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Better publishing of all files (#49)
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* better Publish path

* update CHANGELOG

* better publish + fix path

* update .gitignore and snapshots
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@maxulysse
maxulysse authored Dec 3, 2024
1 parent c4a5538 commit 8ef2074
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -38,6 +38,7 @@ Initial release of nf-core/references, created with the [nf-core](https://nf-co.
- [41](https://github.com/nf-core/references/pull/41) - Better sarek tests
- [41](https://github.com/nf-core/references/pull/41) - Better publishing for sarek related files
- [43](https://github.com/nf-core/references/pull/43) - Fasta is no longer a required asset
- [49](https://github.com/nf-core/references/pull/49) - Better publishing for all files

### Fixed

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27 changes: 15 additions & 12 deletions main.nf
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Expand Up @@ -103,10 +103,10 @@ workflow {

output {
'bowtie1' {
path 'bowtie1'
path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/BowtieIndex/" } }
}
'bowtie2' {
path 'bowtie2'
path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/Bowtie2Index/" } }
}
'bwamem1' {
path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/BWAIndex/" } }
Expand All @@ -127,22 +127,19 @@ output {
path { meta, fai -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/WholeGenomeFasta/${file}" } }
}
'fasta_sizes' {
path 'fasta_sizes'
path { meta, sizes -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/WholeGenomeFasta/${file}" } }
}
'gffread' {
path 'gffread'
path { meta, intervals -> { file -> "${meta.species}/${meta.source}/${meta.id}/Annotation/Genes/${file}" } }
}
'hisat2' {
path 'hisat2'
path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/Hisat2Index/" } }
}
'intervals' {
path { meta, intervals -> { file -> "${meta.species}/${meta.source}/${meta.id}/Annotation/intervals/${file}" } }
}
'kallisto' {
path 'kallisto'
}
'make' {
path 'make'
path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/KallistoIndex/" } }
}
'msisensorpro' {
path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Annotation/msisensorpro/${file}" } }
Expand All @@ -157,13 +154,19 @@ output {
path 'multiqc'
}
'rsem' {
path 'rsem'
path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/RSEMIndex/" } }
}
'salmon' {
path 'salmon'
path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/SalmonIndex/" } }
}
'splice_sites' {
path { meta, txt -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/SpliceSites/${file}" } }
}
'star' {
path 'star'
path { meta, index -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/STARIndex/" } }
}
'transcript_fasta' {
path { meta, fasta -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/TranscriptFasta/${file}" } }
}
'tabix_dbsnp' {
path { meta, vcf -> { file -> "${meta.species}/${meta.source}/${meta.id}/Annotation/${meta.source_dbsnp}/${file}" } }
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18 changes: 9 additions & 9 deletions tests/.nftignore
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@@ -1,8 +1,15 @@
.DS_Store
**/KallistoIndex
**/RSEMIndex/Log.out
**/STARIndex/Log.out
**/SalmonIndex/ctable.bin
**/SalmonIndex/pos.bin
**/SalmonIndex/pre_indexing.log
**/SalmonIndex/ref_indexing.log
**/SalmonIndex/seq.bin
**/dragmap/hash_table.cfg
**/dragmap/hash_table.cfg.bin
**/dragmap/hash_table_stats.txt
kallisto/kallisto
.DS_Store
multiqc/multiqc_data/multiqc.log
multiqc/multiqc_data/multiqc_data.json
multiqc/multiqc_data/multiqc_general_stats.txt
Expand All @@ -11,10 +18,3 @@ multiqc/multiqc_data/multiqc_sources.txt
multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
multiqc/multiqc_report.html
pipeline_info/*.{html,json,txt,yml}
rsem/rsem/Log.out
salmon/salmon/ctable.bin
salmon/salmon/pos.bin
salmon/salmon/pre_indexing.log
salmon/salmon/ref_indexing.log
salmon/salmon/seq.bin
star/star/Log.out
64 changes: 37 additions & 27 deletions tests/hisat2.nf.test.snap
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Expand Up @@ -11,16 +11,20 @@
}
},
[
"hisat2",
"hisat2/hisat2",
"hisat2/hisat2/GRCh38_chr21.1.ht2",
"hisat2/hisat2/GRCh38_chr21.2.ht2",
"hisat2/hisat2/GRCh38_chr21.3.ht2",
"hisat2/hisat2/GRCh38_chr21.4.ht2",
"hisat2/hisat2/GRCh38_chr21.5.ht2",
"hisat2/hisat2/GRCh38_chr21.6.ht2",
"hisat2/hisat2/GRCh38_chr21.7.ht2",
"hisat2/hisat2/GRCh38_chr21.8.ht2",
"Homo_sapiens",
"Homo_sapiens/nf-core",
"Homo_sapiens/nf-core/references",
"Homo_sapiens/nf-core/references/GRCh38_chr21",
"Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence",
"Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index",
"Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21.1.ht2",
"Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21.2.ht2",
"Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21.3.ht2",
"Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21.4.ht2",
"Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21.5.ht2",
"Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21.6.ht2",
"Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21.7.ht2",
"Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21.8.ht2",
"multiqc",
"multiqc/multiqc_data",
"multiqc/multiqc_data/multiqc.log",
Expand Down Expand Up @@ -48,7 +52,7 @@
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-11-28T09:47:04.908315963"
"timestamp": "2024-12-03T12:55:26.231501216"
},
"Run with profile test for hisat2 | --input GRCh38_chr21.yml": {
"content": [
Expand All @@ -68,19 +72,25 @@
}
},
[
"gffread",
"gffread/GRCh38_chr21.gtf",
"hisat2",
"hisat2/GRCh38_chr21.splice_sites.txt",
"hisat2/hisat2",
"hisat2/hisat2/GRCh38_chr21.1.ht2",
"hisat2/hisat2/GRCh38_chr21.2.ht2",
"hisat2/hisat2/GRCh38_chr21.3.ht2",
"hisat2/hisat2/GRCh38_chr21.4.ht2",
"hisat2/hisat2/GRCh38_chr21.5.ht2",
"hisat2/hisat2/GRCh38_chr21.6.ht2",
"hisat2/hisat2/GRCh38_chr21.7.ht2",
"hisat2/hisat2/GRCh38_chr21.8.ht2",
"Homo_sapiens",
"Homo_sapiens/nf-core",
"Homo_sapiens/nf-core/references",
"Homo_sapiens/nf-core/references/GRCh38_chr21",
"Homo_sapiens/nf-core/references/GRCh38_chr21/Annotation",
"Homo_sapiens/nf-core/references/GRCh38_chr21/Annotation/Genes",
"Homo_sapiens/nf-core/references/GRCh38_chr21/Annotation/Genes/GRCh38_chr21.gtf",
"Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence",
"Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index",
"Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21.1.ht2",
"Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21.2.ht2",
"Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21.3.ht2",
"Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21.4.ht2",
"Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21.5.ht2",
"Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21.6.ht2",
"Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21.7.ht2",
"Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/Hisat2Index/GRCh38_chr21.8.ht2",
"Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SpliceSites",
"Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/SpliceSites/GRCh38_chr21.splice_sites.txt",
"multiqc",
"multiqc/multiqc_data",
"multiqc/multiqc_data/multiqc.log",
Expand All @@ -94,7 +104,6 @@
],
[
"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 @@ -103,13 +112,14 @@
"GRCh38_chr21.6.ht2:md5,242e36d01cd1719b6bd05f157c644eed",
"GRCh38_chr21.7.ht2:md5,24e7d0673a77e07fbe40400f9a6b3db6",
"GRCh38_chr21.8.ht2:md5,5e0626bdb7f7a267990f72ae45c3e44a",
"GRCh38_chr21.splice_sites.txt:md5,291af43cd5b00eeb15277f90a76e77f8",
"multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-11-28T09:41:32.891380441"
"timestamp": "2024-12-03T13:57:17.25040689"
}
}
}
31 changes: 20 additions & 11 deletions tests/kallisto.nf.test.snap
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Expand Up @@ -18,12 +18,17 @@
}
},
[
"gffread",
"gffread/GRCh38_chr21.gtf",
"kallisto",
"kallisto/kallisto",
"make",
"make/genome.transcripts.fa",
"Homo_sapiens",
"Homo_sapiens/nf-core",
"Homo_sapiens/nf-core/references",
"Homo_sapiens/nf-core/references/GRCh38_chr21",
"Homo_sapiens/nf-core/references/GRCh38_chr21/Annotation",
"Homo_sapiens/nf-core/references/GRCh38_chr21/Annotation/Genes",
"Homo_sapiens/nf-core/references/GRCh38_chr21/Annotation/Genes/GRCh38_chr21.gtf",
"Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence",
"Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex",
"Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/TranscriptFasta",
"Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/TranscriptFasta/genome.transcripts.fa",
"multiqc",
"multiqc/multiqc_data",
"multiqc/multiqc_data/multiqc.log",
Expand All @@ -45,7 +50,7 @@
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-11-28T09:49:13.419658545"
"timestamp": "2024-12-03T14:31:39.422746281"
},
"Run with profile test for kallisto | --input assets/genomes/test/default_extended.yml": {
"content": [
Expand All @@ -59,8 +64,12 @@
}
},
[
"kallisto",
"kallisto/kallisto",
"Homo_sapiens",
"Homo_sapiens/nf-core",
"Homo_sapiens/nf-core/references",
"Homo_sapiens/nf-core/references/GRCh38_chr21",
"Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence",
"Homo_sapiens/nf-core/references/GRCh38_chr21/Sequence/KallistoIndex",
"multiqc",
"multiqc/multiqc_data",
"multiqc/multiqc_data/multiqc.log",
Expand All @@ -80,6 +89,6 @@
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-11-28T09:48:51.312930217"
"timestamp": "2024-12-03T14:31:07.501838885"
}
}
}
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