/starfusion/*_genome_lib_build_dir/ref_annot.cdsplus.fa
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references/starfusion/*_genome_lib_build_dir/ref_annot.cdsplus.fa.idx
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references/starfusion/*_genome_lib_build_dir/ref_annot.gtf.gene_spans
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references/starfusion/*_genome_lib_build_dir/ref_annot.pep
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references/starfusion/*_genome_lib_build_dir/ref_annot.prot_info.dbm
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references/starfusion/*_genome_lib_build_dir/ref_genome.fa.nin
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references/starfusion/*_genome_lib_build_dir/ref_genome.fa.njs
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references/starfusion/*_genome_lib_build_dir/ref_genome.fa.star.idx/Log.out
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references/starfusion/*_genome_lib_build_dir/trans.blast.align_coords.align_coords.dbm
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references/star/genomeParameters.txt
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references/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/genomeParameters.txt
35+
references/starfusion/*_genome_lib_build_dir/ref_genome.fa.star.idx/genomeParameters.txt
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references/fusion_report_db/mitelman.db
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references/fusion_report_db/fusiongdb2.db

‎tests/test_build.nf.test‎

Lines changed: 1 addition & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -11,20 +11,7 @@ nextflow_pipeline {
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when {
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params {
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config_profile_name = 'Test build references profile'
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config_profile_description = 'Minimal test dataset to check pipeline function'
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// Input data
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references_only = true
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input = "${projectDir}/tests/csv/fastq.csv"
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no_cosmic = true
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tools = "arriba,starfusion,fusionreport,salmon,fusioninspector"
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fasta = 'https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/master/minigenome.fa'
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gtf = 'https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/master/minigenome.gtf'
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fusion_annot_lib = 'https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/master/CTAT_HumanFusionLib.mini.dat.gz'
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species = 'homo_sapiens'
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dfam_version = 3.4
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outdir = "$outputDir"
14+
outdir = "$outputDir"
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}
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}
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‎tests/test_build.nf.test.snap‎

Lines changed: 1 addition & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -222,7 +222,6 @@
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"sjdbList.out.tab:md5,5d78dd49d5db24ca2c056b7ebe5c2059",
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"transcriptInfo.tab:md5,b758c0ccaddcf0453bab5905b3cec4a2",
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"AnnotFilterRule.pm:md5,f94966013cd0df9624a6dda0b75fefa0",
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"PFAM.domtblout.dat.gz:md5,54f921cd70902acb83ff5b14aebd604a",
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"_fusion_annot_lib.idx.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
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"_prot_info_db.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
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"annotfiltrule_cp.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -246,35 +245,20 @@
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"trans.blast.dat.cp.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
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"trans.blast.dat.index.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
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"validate_ctat_genome_lib.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
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"blast_pairs.dat.gz:md5,ebc8f093656956b218544cc3d6c714e6",
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"blast_pairs.idx:md5,bc62513f72fe691d044b40450a2f759d",
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"fusion_annot_lib.gz:md5,23d82a5da81f91ca4e1ecd6481992a12",
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"fusion_annot_lib.idx:md5,6d5f914c3ef873129864704ace7b6023",
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"pfam_domains.dbm:md5,fa101bda7d051bcd3f5943ed241d512f",
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"ref_annot.cdna.fa:md5,dae68f2c6b2b910fc7fba7be851ff8aa",
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"ref_annot.cdna.fa.idx:md5,49a67627a7738284db86cf5315f4581a",
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"ref_annot.cds:md5,c194a1e03db28d0e6e9c2fda8b57b2d3",
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"ref_annot.cdsplus.fa:md5,1be8e201b908d0d1e3b67588a295e092",
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"ref_annot.cdsplus.fa.idx:md5,b75b353e4fe32628d243f1bb6cc293d6",
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"ref_annot.gtf:md5,5ce8afe99ef3940a877a04caeacf9181",
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"ref_annot.gtf.gene_spans:md5,5b3b025a5ac4fe18273e591227b807c6",
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"ref_annot.gtf.mini.sortu:md5,1d29ccecdbb7b40a99c84a02d6c2c1be",
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"ref_annot.gtf.mm2.splice.bed:md5,340585ea1843bf06bf555575ddecf28c",
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"ref_annot.pep:md5,2a5ba213d81f6b0215a9a5b56ee5243a",
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"ref_annot.prot_info.dbm:md5,353f077ac7d0d9aea47aac057e706953",
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"ref_genome.fa:md5,ad699c56ed38566c7d3e9579486b1706",
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"ref_genome.fa.fai:md5,e3f74a27219b33ae80fd5de5cbeaf32b",
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"ref_genome.fa.mm2:md5,ce50979ea284748eb9f84ae88cfd930e",
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"ref_genome.fa.ndb:md5,6ea574753b557610f62f6e4ab79e19f5",
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"ref_genome.fa.nhr:md5,50f28dae71683c4394bfaf94a1ef4392",
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"ref_genome.fa.nin:md5,db10a8b187c7cdb0c36a93424d15f07c",
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"ref_genome.fa.njs:md5,60536e1c49690c3d8bb76370219b08e1",
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"ref_genome.fa.not:md5,1e53e9d08f1d23af0299cfa87478a7bb",
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"ref_genome.fa.nsq:md5,d2361e7871ce4cf51181c112a48f191b",
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"ref_genome.fa.ntf:md5,de1250813f0c7affc6d12dac9d0fb6bb",
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"ref_genome.fa.nto:md5,33cdeccccebe80329f1fdbee7f5874cb",
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"Genome:md5,9e3efdd0901cabb5a2d589664a63b372",
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"Log.out:md5,43ee8d90b889391994d21a684dd85104",
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"SA:md5,7dd9083264be9c6a2194d990bc10d237",
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"SAindex:md5,ac4711df685109e04356db9e9cb9fb7f",
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"build.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -285,13 +269,11 @@
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"exonGeTrInfo.tab:md5,3c35618d07a8e35a0f9108699fcdda42",
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"exonInfo.tab:md5,bcbb3f32fa31fe504cc737f337ad341c",
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"geneInfo.tab:md5,db5db4b6e003904e9908fce7c05f0125",
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"genomeParameters.txt:md5,33d7b726ef158db446859f89c8c3525f",
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"sjdbInfo.txt:md5,e4cc1bbf8bd687cfc3d7c2c702e6def7",
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"sjdbList.fromGTF.out.tab:md5,8f3e8604b00d4067e4eb80aa476a8113",
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"sjdbList.out.tab:md5,5d78dd49d5db24ca2c056b7ebe5c2059",
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"transcriptInfo.tab:md5,b758c0ccaddcf0453bab5905b3cec4a2",
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"trans.blast.align_coords.align_coords.dat:md5,9f6b7a75aea03a9671190be25ecdd4c2",
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"trans.blast.align_coords.align_coords.dbm:md5,edc8b34f6f5057414f947950efa48175",
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"trans.blast.dat.gz:md5,85ba5ea96c566f751ad83a3e4b8ab128"
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]
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],
@@ -301,4 +283,4 @@
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},
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"timestamp": "2025-07-17T18:35:50.278173296"
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}
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}
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}

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