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Updated SYRI to 1.7.0 #107

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Jul 22, 2024
Merged

Updated SYRI to 1.7.0 #107

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11 changes: 6 additions & 5 deletions CHANGELOG.md
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Expand Up @@ -13,16 +13,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
4. Added a test to verify the fix for the bug which resulted in a pipeline crash for assemblies without LTRs
5. Locally patched `FASTA_LTRRETRIEVER_LAI` sub-workflow to emit the `LTRRETRIEVER_LTRRETRIEVER` log as one of the outputs
6. Locally patched `LTRRETRIEVER_LTRRETRIEVER` module to not fail when `LTR_retriever` exits with an error
7. Updated NCBI FCS GX to 0.5.4 [#93](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/93)
8. Updated `SYRI` to 1.7.0 [#104](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/104)

### `Fixed`

1. Fixed a bug where `intron_length_distribution` was used instead of `cds_length_distribution` when creating the CDS Length Distribution Graph [#95](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/95)
2. Fixed a bug where 'Subsequent pipeline modules are skipped.' was printed in the `report.html` even when `contamination_stops_pipeline` was set to false
3. Updated NCBI FCS GX to 0.5.4 [#93](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/93)
4. Now NCBI FCS GX module uses all the cores available from the Nextflow task
5. Fixed a bug which caused `PLOTSR` to fail for certain assembly names [#102](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/102)
6. Now `LTRRETRIEVER_LTRRETRIEVER` does not crash when the input assembly does not contain any LTRs [#92](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/92)
7. Now `LTRRETRIEVER_LTRRETRIEVER` does not crash when the input assembly is not writable [#98](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/98)
3. Now NCBI FCS GX module uses all the cores available from the Nextflow task
4. Fixed a bug which caused `PLOTSR` to fail for certain assembly names [#102](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/102)
5. Now `LTRRETRIEVER_LTRRETRIEVER` does not crash when the input assembly does not contain any LTRs [#92](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/92)
6. Now `LTRRETRIEVER_LTRRETRIEVER` does not crash when the input assembly is not writable [#98](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/98)

### `Dependencies`

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16 changes: 11 additions & 5 deletions modules.json
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Expand Up @@ -2,6 +2,17 @@
"name": "plant-food-research-open/assemblyqc",
"homePage": "https://github.com/plant-food-research-open/assemblyqc",
"repos": {
"https://github.com/GallVp/nxf-components.git": {
"modules": {
"gallvp": {
"syri": {
"branch": "main",
"git_sha": "836bb223521eeaa08d65c1b7f4b82be1272a1964",
"installed_by": ["modules"]
}
}
}
},
"https://github.com/PlantandFoodResearch/nxf-modules.git": {
"modules": {
"pfr": {
Expand Down Expand Up @@ -104,11 +115,6 @@
"branch": "main",
"git_sha": "84f31d4be03e2ae6bee8e0b9fdea466be8e997bb",
"installed_by": ["gff3_gt_gff3_gff3validator_stat"]
},
"syri": {
"branch": "main",
"git_sha": "295e1d8666c746cb05e79563393035e81c9739fc",
"installed_by": ["modules"]
}
}
},
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2 changes: 1 addition & 1 deletion modules/pfr/syri/environment.yml → modules/gallvp/syri/environment.yml
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Expand Up @@ -6,4 +6,4 @@ channels:
- bioconda
- defaults
dependencies:
- "bioconda::syri=1.6.3"
- "bioconda::syri=1.7.0"
4 changes: 2 additions & 2 deletions modules/pfr/syri/main.nf → modules/gallvp/syri/main.nf
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Expand Up @@ -4,8 +4,8 @@ process SYRI {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/syri:1.6.3--py38hdbdd923_2':
'biocontainers/syri:1.6.3--py38hdbdd923_2' }"
'https://depot.galaxyproject.org/singularity/syri:1.7.0--py310hdbdd923_0':
'biocontainers/syri:1.7.0--py310hdbdd923_0' }"

input:
tuple val(meta), path(infile)
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0 modules/pfr/syri/meta.yml → modules/gallvp/syri/meta.yml
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21 changes: 11 additions & 10 deletions modules/pfr/syri/tests/main.nf.test → modules/gallvp/syri/tests/main.nf.test
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Expand Up @@ -6,26 +6,27 @@ nextflow_process {
process "SYRI"

