Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add decompress subworkflows + source_gff -> reference_version #55

Merged
merged 7 commits into from
Dec 6, 2024
Merged

Add decompress subworkflows + source_gff -> reference_version #55

Show file tree
Hide file tree
Changes from 4 commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
04e6613
complete asset
maxulysse Dec 6, 2024
b3e519b
source_gff -> reference_version
maxulysse Dec 6, 2024
a1bb30c
add gunzip
maxulysse Dec 6, 2024
444c65c
add uncompress subworkflows and tests
maxulysse Dec 6, 2024
0f30f66
no need for gff here
maxulysse Dec 6, 2024
058f482
update test file
maxulysse Dec 6, 2024
279f74f
no need to convert gff to gtf if no fasta
maxulysse Dec 6, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
14 changes: 14 additions & 0 deletions assets/genomes/Caenorhabditis_elegans/NCBI/WBcel235.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
- genome: WBcel235
fasta: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/985/GCF_000002985.6_WBcel235/GCF_000002985.6_WBcel235_genomic.fna.gz
gff: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/985/GCF_000002985.6_WBcel235/GCF_000002985.6_WBcel235_genomic.gff.gz
gtf: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/985/GCF_000002985.6_WBcel235/GCF_000002985.6_WBcel235_genomic.gtf.gz
reference_version: GCF_000002985.6
site: https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000002985.6
source: NCBI
species: Caenorhabditis_elegans
- genome: WBcel235
gff: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/985/GCF_000002985.6_WBcel235/GCF_000002985.6_WBcel235_genomic.gff.gz
reference_version: GCF_000002985.6
site: https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000002985.6
source: NCBI
species: Caenorhabditis_elegans
6 changes: 4 additions & 2 deletions assets/genomes/Homo_sapiens/Gencode/GRCh38.p14.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,9 @@
# FIXME Some check this
- genome: GRCh38.p14
fasta: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_45/GRCh38.primary_assembly.genome.fa.gz
gff: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_45/gencode.v45.chr_patch_hapl_scaff.annotation.gff3.gz
gtf: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_45/gencode.v45.chr_patch_hapl_scaff.annotation.gtf.gz
mito_name: MT
site: https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001405.40
reference_version: GCF_000001405.40
site: https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001405.40
source: Gencode
species: Homo_sapiens
8 changes: 8 additions & 0 deletions assets/genomes/Homo_sapiens/NCBI/GRCh38.p14.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,8 @@
- genome: GRCh38.p14
fasta: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.40_GRCh38.p14/GRCh38_major_release_seqs_for_alignment_pipelines/GCA_000001405.15_GRCh38_full_analysis_set.fna.gz
gff: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.40_GRCh38.p14/GCF_000001405.40_GRCh38.p14_genomic.gff.gz
gtf: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.40_GRCh38.p14/GCF_000001405.40_GRCh38.p14_genomic.gtf.gz
mito_name: MT
reference_version: GCF_000001405.40
source: NCBI
species: Homo_sapiens
12 changes: 6 additions & 6 deletions assets/schema_input.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -15,24 +15,24 @@
},
"source": {
"type": "string",
"errorMessage": "Where the references came from",
"errorMessage": "Source of genome must be provided and cannot contain spaces",
"meta": ["source"]
},
"source_vcf": {
"type": "string",
"errorMessage": "Where the references came from",
"errorMessage": "Source of the VCF file must be provided and cannot contain spaces",
"default": "unknown",
"meta": ["source_vcf"]
},
"source_gff": {
"reference_version": {
"type": "string",
"errorMessage": "Where the references came from",
"errorMessage": "What is the version of the reference used to create gff/gtf and transcript related files",
