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Merge pull request #664 from nf-core/starfusion_update
Starfusion update
2 parents dc671e1 + e5025e4 commit cf214a2

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‎CHANGELOG.md‎

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@@ -42,6 +42,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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- Added the `seq_platform` and `seq_center` fields to the samplesheet. These values can be used to overwrite the value of `--seq_platform` and `--seq_center` on a sample-by-sample basis [#654](https://github.com/nf-core/rnafusion/pull/654)
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- Moved strandedness determination for picard collectrnaseqmetrics into modules.config [#658](https://github.com/nf-core/rnafusion/pull/658)
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- Using option `--human_gencode_filter` while building STARFusion references for human species [#657](https://github.com/nf-core/rnafusion/pull/657)
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- Update STAR-Fusion to 1.15.0 and update nf-core modules [#664](https://github.com/nf-core/rnafusion/pull/664)
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- Update fusionreport 4.0.0 that replaces the score of a fusion with a Fusion Indication Index [#667](https://github.com/nf-core/rnafusion/pull/667)
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### Changed

‎modules.json‎

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@@ -7,7 +7,7 @@
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"nf-core": {
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"agat/convertspgff2tsv": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
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"installed_by": ["modules"]
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},
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"arriba/arriba": {
@@ -17,27 +17,27 @@
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},
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"arriba/download": {
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"branch": "master",
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"git_sha": "467c202a876d26af544fa8c4b22a050a535462a7",
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
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"installed_by": ["modules"]
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},
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"cat/cat": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
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"installed_by": ["modules"]
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},
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"cat/fastq": {
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"branch": "master",
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"git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc",
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
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"installed_by": ["modules"]
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},
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"fastp": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "d082103d7976a2804f21225446cc110cbd822f4c",
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"installed_by": ["modules"]
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},
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"fastqc": {
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"branch": "master",
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"git_sha": "08108058ea36a63f141c25c4e75f9f872a5b2296",
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"git_sha": "b1966f36ec9de31927b2603d8f499960b2a4c294",
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"installed_by": ["modules"]
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},
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"fusioncatcher/fusioncatcher": {
@@ -47,108 +47,97 @@
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},
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"gatk4/bedtointervallist": {
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"branch": "master",
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"git_sha": "1999eff2c530b2b185a25cc42117a1686f09b685",
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
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"installed_by": ["modules"]
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},
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"gatk4/createsequencedictionary": {
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"branch": "master",
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"git_sha": "1999eff2c530b2b185a25cc42117a1686f09b685",
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
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"installed_by": ["modules"]
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},
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"gatk4/markduplicates": {
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"branch": "master",
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"git_sha": "1999eff2c530b2b185a25cc42117a1686f09b685",
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"git_sha": "1ec937ab3edc307bc0d79a2200d784e9f0868359",
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"installed_by": ["modules"]
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},
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"gffread": {
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"branch": "master",
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"git_sha": "bd5f75ccaf2345269810e66e85de8a70e4de8764",
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
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"installed_by": ["modules"]
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},
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"multiqc": {
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"branch": "master",
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"git_sha": "f0719ae309075ae4a291533883847c3f7c441dad",
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"git_sha": "7b50cb7be890e4b28cffb82e438cc6a8d7805d3f",
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"installed_by": ["modules"]
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},
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"picard/collectinsertsizemetrics": {
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"branch": "master",
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"git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
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"git_sha": "980a4964be91da75fb3ccf576118a18e247f6d15",
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"installed_by": ["modules"]
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},
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"picard/collectrnaseqmetrics": {
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"branch": "master",
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"git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
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"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
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"installed_by": ["modules"]
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},
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"picard/collectwgsmetrics": {
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"branch": "master",
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"git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
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"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
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"installed_by": ["modules"]
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},
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"rrnatranscripts": {
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"branch": "master",
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"git_sha": "812edf8cf702de42d2d8c7314d6f03b97e20abeb",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/rrnatranscripts/rrnatranscripts.diff"
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},
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"salmon/index": {
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"branch": "master",
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"git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
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"installed_by": ["modules"]
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},
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"salmon/quant": {
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"branch": "master",
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"git_sha": "85b5f8a0d9df9ce7587af50e2ee75b37c97515c6",
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"git_sha": "db5a84497b80c4932b4498ec231f19403d19bcff",
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"installed_by": ["modules"]
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},
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"samtools/convert": {
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"branch": "master",
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"git_sha": "b823b7220bac94079f9ea65113401956ca7d633e",
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
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"installed_by": ["modules"]
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},
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"samtools/faidx": {
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"branch": "master",
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"git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
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"installed_by": ["modules"]
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},
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"samtools/index": {
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"branch": "master",
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"git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
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"installed_by": ["modules"]
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},
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"samtools/sort": {
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"branch": "master",
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"git_sha": "b7800db9b069ed505db3f9d91b8c72faea9be17b",
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"installed_by": ["modules"]
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},
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"samtools/view": {
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"branch": "master",
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"git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
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"installed_by": ["modules"]
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},
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"star/align": {
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"branch": "master",
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"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
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"installed_by": ["modules"]
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},
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"star/genomegenerate": {
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"branch": "master",
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"git_sha": "a5ad53288c79fa52c5ae708c317e09ec2dd149ab",
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
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"installed_by": ["modules"]
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},
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"stringtie/merge": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
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"installed_by": ["modules"]
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},
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"stringtie/stringtie": {
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"branch": "master",
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"git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
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"installed_by": ["modules"]
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},
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"ucsc/gtftogenepred": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
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"installed_by": ["modules"]
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}
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}

