From 14a75fccc46a0339408edaef8025873bc60eb8dc Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 28 Nov 2024 10:10:28 +0100 Subject: [PATCH 1/2] fix gtf generation and dependencies --- main.nf | 2 +- tests/hisat2.nf.test.snap | 22 ++++++++++------ tests/kallisto.nf.test.snap | 38 +++++++++++++++------------ tests/rnaseq.nf.test.snap | 16 ++++++------ tests/rsem.nf.test.snap | 50 ++++++++++++++++++++---------------- tests/salmon.nf.test.snap | 36 +++++++++++++++----------- workflows/references/main.nf | 40 +++++++++++++++++------------ 7 files changed, 118 insertions(+), 86 deletions(-) diff --git a/main.nf b/main.nf index 20757ae..195eef3 100644 --- a/main.nf +++ b/main.nf @@ -195,7 +195,7 @@ workflow NFCORE_REFERENCES { faidx = REFERENCES.out.faidx fasta = REFERENCES.out.fasta germline_resource_vcf_tbi = REFERENCES.out.germline_resource_vcf_tbi - gffread = REFERENCES.out.gffread + gffread = REFERENCES.out.gff_gtf hisat2 = REFERENCES.out.hisat2 hisat2_splice_sites = REFERENCES.out.hisat2_splice_sites intervals = REFERENCES.out.intervals_bed diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index 4279ee4..ffe6ec9 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -46,14 +46,17 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "24.10.2" }, - "timestamp": "2024-11-27T10:40:01.494387729" + "timestamp": "2024-11-28T09:47:04.908315963" }, "Run with profile test for hisat2 | --input GRCh38_chr21.yml": { "content": [ - 3, + 4, { + "GFFREAD": { + "gffread": "0.12.7" + }, "HISAT2_BUILD": { "hisat2": "2.2.1" }, @@ -65,8 +68,10 @@ } }, [ + "gffread", + "gffread/GRCh38_chr21.gtf", "hisat2", - "hisat2/genes_chr21.splice_sites.txt", + "hisat2/GRCh38_chr21.splice_sites.txt", "hisat2/hisat2", "hisat2/hisat2/GRCh38_chr21.1.ht2", "hisat2/hisat2/GRCh38_chr21.2.ht2", @@ -88,7 +93,8 @@ "pipeline_info/nf_core_references_software_mqc_versions.yml" ], [ - "genes_chr21.splice_sites.txt:md5,291af43cd5b00eeb15277f90a76e77f8", + "GRCh38_chr21.gtf:md5,c552c0aee5f1becb1d3991d21e63a5c1", + "GRCh38_chr21.splice_sites.txt:md5,291af43cd5b00eeb15277f90a76e77f8", "GRCh38_chr21.1.ht2:md5,eb322cf410ecc616d7fe63cc1be2785b", "GRCh38_chr21.2.ht2:md5,46be3356d4c236ebd5d1e52e9eaf4e12", "GRCh38_chr21.3.ht2:md5,dbf5af96efd98d6b03f1e5d2baed848a", @@ -102,8 +108,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "24.10.2" }, - "timestamp": "2024-11-27T11:34:29.562342157" + "timestamp": "2024-11-28T09:41:32.891380441" } -} +} \ No newline at end of file diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index efca08c..3689f41 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -1,18 +1,29 @@ { - "Run with profile test for kallisto | --input assets/genomes/test/pipelines/default_extended.yml": { + "Run with profile test for kallisto | --input GRCh38_chr21.yml": { "content": [ - 2, + 4, { + "GFFREAD": { + "gffread": "0.12.7" + }, "KALLISTO_INDEX": { "kallisto": "0.51.1" }, + "MAKE_TRANSCRIPTS_FASTA": { + "rsem": "1.3.1", + "star": "2.7.10a" + }, "Workflow": { "nf-core/references": "v1.0dev" } }, [ + "gffread", + "gffread/GRCh38_chr21.gtf", "kallisto", "kallisto/kallisto", + "make", + "make/genome.transcripts.fa", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/multiqc.log", @@ -25,26 +36,24 @@ "pipeline_info/nf_core_references_software_mqc_versions.yml" ], [ + "GRCh38_chr21.gtf:md5,c552c0aee5f1becb1d3991d21e63a5c1", + "genome.transcripts.fa:md5,fd4e06fc250a19351a611a44861b9aea", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "24.10.2" }, - "timestamp": "2024-11-27T10:41:51.31627571" + "timestamp": "2024-11-28T09:49:13.419658545" }, - "Run with profile test for kallisto | --input GRCh38_chr21.yml": { + "Run with profile test for kallisto | --input assets/genomes/test/pipelines/default_extended.yml": { "content": [ - 3, + 2, { "KALLISTO_INDEX": { "kallisto": "0.51.1" }, - "MAKE_TRANSCRIPTS_FASTA": { - "rsem": "1.3.1", - "star": "2.7.10a" - }, "Workflow": { "nf-core/references": "v1.0dev" } @@ -52,8 +61,6 @@ [ "kallisto", "kallisto/kallisto", - "make", - "make/genome.transcripts.fa", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/multiqc.log", @@ -66,14 +73,13 @@ "pipeline_info/nf_core_references_software_mqc_versions.yml" ], [ - "genome.transcripts.fa:md5,fd4e06fc250a19351a611a44861b9aea", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "24.10.2" }, - "timestamp": "2024-11-27T10:42:14.938884156" + "timestamp": "2024-11-28T09:48:51.312930217" } -} +} \ No newline at end of file diff --git a/tests/rnaseq.nf.test.snap b/tests/rnaseq.nf.test.snap index 243e270..f09858c 100644 --- a/tests/rnaseq.nf.test.snap +++ b/tests/rnaseq.nf.test.snap @@ -99,20 +99,20 @@ "chrName.txt:md5,e99d7d1051eee43ceab5563c2d09fcee", "chrNameLength.txt:md5,c985a141685e8431ec27c782816cb744", "chrStart.txt:md5,6925b594ea2eeb964ba87cd6d42ab98f", - "exonGeTrInfo.tab:md5,ea42dd46e177f95a72a8f6a2925f7348", - "exonInfo.tab:md5,42a3ce2024f396b2298c0a84b07fb6e4", - "geneInfo.tab:md5,d0092fb1ea6fcdac270c4df788de70fb", - "genomeParameters.txt:md5,39e3bd7dc3a55e54b002b3e8921f5be8", + "exonGeTrInfo.tab:md5,a36b92eeceaaf921b9d19cd8e806a98e", + "exonInfo.tab:md5,bb892190d1ebdd59bf55652916121479", + "geneInfo.tab:md5,4303e97d841035b5c0fcc3686b2f5a36", + "genomeParameters.txt:md5,79725c6405e5c67a8cc75c0ee45f73c2", "sjdbInfo.txt:md5,12fb05dc7cea89735a0c19e1c0df61cb", - "sjdbList.fromGTF.out.tab:md5,5d9761b49920fb70a77d74e390d196b9", + "sjdbList.fromGTF.out.tab:md5,d9e4a184cde15a5ab282ff66e740a4a2", "sjdbList.out.tab:md5,766fbca932681f8666b3a9e5fb3640bd", - "transcriptInfo.tab:md5,21c1f470ffe3b55b23900e7b7eaec2f4" + "transcriptInfo.tab:md5,ad9baa68c5432908b42693edb9aed02a" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "24.10.2" }, - "timestamp": "2024-11-27T11:11:41.979250318" + "timestamp": "2024-11-28T09:51:05.948550848" } } \ No newline at end of file diff --git a/tests/rsem.nf.test.snap b/tests/rsem.nf.test.snap index 019403f..a4b5147 100644 --- a/tests/rsem.nf.test.snap +++ b/tests/rsem.nf.test.snap @@ -1,12 +1,8 @@ { - "Run with profile test for rsem | --input GRCh38_chr21.yml": { + "Run with profile test for rsem | --input assets/genomes/test/pipelines/default_extended.yml": { "content": [ - 3, + 2, { - "MAKE_TRANSCRIPTS_FASTA": { - "rsem": "1.3.1", - "star": "2.7.10a" - }, "RSEM_PREPAREREFERENCE_GENOME": { "rsem": "1.3.1", "star": "2.7.10a" @@ -16,8 +12,6 @@ } }, [ - "make", - "make/genome.transcripts.fa", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/multiqc.log", @@ -56,7 +50,6 @@ "rsem/rsem/transcriptInfo.tab" ], [ - "genome.transcripts.fa:md5,fd4e06fc250a19351a611a44861b9aea", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", "GRCh38_chr21.fa:md5,c675070fcf168d7b64cfadc30b5d7b4d", "Genome:md5,612664e3cfde5e1b73ad541d93752b31", @@ -87,12 +80,19 @@ "nf-test": "0.9.2", "nextflow": "24.10.1" }, - "timestamp": "2024-11-27T11:06:55.293456882" + "timestamp": "2024-11-27T11:05:05.450221738" }, - "Run with profile test for rsem | --input assets/genomes/test/pipelines/default_extended.yml": { + "Run with profile test for rsem | --input GRCh38_chr21.yml": { "content": [ - 2, + 4, { + "GFFREAD": { + "gffread": "0.12.7" + }, + "MAKE_TRANSCRIPTS_FASTA": { + "rsem": "1.3.1", + "star": "2.7.10a" + }, "RSEM_PREPAREREFERENCE_GENOME": { "rsem": "1.3.1", "star": "2.7.10a" @@ -102,6 +102,10 @@ } }, [ + "gffread", + "gffread/GRCh38_chr21.gtf", + "make", + "make/genome.transcripts.fa", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/multiqc.log", @@ -140,6 +144,8 @@ "rsem/rsem/transcriptInfo.tab" ], [ + "GRCh38_chr21.gtf:md5,c552c0aee5f1becb1d3991d21e63a5c1", + "genome.transcripts.fa:md5,fd4e06fc250a19351a611a44861b9aea", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", "GRCh38_chr21.fa:md5,c675070fcf168d7b64cfadc30b5d7b4d", "Genome:md5,612664e3cfde5e1b73ad541d93752b31", @@ -149,27 +155,27 @@ "chrName.txt:md5,e99d7d1051eee43ceab5563c2d09fcee", "chrNameLength.txt:md5,c985a141685e8431ec27c782816cb744", "chrStart.txt:md5,6925b594ea2eeb964ba87cd6d42ab98f", - "exonGeTrInfo.tab:md5,ea42dd46e177f95a72a8f6a2925f7348", - "exonInfo.tab:md5,42a3ce2024f396b2298c0a84b07fb6e4", - "geneInfo.tab:md5,d0092fb1ea6fcdac270c4df788de70fb", + "exonGeTrInfo.tab:md5,a36b92eeceaaf921b9d19cd8e806a98e", + "exonInfo.tab:md5,bb892190d1ebdd59bf55652916121479", + "geneInfo.tab:md5,4303e97d841035b5c0fcc3686b2f5a36", "genome.chrlist:md5,c985a141685e8431ec27c782816cb744", "genome.grp:md5,f75057a7bf6943f88c04f164cd641105", "genome.idx.fa:md5,fd4e06fc250a19351a611a44861b9aea", "genome.n2g.idx.fa:md5,fd4e06fc250a19351a611a44861b9aea", "genome.seq:md5,03f87c5a63ec7cb6e681e8e4e042153e", - "genome.ti:md5,38ba06dd31c6feaa10c8d9b42662358c", + "genome.ti:md5,283306157cf36e6827e4274c896844ba", "genome.transcripts.fa:md5,fd4e06fc250a19351a611a44861b9aea", - "genomeParameters.txt:md5,18fd87d37983d4d39bef7e9b773b5c23", + "genomeParameters.txt:md5,f26eb5881ea7e6fe1ad0c58e635a5a3d", "sjdbInfo.txt:md5,12fb05dc7cea89735a0c19e1c0df61cb", - "sjdbList.fromGTF.out.tab:md5,5d9761b49920fb70a77d74e390d196b9", + "sjdbList.fromGTF.out.tab:md5,d9e4a184cde15a5ab282ff66e740a4a2", "sjdbList.out.tab:md5,766fbca932681f8666b3a9e5fb3640bd", - "transcriptInfo.tab:md5,21c1f470ffe3b55b23900e7b7eaec2f4" + "transcriptInfo.tab:md5,ad9baa68c5432908b42693edb9aed02a" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "24.10.2" }, - "timestamp": "2024-11-27T11:05:05.450221738" + "timestamp": "2024-11-28T10:01:45.020113604" } -} +} \ No newline at end of file diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap index 244061d..04394f7 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -1,12 +1,8 @@ { - "Run with profile test for salmon | --input GRCh38_chr21.yml": { + "Run with profile test for salmon | --input assets/genomes/test/pipelines/default_extended.yml": { "content": [ - 3, + 2, { - "MAKE_TRANSCRIPTS_FASTA": { - "rsem": "1.3.1", - "star": "2.7.10a" - }, "SALMON_INDEX": { "salmon": "1.10.3" }, @@ -15,8 +11,6 @@ } }, [ - "make", - "make/genome.transcripts.fa", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/multiqc.log", @@ -46,7 +40,6 @@ "salmon/salmon/versionInfo.json" ], [ - "genome.transcripts.fa:md5,fd4e06fc250a19351a611a44861b9aea", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", "complete_ref_lens.bin:md5,ec4126a76984f26dc11baa2aaec7c325", "ctg_offsets.bin:md5,6f41c3fe64790ba0399be18d30436bb6", @@ -64,12 +57,19 @@ "nf-test": "0.9.2", "nextflow": "24.10.1" }, - "timestamp": "2024-11-27T10:47:56.770600657" + "timestamp": "2024-11-27T10:47:00.694933333" }, - "Run with profile test for salmon | --input assets/genomes/test/pipelines/default_extended.yml": { + "Run with profile test for salmon | --input GRCh38_chr21.yml": { "content": [ - 2, + 4, { + "GFFREAD": { + "gffread": "0.12.7" + }, + "MAKE_TRANSCRIPTS_FASTA": { + "rsem": "1.3.1", + "star": "2.7.10a" + }, "SALMON_INDEX": { "salmon": "1.10.3" }, @@ -78,6 +78,10 @@ } }, [ + "gffread", + "gffread/GRCh38_chr21.gtf", + "make", + "make/genome.transcripts.fa", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/multiqc.log", @@ -107,6 +111,8 @@ "salmon/salmon/versionInfo.json" ], [ + "GRCh38_chr21.gtf:md5,c552c0aee5f1becb1d3991d21e63a5c1", + "genome.transcripts.fa:md5,fd4e06fc250a19351a611a44861b9aea", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", "complete_ref_lens.bin:md5,ec4126a76984f26dc11baa2aaec7c325", "ctg_offsets.bin:md5,6f41c3fe64790ba0399be18d30436bb6", @@ -122,8 +128,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "24.10.2" }, - "timestamp": "2024-11-27T10:47:00.694933333" + "timestamp": "2024-11-28T09:54:40.423362524" } -} +} \ No newline at end of file diff --git a/workflows/references/main.nf b/workflows/references/main.nf index a00cdd2..af1cfe3 100644 --- a/workflows/references/main.nf +++ b/workflows/references/main.nf @@ -34,7 +34,7 @@ workflow REFERENCES { bowtie1 = Channel.empty() bowtie2 = Channel.empty() faidx = Channel.empty() - gffread = Channel.empty() + gff_gtf = Channel.empty() hisat2 = Channel.empty() hisat2_splice_sites = Channel.empty() kallisto = Channel.empty() @@ -73,6 +73,7 @@ workflow REFERENCES { known_snps_vcf: tools.contains('tabix') && known_snps_vcf ? [meta, known_snps_vcf] : [[:], []] known_indels_vcf: tools.contains('tabix') && known_indels_vcf ? [meta, known_indels_vcf] : [[:], []] germline_resource_vcf: tools.contains('tabix') && germline_resource_vcf ? [meta, germline_resource_vcf] : [[:], []] + gff_gffread: !gtf && (tools.contains('gffread') || tools.contains('hisat2') || tools.contains('kallisto') || tools.contains('rsem') || tools.contains('salmon') || tools.contains('star')) ? [meta, gff] : [[:], []] } // I should be able to output null instead of `[[:], []] and have that registered as an empty channel and not trigger downstream processes // but not working currently @@ -186,19 +187,25 @@ workflow REFERENCES { ) germline_resource_vcf_tbi = TABIX_GERMLINE_RESOURCE.out.tbi + GFFREAD( + input.gff_gffread.map { meta, file -> + return file ? [meta, file] : null + }, + [] + ) - if (tools.contains('gffread')) { - GFFREAD(input.gff, []) - - gffread = GFFREAD.out.gtf.map { it[1] } - versions = versions.mix(GFFREAD.out.versions) - } + gff_gtf = input.gtf + .mix(GFFREAD.out.gtf) + .groupTuple() + .map { meta, file -> + return file[1] ? [meta, file[1]] : [meta, file] + } if (tools.contains('hisat2')) { // TODO: be smarter about input assets // Here we either return an empty channel if we have a splice_sites so that HISAT2_EXTRACTSPLICESITES is not triggered // Or we return the provided gtf so that HISAT2_EXTRACTSPLICESITES is run - gtf_hisat2 = input.gtf + gtf_hisat2 = gff_gtf .join(input.splice_sites) .groupTuple() .map { meta, gtf, splice_sites -> @@ -219,7 +226,7 @@ workflow REFERENCES { } if (tools && tools.split(',').contains('hisat2')) { - HISAT2_BUILD(input.fasta, input.gtf, hisat2_splice_sites) + HISAT2_BUILD(input.fasta, gff_gtf, hisat2_splice_sites) hisat2 = HISAT2_BUILD.out.index versions = versions.mix(HISAT2_BUILD.out.versions) @@ -230,7 +237,7 @@ workflow REFERENCES { // TODO: be smarter about input assets // Here we either return an empty channel if we have a transcript_fasta so that MAKE_TRANSCRIPTS_FASTA is not triggered // Or we return the provided gtf so that MAKE_TRANSCRIPTS_FASTA is run - gtf_rsem = input.gtf + gtf_rsem = gff_gtf .join(input.transcript_fasta) .groupTuple() .map { meta, gtf, transcript_fasta -> @@ -273,14 +280,14 @@ workflow REFERENCES { } if (tools && tools.split(',').contains('rsem')) { - RSEM_PREPAREREFERENCE_GENOME(input.fasta, input.gtf) + RSEM_PREPAREREFERENCE_GENOME(input.fasta, gff_gtf) rsem = RSEM_PREPAREREFERENCE_GENOME.out.index versions = versions.mix(RSEM_PREPAREREFERENCE_GENOME.out.versions) } if (tools.contains('star')) { - STAR_GENOMEGENERATE(input.fasta, input.gtf) + STAR_GENOMEGENERATE(input.fasta, gff_gtf) star = STAR_GENOMEGENERATE.out.index versions = versions.mix(STAR_GENOMEGENERATE.out.versions) @@ -292,11 +299,12 @@ workflow REFERENCES { versions = versions.mix(BWAMEM2_INDEX.out.versions) versions = versions.mix(DRAGMAP_HASHTABLE.out.versions) versions = versions.mix(GATK4_CREATESEQUENCEDICTIONARY.out.versions) + versions = versions.mix(GFFREAD.out.versions) versions = versions.mix(SAMTOOLS_FAIDX.out.versions) versions = versions.mix(TABIX_DBSNP.out.versions) - versions = versions.mix(TABIX_KNOWN_SNPS.out.versions) - versions = versions.mix(TABIX_KNOWN_INDELS.out.versions) versions = versions.mix(TABIX_GERMLINE_RESOURCE.out.versions) + versions = versions.mix(TABIX_KNOWN_INDELS.out.versions) + versions = versions.mix(TABIX_KNOWN_SNPS.out.versions) // input fasta fasta = input.fasta @@ -313,7 +321,7 @@ workflow REFERENCES { faidx = faidx fasta = input.fasta germline_resource_vcf_tbi = germline_resource_vcf_tbi - gffread = gffread + gff_gtf = gff_gtf hisat2 = hisat2 hisat2_splice_sites = hisat2_splice_sites kallisto = kallisto @@ -339,7 +347,7 @@ workflow REFERENCES { faidx >> 'samtools' fasta >> 'fasta' germline_resource_vcf_tbi >> 'tabix' - gffread >> 'gffread' + gff_gtf >> 'gffread' hisat2 >> 'hisat2' hisat2_splice_sites >> 'hisat2' kallisto >> 'kallisto' From 00ed802deb1bdf06ad1a96775fc0f27b646eb161 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 28 Nov 2024 11:28:27 +0100 Subject: [PATCH 2/2] update gtf file --- .../test/pipelines/default_extended.yml | 2 +- assets/genomes/test/pipelines/default_full.yml | 2 +- tests/rsem.nf.test.snap | 18 +++++++++--------- 3 files changed, 11 insertions(+), 11 deletions(-) diff --git a/assets/genomes/test/pipelines/default_extended.yml b/assets/genomes/test/pipelines/default_extended.yml index 4d9a3d9..accc47a 100644 --- a/assets/genomes/test/pipelines/default_extended.yml +++ b/assets/genomes/test/pipelines/default_extended.yml @@ -4,7 +4,7 @@ fasta_fai: "https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/GRCh38_chr21.fa.fai" fasta_sizes: "https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/GRCh38_chr21.fa.sizes" gff: "https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/genes_chr21.gff" - gtf: "https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/genes_chr21.gtf" + gtf: "https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/GRCh38_chr21.gtf" mito_name: "MT" readme: "https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/README.md" source: "nf-core/references" diff --git a/assets/genomes/test/pipelines/default_full.yml b/assets/genomes/test/pipelines/default_full.yml index e7a745c..710dadc 100644 --- a/assets/genomes/test/pipelines/default_full.yml +++ b/assets/genomes/test/pipelines/default_full.yml @@ -5,7 +5,7 @@ fasta_fai: "https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/GRCh38_chr21.fa.fai" fasta_sizes: "https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/GRCh38_chr21.fa.sizes" gff: "https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/genes_chr21.gff" - gtf: "https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/genes_chr21.gtf" + gtf: "https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/GRCh38_chr21.gtf" mito_name: "MT" readme: "https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/README.md" source: "nf-core/references" diff --git a/tests/rsem.nf.test.snap b/tests/rsem.nf.test.snap index a4b5147..d9c7c8f 100644 --- a/tests/rsem.nf.test.snap +++ b/tests/rsem.nf.test.snap @@ -59,28 +59,28 @@ "chrName.txt:md5,e99d7d1051eee43ceab5563c2d09fcee", "chrNameLength.txt:md5,c985a141685e8431ec27c782816cb744", "chrStart.txt:md5,6925b594ea2eeb964ba87cd6d42ab98f", - "exonGeTrInfo.tab:md5,ea42dd46e177f95a72a8f6a2925f7348", - "exonInfo.tab:md5,42a3ce2024f396b2298c0a84b07fb6e4", - "geneInfo.tab:md5,d0092fb1ea6fcdac270c4df788de70fb", + "exonGeTrInfo.tab:md5,a36b92eeceaaf921b9d19cd8e806a98e", + "exonInfo.tab:md5,bb892190d1ebdd59bf55652916121479", + "geneInfo.tab:md5,4303e97d841035b5c0fcc3686b2f5a36", "genome.chrlist:md5,c985a141685e8431ec27c782816cb744", "genome.grp:md5,f75057a7bf6943f88c04f164cd641105", "genome.idx.fa:md5,fd4e06fc250a19351a611a44861b9aea", "genome.n2g.idx.fa:md5,fd4e06fc250a19351a611a44861b9aea", "genome.seq:md5,03f87c5a63ec7cb6e681e8e4e042153e", - "genome.ti:md5,38ba06dd31c6feaa10c8d9b42662358c", + "genome.ti:md5,283306157cf36e6827e4274c896844ba", "genome.transcripts.fa:md5,fd4e06fc250a19351a611a44861b9aea", - "genomeParameters.txt:md5,18fd87d37983d4d39bef7e9b773b5c23", + "genomeParameters.txt:md5,f26eb5881ea7e6fe1ad0c58e635a5a3d", "sjdbInfo.txt:md5,12fb05dc7cea89735a0c19e1c0df61cb", - "sjdbList.fromGTF.out.tab:md5,5d9761b49920fb70a77d74e390d196b9", + "sjdbList.fromGTF.out.tab:md5,d9e4a184cde15a5ab282ff66e740a4a2", "sjdbList.out.tab:md5,766fbca932681f8666b3a9e5fb3640bd", - "transcriptInfo.tab:md5,21c1f470ffe3b55b23900e7b7eaec2f4" + "transcriptInfo.tab:md5,ad9baa68c5432908b42693edb9aed02a" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "24.10.2" }, - "timestamp": "2024-11-27T11:05:05.450221738" + "timestamp": "2024-11-28T11:21:44.429667988" }, "Run with profile test for rsem | --input GRCh38_chr21.yml": { "content": [