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fix gtf generation and dependencies #39

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merged 2 commits into from
Nov 28, 2024
Merged

fix gtf generation and dependencies #39

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14a75fc
fix gtf generation and dependencies
maxulysse Nov 28, 2024
00ed802
update gtf file
maxulysse Nov 28, 2024
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2 changes: 1 addition & 1 deletion assets/genomes/test/pipelines/default_extended.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
Expand Down
2 changes: 1 addition & 1 deletion assets/genomes/test/pipelines/default_full.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
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2 changes: 1 addition & 1 deletion main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
22 changes: 14 additions & 8 deletions tests/hisat2.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
},
Expand All @@ -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",
Expand All @@ -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",
Expand All @@ -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"
}
}
}
38 changes: 22 additions & 16 deletions tests/kallisto.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -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",
Expand All @@ -25,35 +36,31 @@
"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"
}
},
[
"kallisto",
"kallisto/kallisto",
"make",
"make/genome.transcripts.fa",
"multiqc",
"multiqc/multiqc_data",
"multiqc/multiqc_data/multiqc.log",
Expand All @@ -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"
}
}
}
16 changes: 8 additions & 8 deletions tests/rnaseq.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
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"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"
}
}
66 changes: 36 additions & 30 deletions tests/rsem.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -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"
Expand All @@ -16,8 +12,6 @@
}
},
[
"make",
"make/genome.transcripts.fa",
"multiqc",
"multiqc/multiqc_data",
"multiqc/multiqc_data/multiqc.log",
Expand Down Expand Up @@ -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",
Expand All @@ -66,33 +59,40 @@
"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": "2024-11-27T11:06:55.293456882"
"timestamp": "2024-11-28T11:21:44.429667988"
},
"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"
Expand All @@ -102,6 +102,10 @@
}
},
[
"gffread",
"gffread/GRCh38_chr21.gtf",
"make",
"make/genome.transcripts.fa",
"multiqc",
"multiqc/multiqc_data",
"multiqc/multiqc_data/multiqc.log",
Expand Down Expand Up @@ -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",
Expand All @@ -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"
}
}
}
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