‎modules/local/starfusion/build/environment.yml‎

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@@ -4,5 +4,5 @@ channels:
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dependencies:
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- bioconda::dfam=3.7
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- bioconda::hmmer=3.4
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- bioconda::minimap2=2.28
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- bioconda::star-fusion=1.14.0
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- bioconda::minimap2=2.29
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- bioconda::star-fusion=1.15.0

‎modules/local/starfusion/build/main.nf‎

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@@ -4,15 +4,16 @@ process STARFUSION_BUILD {
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conda "${moduleDir}/environment.yml"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
7-
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/be/bed86145102fdf7e381e1a506a4723676f98b4bbe1db5085d02213cef18525c9/data' :
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'community.wave.seqera.io/library/dfam_hmmer_minimap2_star-fusion:aa3a8e3951498552'}"
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'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b0/b0a58b9d30f9c72b22135f85746e10596d568c40a7d9634b13e0a0749cacd21b/data' :
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'community.wave.seqera.io/library/dfam_hmmer_minimap2_star-fusion:c2bc5374f142ac93'}"
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input:
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tuple val(meta), path(fasta)
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tuple val(meta2), path(gtf)
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path fusion_annot_lib
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val dfam_species
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val dfam_version
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val pfam_version
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output:
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tuple val(meta), path("ctat_genome_lib_build_dir"), emit: reference
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script:
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def args = task.ext.args ?: ''
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"""
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wget http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam34.0/Pfam-A.hmm.gz --no-check-certificate
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wget http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam${pfam_version}/Pfam-A.hmm.gz --no-check-certificate
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wget https://www.dfam.org/releases/Dfam_${dfam_version}/infrastructure/dfamscan/${dfam_species}_dfam.hmm --no-check-certificate
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wget https://www.dfam.org/releases/Dfam_${dfam_version}/infrastructure/dfamscan/${dfam_species}_dfam.hmm.h3f --no-check-certificate
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wget https://www.dfam.org/releases/Dfam_${dfam_version}/infrastructure/dfamscan/${dfam_species}_dfam.hmm.h3i --no-check-certificate
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wget https://www.dfam.org/releases/Dfam_${dfam_version}/infrastructure/dfamscan/${dfam_species}_dfam.hmm.h3m --no-check-certificate
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wget https://www.dfam.org/releases/Dfam_${dfam_version}/infrastructure/dfamscan/${dfam_species}_dfam.hmm.h3p --no-check-certificate
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gunzip Pfam-A.hmm.gz && hmmpress Pfam-A.hmm
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wget https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/AnnotFilterRule.pm -O AnnotFilterRule.pm --no-check-certificate
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prep_genome_lib.pl \\
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--genome_fa $fasta \\
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--gtf $gtf \\
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--dfam_db ${dfam_species}_dfam.hmm \\
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--pfam_db Pfam-A.hmm \\
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--fusion_annot_lib $fusion_annot_lib \\
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--annot_filter_rule AnnotFilterRule.pm \\
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--CPU $task.cpus \\
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${args}
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‎modules/local/starfusion/build/meta.yml‎