tag "modules"
tag "modules_nfcore"
tag "modules_gallvp"
tag "syri"
tag "minimap2/align"

setup {
run("MINIMAP2_ALIGN") {
script "modules/pfr/minimap2/align/main.nf"
script "../../minimap2/align"
process {
"""
input[0] = [
[id: 'test'],
file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
]
input[1] = [
[id: 'reference'],
file(params.test_data['homo_sapiens']['genome']['genome2_fasta'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome2.fasta', checkIfExists: true)
]
input[2] = true // bam_format
input[3] = false // cigar_paf_format
input[4] = false // cigar_bam
input[3] = 'bai' // bam_index_extension
input[4] = false // cigar_paf_format
input[5] = false // cigar_bam
"""
}
}
Expand All @@ -37,8 +38,8 @@ nextflow_process {
process {
"""
input[0] = MINIMAP2_ALIGN.out.bam
input[1] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
input[2] = file(params.test_data['homo_sapiens']['genome']['genome2_fasta'], checkIfExists: true)
input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome2.fasta', checkIfExists: true)
input[3] = 'B'
"""
}
Expand All @@ -61,8 +62,8 @@ nextflow_process {
process {
"""
input[0] = MINIMAP2_ALIGN.out.bam
input[1] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
input[2] = file(params.test_data['homo_sapiens']['genome']['genome2_fasta'], checkIfExists: true)
input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome2.fasta', checkIfExists: true)
input[3] = 'B'
"""
}
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16 changes: 8 additions & 8 deletions modules/pfr/syri/tests/main.nf.test.snap → modules/gallvp/syri/tests/main.nf.test.snap
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Expand Up @@ -14,7 +14,7 @@

],
"2": [
"versions.yml:md5,05cf55e24c29c2661a2b9301d3c7c2a0"
"versions.yml:md5,0c85b0fa3d80a73807daf08b7e4c51f6"
],
"error": [

Expand All @@ -28,15 +28,15 @@
]
],
"versions": [
"versions.yml:md5,05cf55e24c29c2661a2b9301d3c7c2a0"
"versions.yml:md5,0c85b0fa3d80a73807daf08b7e4c51f6"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.1"
"nextflow": "24.04.3"
},
"timestamp": "2024-05-25T21:30:50.653501"
"timestamp": "2024-07-22T14:11:06.589243"
},
"homo_sapiens - genome - stub": {
"content": [
Expand All @@ -53,7 +53,7 @@

],
"2": [
"versions.yml:md5,05cf55e24c29c2661a2b9301d3c7c2a0"
"versions.yml:md5,0c85b0fa3d80a73807daf08b7e4c51f6"
],
"error": [

Expand All @@ -67,14 +67,14 @@
]
],
"versions": [
"versions.yml:md5,05cf55e24c29c2661a2b9301d3c7c2a0"
"versions.yml:md5,0c85b0fa3d80a73807daf08b7e4c51f6"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.1"
"nextflow": "24.04.3"
},
"timestamp": "2024-05-25T21:22:31.028411"
"timestamp": "2024-07-22T14:11:12.583161"
}
}
0 modules/pfr/syri/tests/nextflow.config → modules/gallvp/syri/tests/nextflow.config
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2 changes: 0 additions & 2 deletions modules/pfr/syri/tests/tags.yml
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This file was deleted.

2 changes: 1 addition & 1 deletion subworkflows/local/fasta_synteny.nf
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Expand Up @@ -13,7 +13,7 @@ include { CIRCOS } from '../../modules/local/circos'
include { LINEARSYNTENY } from '../../modules/local/linearsynteny'
include { CUSTOM_RELABELFASTA } from '../../modules/pfr/custom/relabelfasta/main'
include { MINIMAP2_ALIGN } from '../../modules/nf-core/minimap2/align/main'
include { SYRI } from '../../modules/pfr/syri/main'
include { SYRI } from '../../modules/gallvp/syri/main'
include { PLOTSR } from '../../modules/pfr/plotsr/main'

workflow FASTA_SYNTENY {
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