"default": "unknown",
"meta": ["source_gff"]
"meta": ["reference_version"]
},
"species": {
"type": "string",
"errorMessage": "Species of the reference",
"errorMessage": "Species of the reference, cannot contain spaces",
"meta": ["species"]
},
"intervals_bed": {
Expand Down
25 changes: 14 additions & 11 deletions main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -129,15 +129,18 @@ output {
'fasta_sizes' {
path { meta, sizes -> { file -> "${meta.species}/${meta.source}/${meta.id}/Sequence/WholeGenomeFasta/${file}" } }
}
'gff' {
path { meta, gff -> { file -> "${meta.species}/${meta.source}/${meta.id}/Annotation/Genes/${file}" } }
}
'gtf' {
path { meta, intervals -> { file -> "${meta.species}/${meta.source}/${meta.id}/Annotation/Genes/${file}" } }
path { meta, gtf -> { file -> "${meta.species}/${meta.source}/${meta.id}/Annotation/Genes/${file}" } }
}
'hisat2_index' {
path { meta, index ->
{ file ->
meta.source_gff == "unknown"
meta.reference_version == "unknown"
? "${meta.species}/${meta.source}/${meta.id}/Sequence/Hisat2Index/version2.2.1"
: "${meta.species}/${meta.source}/${meta.id}/Sequence/Hisat2Index/${meta.source_gff}/version2.2.1"
: "${meta.species}/${meta.source}/${meta.id}/Sequence/Hisat2Index/${meta.reference_version}/version2.2.1"
}
}
}
Expand All @@ -147,9 +150,9 @@ output {
'kallisto_index' {
path { meta, index ->
{ file ->
meta.source_gff == "unknown"
meta.reference_version == "unknown"
? "${meta.species}/${meta.source}/${meta.id}/Sequence/KallistoIndex/version0.51.1/${file}"
: "${meta.species}/${meta.source}/${meta.id}/Sequence/KallistoIndex/${meta.source_gff}/version0.51.1/${file}"
: "${meta.species}/${meta.source}/${meta.id}/Sequence/KallistoIndex/${meta.reference_version}/version0.51.1/${file}"
}
}
}
Expand All @@ -168,18 +171,18 @@ output {
'rsem_index' {
path { meta, index ->
{ file ->
meta.source_gff == "unknown"
meta.reference_version == "unknown"
? "${meta.species}/${meta.source}/${meta.id}/Sequence/RSEMIndex/version1.3.1"
: "${meta.species}/${meta.source}/${meta.id}/Sequence/RSEMIndex/${meta.source_gff}/version1.3.1"
: "${meta.species}/${meta.source}/${meta.id}/Sequence/RSEMIndex/${meta.reference_version}/version1.3.1"
}
}
}
'salmon_index' {
path { meta, index ->
{ file ->
meta.source_gff == "unknown"
meta.reference_version == "unknown"
? "${meta.species}/${meta.source}/${meta.id}/Sequence/SalmonIndex/version1.10.3"
: "${meta.species}/${meta.source}/${meta.id}/Sequence/SalmonIndex/${meta.source_gff}/version1.10.3"
: "${meta.species}/${meta.source}/${meta.id}/Sequence/SalmonIndex/${meta.reference_version}/version1.10.3"
}
}
}
Expand All @@ -189,9 +192,9 @@ output {
'star_index' {
path { meta, index ->
{ file ->
meta.source_gff == "unknown"
meta.reference_version == "unknown"
? "${meta.species}/${meta.source}/${meta.id}/Sequence/STARIndex/version2.7.11b"
: "${meta.species}/${meta.source}/${meta.id}/Sequence/STARIndex/${meta.source_gff}/version2.7.11b"
: "${meta.species}/${meta.source}/${meta.id}/Sequence/STARIndex/${meta.reference_version}/version2.7.11b"
}
}
}
Expand Down
5 changes: 5 additions & 0 deletions modules.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -56,6 +56,11 @@
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"gunzip": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"hisat2/build": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
Expand Down
7 changes: 7 additions & 0 deletions modules/nf-core/gunzip/environment.yml
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

55 changes: 55 additions & 0 deletions modules/nf-core/gunzip/main.nf
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

47 changes: 47 additions & 0 deletions modules/nf-core/gunzip/meta.yml
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

121 changes: 121 additions & 0 deletions modules/nf-core/gunzip/tests/main.nf.test
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

Loading
Loading