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- dfam_version:
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type: string
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description: DNA transposable element database version, required for repeat masking. Values such as '3.4' are accepted (will automatically pull the resources from dfam).
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- pfam_version:
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type: string
35+
description: Protein families database version, to get domain information. Values such as '37.4' are accepted (will automatically pull the resources from Pfam).
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output:
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- reference:

‎modules/local/starfusion/build/tests/main.nf.test‎

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input [2] = file("https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/master/CTAT_HumanFusionLib.mini.dat.gz")
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input [3] = "homo_sapiens"
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input [4] = "3.4"
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input [4] = "3.8"
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input [5] = "37.4"
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2526
"""
2627
}
@@ -125,7 +126,8 @@ nextflow_process {
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126127
input [2] = file("https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/master/CTAT_HumanFusionLib.mini.dat.gz")
127128
input [3] = "homo_sapiens"
128-
input [4] = "3.4"
129+
input [4] = "3.8"
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input [5] = "37.4"
129131

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"""
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}

‎modules/local/starfusion/build/tests/main.nf.test.snap‎

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{
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"STARFUSION_BUILD - human - minigenome": {
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"content": [
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"AnnotFilterRule.pm:md5,5391fcc58d9c71cd1f0e45668c5ec597",
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"AnnotFilterRule.pm:md5,f94966013cd0df9624a6dda0b75fefa0",
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true,
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true,
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"annotfiltrule_cp.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -75,14 +75,14 @@
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true,
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"trans.blast.dat.gz:md5,85ba5ea96c566f751ad83a3e4b8ab128",
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[
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"versions.yml:md5,4a6ed47cb345f2a5af4d9f12b7918cdb"
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"versions.yml:md5,99533491facb961016dafc1d45a8101e"
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]
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "24.10.5"
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"nf-test": "0.8.4",
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"nextflow": "24.10.6"
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},
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"timestamp": "2025-04-15T17:34:00.624179533"
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"timestamp": "2025-05-07T20:31:12.177376155"
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},
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"STARFUSION_BUILD - human - minigenome - stub": {
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"content": [
@@ -173,7 +173,7 @@
173173
]
174174
],
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"1": [
176-
"versions.yml:md5,4a6ed47cb345f2a5af4d9f12b7918cdb"
176+
"versions.yml:md5,99533491facb961016dafc1d45a8101e"
177177
],
178178
"reference": [
179179
[
@@ -261,14 +261,14 @@
261261
]
262262
],
263263
"versions": [
264-
"versions.yml:md5,4a6ed47cb345f2a5af4d9f12b7918cdb"
264+
"versions.yml:md5,99533491facb961016dafc1d45a8101e"
265265
]
266266
}
267267
],
268268
"meta": {
269-
"nf-test": "0.9.2",
270-
"nextflow": "24.10.5"
269+
"nf-test": "0.8.4",
270+
"nextflow": "24.10.6"
271271
},
272-
"timestamp": "2025-04-15T17:34:36.490161525"
272+
"timestamp": "2025-05-07T20:31:53.437179641"
273273
}
274-
}
274+
}

‎modules/local/starfusion/detect/main.nf‎

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Original file line numberDiff line numberDiff line change
@@ -4,8 +4,8 @@ process STARFUSION {
44

55
conda "${moduleDir}/environment.yml"
66
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
7-
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/be/bed86145102fdf7e381e1a506a4723676f98b4bbe1db5085d02213cef18525c9/data' :
8-
'community.wave.seqera.io/library/dfam_hmmer_minimap2_star-fusion:aa3a8e3951498552'}"
7+
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b0/b0a58b9d30f9c72b22135f85746e10596d568c40a7d9634b13e0a0749cacd21b/data' :
8+
'community.wave.seqera.io/library/dfam_hmmer_minimap2_star-fusion:c2bc5374f142ac93'}"
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1111
tuple val(meta), path(reads), path(junction)

‎modules/nf-core/agat/convertspgff2tsv/environment.yml‎

Lines changed: 3 additions & 1 deletion
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‎modules/nf-core/agat/convertspgff2tsv/main.nf‎

Lines changed: 2 additions & 3 deletions
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