diff --git a/tests/.nftignore b/tests/.nftignore index ec58fdc..e5170cd 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -1,3 +1,6 @@ +gatk4/*.{vcf.gz,vcf.gz.tbi} +gatk4/test/* +gatk4/test/** multiqc/multiqc_data/multiqc.log multiqc/multiqc_data/multiqc_data.json multiqc/multiqc_data/multiqc_general_stats.txt diff --git a/tests/mutect2.nf.test b/tests/mutect2.nf.test index 4e63875..61a62f6 100644 --- a/tests/mutect2.nf.test +++ b/tests/mutect2.nf.test @@ -16,7 +16,7 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}', 'gatk4/test/**/*']) // stable_path: All files in ${params.outdir}/ with stable content def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( diff --git a/tests/mutect2.nf.test.snap b/tests/mutect2.nf.test.snap index c9c5f88..dd8e352 100644 --- a/tests/mutect2.nf.test.snap +++ b/tests/mutect2.nf.test.snap @@ -30,167 +30,8 @@ "gatk4/test/__tiledb_workspace.tdb", "gatk4/test/callset.json", "gatk4/test/chr21$2$23354000", - "gatk4/test/chr21$2$23354000/.__consolidation_lock", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/AD.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/AD_var.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/AF.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/AF_var.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/ALT.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/ALT_var.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/AS_SB_TABLE.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/AS_SB_TABLE_var.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/AS_UNIQ_ALT_READ_COUNT.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/AS_UNIQ_ALT_READ_COUNT_var.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/CONTQ.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/DP.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/DP_FORMAT.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/ECNT.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/END.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/F1R2.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/F1R2_var.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/F2R1.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/F2R1_var.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/FAD.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/FAD_var.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/FILTER.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/FILTER_var.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/GERMQ.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/GQ.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/GT.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/GT_var.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/ID.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/ID_var.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/MBQ.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/MBQ_var.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/MFRL.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/MFRL_var.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/MMQ.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/MMQ_var.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/MPOS.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/MPOS_var.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/NALOD.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/NALOD_var.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/NCount.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/NLOD.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/NLOD_var.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/OCM.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/PGT.