Skip to content

Commit 86d1b14

Browse files
atrigilaatrigila
authored
Merge branch 'dev' into remove_sbwf_starfusion
2 parents b7987ce + d0cef33 commit 86d1b14

44 files changed

Lines changed: 637 additions & 466 deletions

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

‎CHANGELOG.md‎

Lines changed: 3 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -82,6 +82,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
8282
- `all` => This will automatically run all of the above tools
8383
- Updated all `wget` containers to `conda-forge::wget=1.21.4` [#655](https://github.com/nf-core/rnafusion/pull/655)
8484
- Using FusionInspector abridged output (that now contains coding effects) for downstream analysis [#669](https://github.com/nf-core/rnafusion/pull/669)
85+
- Replaced local `FUSIONREPORT` and `FUSIONREPORT_DOWNLOAD` with `FUSIONREPORT_DETECT` and `FUSIONREPORT_DOWNLOAD` from nf-core [#703](https://github.com/nf-core/rnafusion/pull/703)
86+
- Updated arriba to v2.5.0 [#693](https://github.com/nf-core/rnafusion/pull/693)
8587

8688
### Fixed
8789

@@ -100,6 +102,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
100102
- Fix bug in argument handling for FusionInspector [#669](https://github.com/nf-core/rnafusion/pull/669)
101103
- Upgrade STAR-Fusion to 1.15.1 to solve problem building STAR-Fusion references with `--human_gencode_filter` [#683](https://github.com/nf-core/rnafusion/pull/683)
102104
- Fix missing memory unit for fusioncatcher [#674](https://github.com/nf-core/rnafusion/pull/674)
105+
- Fix fusioncatcher download link [#693](https://github.com/nf-core/rnafusion/pull/693)
103106

104107
### Removed
105108

‎conf/modules.config‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -128,7 +128,7 @@ process {
128128
]
129129
}
130130

131-
withName: 'FUSIONREPORT' {
131+
withName: 'FUSIONREPORT_DETECT' {
132132
ext.args = { params.no_cosmic ? "--no-cosmic" : "" }
133133
ext.args2 = "--export csv"
134134
publishDir = [

‎modules.json‎

Lines changed: 12 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -12,12 +12,12 @@
1212
},
1313
"arriba/arriba": {
1414
"branch": "master",
15-
"git_sha": "1719e20e3881b37b9e1e8498ea669a2b92e54b9a",
15+
"git_sha": "077818897bfe993e1ed91a0339bcbe53fe13edc7",
1616
"installed_by": ["modules"]
1717
},
1818
"arriba/download": {
1919
"branch": "master",
20-
"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
20+
"git_sha": "98bd7be6d2191b0d5900ee698d91b52eeab90311",
2121
"installed_by": ["modules"]
2222
},
2323
"cat/cat": {
@@ -45,6 +45,16 @@
4545
"git_sha": "1037205706929921360f57e8042eae6819825e31",
4646
"installed_by": ["modules"]
4747
},
48+
"fusionreport/detect": {
49+
"branch": "master",
50+
"git_sha": "412d1e0614c3be267b8feb448588864a16a48293",
51+
"installed_by": ["modules"]
52+
},
53+
"fusionreport/download": {
54+
"branch": "master",
55+
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
56+
"installed_by": ["modules"]
57+
},
4858
"gatk4/bedtointervallist": {
4959
"branch": "master",
5060
"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",

‎modules/local/arriba/visualisation/environment.yml‎

Lines changed: 8 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,8 @@
1+
---
2+
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
3+
channels:
4+
- conda-forge
5+
- bioconda
6+
dependencies:
7+
- bioconda::arriba=2.5.0
8+
- conda-forge::wget=1.21.4

‎modules/local/arriba/visualisation/main.nf‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -2,10 +2,10 @@ process ARRIBA_VISUALISATION {
22
tag "$meta.id"
33
label 'process_medium'
44

