Starfusion update

CHANGELOG.md

@@ -42,6 +42,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - 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)
 - Moved strandedness determination for picard collectrnaseqmetrics into modules.config [#658](https://github.com/nf-core/rnafusion/pull/658)
 - Using option `--human_gencode_filter` while building STARFusion references for human species [#657](https://github.com/nf-core/rnafusion/pull/657)
+- Update STAR-Fusion to 1.15.0 and update nf-core modules [#664](https://github.com/nf-core/rnafusion/pull/664)
 
 ### Changed
 

modules.json

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

modules/local/starfusion/build/environment.yml

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

modules/local/starfusion/build/main.nf

@@ -4,8 +4,8 @@ process STARFUSION_BUILD {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/be/bed86145102fdf7e381e1a506a4723676f98b4bbe1db5085d02213cef18525c9/data' :
-        'community.wave.seqera.io/library/dfam_hmmer_minimap2_star-fusion:aa3a8e3951498552'}"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b0/b0a58b9d30f9c72b22135f85746e10596d568c40a7d9634b13e0a0749cacd21b/data' :
+        'community.wave.seqera.io/library/dfam_hmmer_minimap2_star-fusion:c2bc5374f142ac93'}"
 
     input:
     tuple val(meta), path(fasta)
@@ -21,21 +21,23 @@ process STARFUSION_BUILD {
     script:
     def args = task.ext.args ?: ''
     """
-    wget http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam34.0/Pfam-A.hmm.gz --no-check-certificate
-
+    wget http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam37.4/Pfam-A.hmm.gz --no-check-certificate
     wget https://www.dfam.org/releases/Dfam_${dfam_version}/infrastructure/dfamscan/${dfam_species}_dfam.hmm --no-check-certificate
     wget https://www.dfam.org/releases/Dfam_${dfam_version}/infrastructure/dfamscan/${dfam_species}_dfam.hmm.h3f --no-check-certificate
     wget https://www.dfam.org/releases/Dfam_${dfam_version}/infrastructure/dfamscan/${dfam_species}_dfam.hmm.h3i --no-check-certificate
     wget https://www.dfam.org/releases/Dfam_${dfam_version}/infrastructure/dfamscan/${dfam_species}_dfam.hmm.h3m --no-check-certificate
     wget https://www.dfam.org/releases/Dfam_${dfam_version}/infrastructure/dfamscan/${dfam_species}_dfam.hmm.h3p --no-check-certificate
     gunzip Pfam-A.hmm.gz && hmmpress Pfam-A.hmm
+    wget https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/AnnotFilterRule.pm -O AnnotFilterRule.pm --no-check-certificate
+
 
     prep_genome_lib.pl \\
         --genome_fa $fasta \\
         --gtf $gtf \\
         --dfam_db ${dfam_species}_dfam.hmm \\
         --pfam_db Pfam-A.hmm \\
         --fusion_annot_lib $fusion_annot_lib \\
+        --annot_filter_rule AnnotFilterRule.pm \\
         --CPU $task.cpus \\
         ${args}
 

modules/local/starfusion/detect/main.nf

@@ -4,8 +4,8 @@ process STARFUSION {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/be/bed86145102fdf7e381e1a506a4723676f98b4bbe1db5085d02213cef18525c9/data' :
-        'community.wave.seqera.io/library/dfam_hmmer_minimap2_star-fusion:aa3a8e3951498552'}"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b0/b0a58b9d30f9c72b22135f85746e10596d568c40a7d9634b13e0a0749cacd21b/data' :
+        'community.wave.seqera.io/library/dfam_hmmer_minimap2_star-fusion:c2bc5374f142ac93'}"
 
     input:
     tuple val(meta), path(reads), path(junction)