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/PGT_var.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/PID.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/PID_var.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/PL.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/PL_var.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/PON.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/POPAF.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/POPAF_var.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/PS.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/QUAL.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/REF.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/REF_var.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/ROQ.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/RPA.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/RPA_var.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/RU.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/RU_var.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/SB.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/SEQQ.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/STR.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/STRANDQ.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/STRQ.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/TLOD.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/TLOD_var.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/__book_keeping.tdb.gz", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/__coords.tdb", - "gatk4/test/chr21$2$23354000/__6d81792d-3faf-4b0b-a83f-3970900ce0c3140170370176704_1728638204392/__tiledb_fragment.tdb", - "gatk4/test/chr21$2$23354000/__array_schema.tdb", - "gatk4/test/chr21$2$23354000/genomicsdb_meta_dir", - "gatk4/test/chr21$2$23354000/genomicsdb_meta_dir/genomicsdb_column_bounds.json", - "gatk4/test/chr21$2$23354000/genomicsdb_meta_dir/genomicsdb_meta_2fa49a66-d70b-472f-b420-a0eca92715ab.json", "gatk4/test/chr21$24132500$24910998", - "gatk4/test/chr21$24132500$24910998/.__consolidation_lock", - "gatk4/test/chr21$24132500$24910998/__array_schema.tdb", - "gatk4/test/chr21$24132500$24910998/genomicsdb_meta_dir", - "gatk4/test/chr21$24132500$24910998/genomicsdb_meta_dir/genomicsdb_column_bounds.json", - "gatk4/test/chr21$24132500$24910998/genomicsdb_meta_dir/genomicsdb_meta_d23be0e8-765f-4373-887f-74a701b5d7c1.json", "gatk4/test/chr21$25689498$46709983", - "gatk4/test/chr21$25689498$46709983/.__consolidation_lock", - "gatk4/test/chr21$25689498$46709983/__8ec66c56-124d-4e2a-8830-5b3e08932d1b140170370176704_1728638204900", - "gatk4/test/chr21$25689498$46709983/__8ec66c56-124d-4e2a-8830-5b3e08932d1b140170370176704_1728638204900/AD.tdb", - "gatk4/test/chr21$25689498$46709983/__8ec66c56-124d-4e2a-8830-5b3e08932d1b140170370176704_1728638204900/AD_var.tdb", - "gatk4/test/chr21$25689498$46709983/__8ec66c56-124d-4e2a-8830-5b3e08932d1b140170370176704_1728638204900/AF.tdb", - "gatk4/test/chr21$25689498$46709983/__8ec66c56-124d-4e2a-8830-5b3e08932d1b140170370176704_1728638204900/AF_var.tdb", - "gatk4/test/chr21$25689498$46709983/__8ec66c56-124d-4e2a-8830-5b3e08932d1b140170370176704_1728638204900/ALT.tdb", - "gatk4/test/chr21$25689498$46709983/__8ec66c56-124d-4e2a-8830-5b3e08932d1b140170370176704_1728638204900/ALT_var.tdb", - "gatk4/test/chr21$25689498$46709983/__8ec66c56-124d-4e2a-8830-5b3e08932d1b140170370176704_1728638204900/AS_SB_TABLE.tdb", - "gatk4/test/chr21$25689498$46709983/__8ec66c56-124d-4e2a-8830-5b3e08932d1b140170370176704_1728638204900/AS_SB_TABLE_var.tdb", - "gatk4/test/chr21$25689498$46709983/__8ec66c56-124d-4e2a-8830-5b3e08932d1b140170370176704_1728638204900/AS_UNIQ_ALT_READ_COUNT.tdb", - "gatk4/test/chr21$25689498$46709983/__8ec66c56-124d-4e2a-8830-5b3e08932d1b140170370176704_1728638204900/AS_UNIQ_ALT_READ_COUNT_var.tdb", - "gatk4/test/chr21$25689498$46709983/__8ec66c56-124d-4e2a-8830-5b3e08932d1b140170370176704_1728638204900/CONTQ.tdb", - "gatk4/test/chr21$25689498$46709983/__8ec66c56-124d-4e2a-8830-5b3e08932d1b140170370176704_1728638204900/DP.tdb", - "gatk4/test/chr21$25689498$46709983/__8ec66c56-124d-4e2a-8830-5b3e08932d1b140170370176704_1728638204900/DP_FORMAT.tdb", - 