5-
conda "bioconda::arriba=2.4.0"
5+
conda "${moduleDir}/environment.yml"
66
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
7-
'https://depot.galaxyproject.org/singularity/arriba:2.4.0--h0033a41_2' :
8-
'biocontainers/arriba:2.4.0--h0033a41_2' }"
7+
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/27/27475cdcdbcc8c0ffb6b5ca8c2e6567dbe490edb96f5df4e8f01f4f95912dcd3/data' :
8+
'community.wave.seqera.io/library/arriba_wget:a3e48cf793a0b654' }"
99

1010
input:
1111
tuple val(meta), path(bam), path(bai), path(fusions)

‎modules/local/arriba/visualisation/tests/main.nf.test‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -25,11 +25,11 @@ nextflow_process {
2525
]
2626
input[2] = [
2727
[ id:'test_protein_domains' ],
28-
file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/rnafusion/testdata/reference/arriba/protein_domains_hg38_GRCh38_v2.4.0.gff3", checkIfExists: true)
28+
file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/rnafusion/testdata/reference/arriba/protein_domains_hg38_GRCh38_v2.5.0.gff3", checkIfExists: true)
2929
]
3030
input[3] = [
3131
[ id:'test_cytobands' ],
32-
file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/rnafusion/testdata/reference/arriba/cytobands_hg38_GRCh38_v2.4.0.tsv", checkIfExists: true)
32+
file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/rnafusion/testdata/reference/arriba/cytobands_hg38_GRCh38_v2.5.0.tsv", checkIfExists: true)
3333
]
3434
"""
3535
}
@@ -63,11 +63,11 @@ nextflow_process {
6363
]
6464
input[2] = [
6565
[ id:'test_protein_domains' ],
66-
file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/rnafusion/testdata/reference/arriba/protein_domains_hg38_GRCh38_v2.4.0.gff3", checkIfExists: true)
66+
file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/rnafusion/testdata/reference/arriba/protein_domains_hg38_GRCh38_v2.5.0.gff3", checkIfExists: true)
6767
]
6868
input[3] = [
6969
[ id:'test_cytobands' ],
70-
file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/rnafusion/testdata/reference/arriba/cytobands_hg38_GRCh38_v2.4.0.tsv", checkIfExists: true)
70+
file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/rnafusion/testdata/reference/arriba/cytobands_hg38_GRCh38_v2.5.0.tsv", checkIfExists: true)
7171
]
7272
"""
7373
}

‎modules/local/fusioncatcher/download/main.nf‎

Lines changed: 2 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -22,10 +22,8 @@ process FUSIONCATCHER_DOWNLOAD {
2222
def args = task.ext.args ?: ''
2323
meta = [ id: "human_v${genome_gencode_version}" ]
2424
"""
25-
wget --no-check-certificate $args ${params.fusioncatcher_download_link}/human_v${genome_gencode_version}.tar.gz.partaa
26-
wget --no-check-certificate $args ${params.fusioncatcher_download_link}/human_v${genome_gencode_version}.tar.gz.partab
27-
wget --no-check-certificate $args ${params.fusioncatcher_download_link}/human_v${genome_gencode_version}.tar.gz.partac
28-
cat human_v${genome_gencode_version}.tar.gz.* | tar xz
25+
wget --no-check-certificate $args ${params.fusioncatcher_download_link}
26+
tar xz human_v${genome_gencode_version}.tar.gz
2927
rm human_v${genome_gencode_version}.tar*
3028
3129
cat <<-END_VERSIONS > versions.yml

‎modules/local/fusionreport/detect/meta.yml‎

Lines changed: 0 additions & 51 deletions
This file was deleted.

‎modules/local/fusionreport/detect/tests/nextflow.config‎

Lines changed: 0 additions & 10 deletions
This file was deleted.

‎modules/local/fusionreport/download/environment.yml‎

Lines changed: 0 additions & 6 deletions
This file was deleted.

0 commit comments

Comments
 (0)