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"GERMQ.tdb:md5,17ee8dd46c227a6c999de499e46327ca", - "GQ.tdb:md5,17ee8dd46c227a6c999de499e46327ca", - "GT.tdb:md5,8968e4582af714b67f8dceb07e8991ca", - "GT_var.tdb:md5,4ecf12b42be9b68badebb1c690c0809e", - "ID.tdb:md5,59eec9e1c659b9a126a5b23271d964a5", - "ID_var.tdb:md5,d41d8cd98f00b204e9800998ecf8427e", - "MBQ.tdb:md5,d520808c95b3d0ee9847e7923ebaaa6c", - "MBQ_var.tdb:md5,eb85c62a51886544118df9dfaa5045c3", - "MFRL.tdb:md5,d520808c95b3d0ee9847e7923ebaaa6c", - "MFRL_var.tdb:md5,c1bf3db7ef8dd15836dec497574d778f", - "MMQ.tdb:md5,d520808c95b3d0ee9847e7923ebaaa6c", - "MMQ_var.tdb:md5,8f266ac111f437dd74eaeb80f054d3ed", - "MPOS.tdb:md5,89f24fce2fe1ae768a4f87f6c5644dc4", - "MPOS_var.tdb:md5,d330fe7e1921b80da418689d1dbac682", - "NALOD.tdb:md5,59eec9e1c659b9a126a5b23271d964a5", - "NALOD_var.tdb:md5,d41d8cd98f00b204e9800998ecf8427e", - "NCount.tdb:md5,17ee8dd46c227a6c999de499e46327ca", - "NLOD.tdb:md5,59eec9e1c659b9a126a5b23271d964a5", - "NLOD_var.tdb:md5,d41d8cd98f00b204e9800998ecf8427e", - "OCM.tdb:md5,17ee8dd46c227a6c999de499e46327ca", - "PGT.tdb:md5,1c9fcbab7490fde6bf8f1c6c98dd6fe1", - "PGT_var.tdb:md5,b23eb2be3856f3c8e98032041a19d135", - "PID.tdb:md5,9f7589ebbef726f2d4bb518ed2fce1fe", - "PID_var.tdb:md5,47bacc6fe0f1b318747dc56ebb4d6e3e", - "PL.tdb:md5,59eec9e1c659b9a126a5b23271d964a5", - "PL_var.tdb:md5,d41d8cd98f00b204e9800998ecf8427e", - "PON.tdb:md5,7915e8a208af602b1f603ad88ca0613b", - "POPAF.tdb:md5,89f24fce2fe1ae768a4f87f6c5644dc4", - "POPAF_var.tdb:md5,23f91f0f95fe5fce57c2b3ae5027f196", - "PS.tdb:md5,e6ccd6a8ff224f0780b88a533489cefc", - "QUAL.tdb:md5,bdc87df1ac52acb83558b0f32fa08879", - "REF.tdb:md5,c4dedc9bd820cce6afb9558bfb5217a4", - "REF_var.tdb:md5,963bf8052cc72f58a4e9247d476660be", - "ROQ.tdb:md5,bdc87df1ac52acb83558b0f32fa08879", - "RPA.tdb:md5,0b5b1b1ec7a46a2c2ac451de952440f9", - "RPA_var.tdb:md5,0e3ab36d395525c86e4122a613ca2e9c", - "RU.tdb:md5,80e670397dc61b8d4f65dd148758cbcf", - "RU_var.tdb:md5,e856786f8d55b52e3406d8f4f31de900", - "SB.tdb:md5,f13d419074793d70c6c66305d56235e6", - "SEQQ.tdb:md5,17ee8dd46c227a6c999de499e46327ca", - "STR.tdb:md5,da41a617915015415f8b8a5499fa18b0", - "STRANDQ.tdb:md5,17ee8dd46c227a6c999de499e46327ca", - "STRQ.tdb:md5,17ee8dd46c227a6c999de499e46327ca", - "TLOD.tdb:md5,89f24fce2fe1ae768a4f87f6c5644dc4", - "TLOD_var.tdb:md5,0f73e670bb2aca83b861d83cd908ae3a", - "__book_keeping.tdb.gz:md5,7f2bd5c335cf117ff7c0bf13d38f68e3", - "__coords.tdb:md5,78c8fb3250f31495f89a96047ff1f8ac", - "__tiledb_fragment.tdb:md5,d41d8cd98f00b204e9800998ecf8427e", - "__array_schema.tdb:md5,f623aa15e93722a5ab35423bc60adb74", - "genomicsdb_column_bounds.json:md5,41f164432abe9a6d6c559d90e9a7cabc", - "genomicsdb_meta_fbfd9118-39ee-4677-b032-6b3d1bd1112d.json:md5,d65998127173145d94d773e3350881e5", - "vcfheader.vcf:md5,3eed5f181c05191fe5f43cfb64a255f3", - "vidmap.json:md5,bdd4857ec33a3a7a01211bfd21037a7a", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], @@ -378,6 +55,6 @@ "nf-test": "0.9.0", "nextflow": "24.09.0" }, - "timestamp": "2024-10-11T11:16:59.841003" + "timestamp": "2024-10-11T12:02:22.796491" } } \ No newline at end of file