Merge pull request #588 from nf-core/add_singularity_containers

Add singularity containers
nf-core · Dec 19, 2024 · 1ede9b4 · 1ede9b4
2 parents 077eb17 + 27b3f8b
commit 1ede9b4
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Showing 12 changed files with 29 additions and 30 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -19,7 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Add nf-test to local module: `FUSIONREPORT_DOWNLOAD` [#560](https://github.com/nf-core/rnafusion/pull/560)
 - Add nf-test to local subworkflow: `QC_WORKFLOW` [#568](https://github.com/nf-core/rnafusion/pull/568)
 - Add nf-test to local subworkflow: `TRIM_WORKFLOW` [#572](https://github.com/nf-core/rnafusion/pull/572)
-- Add nf-test to local module: `FUSIONREPORT_DETECT`. Improve `FUSIONREPORT_DOWNLOAD` module [#572](https://github.com/nf-core/rnafusion/pull/577)
+- Add nf-test to local module: `FUSIONREPORT_DETECT`. Improve `FUSIONREPORT_DOWNLOAD` module [#577](https://github.com/nf-core/rnafusion/pull/577)
 - Add nf-test to local subworkflow: `ARRIBA_WORKFLOW` [#578](https://github.com/nf-core/rnafusion/pull/578)
 
 ### Changed
@@ -29,6 +29,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Remove local module `RRNA_TRANSCRIPTS` (replaced by nf-core module) [#541](https://github.com/nf-core/rnafusion/pull/541)
 - Allow fastq files without a dot before .fn(.gz)/.fastq(.gz) files [#548](https://github.com/nf-core/rnafusion/pull/548)
 - Remove double nested folder introduced in [#577](https://github.com/nf-core/rnafusion/pull/577), [#581](https://github.com/nf-core/rnafusion/pull/581)
+- Use docker.io and galaxy containers for fusioncatcher and starfusion (incl. fusioninspector) instead of wave as they are not functional on wave [#588](https://github.com/nf-core/rnafusion/pull/588)
+- Update STAR-Fusion to 1.14 [#588](https://github.com/nf-core/rnafusion/pull/588)
 
 ### Fixed
 

diff --git a/modules/local/fusioncatcher/detect/main.nf b/modules/local/fusioncatcher/detect/main.nf
@@ -2,8 +2,7 @@ process FUSIONCATCHER {
     tag "$meta.id"
     label 'process_high'
 
-    conda "${moduleDir}/environment.yml"
-    container "community.wave.seqera.io/library/fusioncatcher:1.33--4733482b637ef92f"
+    container "docker.io/rannickscilifelab/fusioncatcher:1.34"
 
     input:
     tuple val(meta), path(fasta)

diff --git a/modules/local/fusioncatcher/download/main.nf b/modules/local/fusioncatcher/download/main.nf
@@ -2,8 +2,7 @@ process FUSIONCATCHER_DOWNLOAD {
     tag "fusioncatcher_download"
     label 'process_medium'
 
-    conda "${moduleDir}/environment.yml"
-    container "community.wave.seqera.io/library/fusioncatcher:1.33--4733482b637ef92f"
+    container "docker.io/rannickscilifelab/fusioncatcher:1.34"
 
     output:
     path "*"                , emit: reference

diff --git a/modules/local/fusioninspector/environment.yml b/modules/local/fusioninspector/environment.yml
@@ -4,7 +4,5 @@ channels:
 dependencies:
   - bioconda::dfam=3.7
   - bioconda::hmmer=3.4
-  - bioconda::star-fusion=1.7.0
-  - bioconda::trinity=2.15.2
-  - bioconda::samtools=1.21
-  - bioconda::star=2.7.11b
+  - bioconda::minimap2=2.28
+  - bioconda::star-fusion=1.14.0
diff --git a/modules/local/fusioninspector/main.nf b/modules/local/fusioninspector/main.nf
@@ -3,7 +3,9 @@ process FUSIONINSPECTOR {
     label 'process_high'
 
     conda "${moduleDir}/environment.yml"
-    container 'community.wave.seqera.io/library/dfam_hmmer_samtools_star-fusion_pruned:5694d82381bf039e'
+    container "${ 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'}"
 
     input:
     tuple val(meta), path(reads), path(fusion_list)

diff --git a/modules/local/starfusion/build/environment.yml b/modules/local/starfusion/build/environment.yml
@@ -4,7 +4,5 @@ channels:
 dependencies:
   - bioconda::dfam=3.7
   - bioconda::hmmer=3.4
-  - bioconda::star-fusion=1.7.0
-  - bioconda::trinity=2.15.2
-  - bioconda::samtools=1.21
-  - bioconda::star=2.7.11b
+  - bioconda::minimap2=2.28
+  - bioconda::star-fusion=1.14.0
diff --git a/modules/local/starfusion/build/main.nf b/modules/local/starfusion/build/main.nf
@@ -2,7 +2,9 @@ process STARFUSION_BUILD {
     tag 'star-fusion'
 
     conda "${moduleDir}/environment.yml"
-    container 'community.wave.seqera.io/library/dfam_hmmer_samtools_star-fusion_pruned:5694d82381bf039e'
+    container "${ 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'}"
 
     input:
     tuple val(meta), path(fasta)
@@ -12,7 +14,6 @@ process STARFUSION_BUILD {
     path "*"  , emit: reference
 
     script:
-    def binPath = (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1)  ? "prep_genome_lib.pl" : "/usr/local/src/STAR-Fusion/ctat-genome-lib-builder/prep_genome_lib.pl"
     """
     export TMPDIR=/tmp
     wget http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam34.0/Pfam-A.hmm.gz --no-check-certificate
@@ -24,7 +25,7 @@ process STARFUSION_BUILD {
     wget https://www.dfam.org/releases/Dfam_3.4/infrastructure/dfamscan/homo_sapiens_dfam.hmm.h3m --no-check-certificate
     wget https://www.dfam.org/releases/Dfam_3.4/infrastructure/dfamscan/homo_sapiens_dfam.hmm.h3p --no-check-certificate
     gunzip Pfam-A.hmm.gz && hmmpress Pfam-A.hmm
-    $binPath \\
+    prep_genome_lib.pl \\
         --genome_fa $fasta \\
         --gtf $gtf \\
         --annot_filter_rule AnnotFilterRule.pm \\

diff --git a/modules/local/starfusion/detect/environment.yml b/modules/local/starfusion/detect/environment.yml
@@ -4,7 +4,5 @@ channels:
 dependencies:
   - bioconda::dfam=3.7
   - bioconda::hmmer=3.4
-  - bioconda::star-fusion=1.7.0
-  - bioconda::trinity=2.15.2
-  - bioconda::samtools=1.21
-  - bioconda::star=2.7.11b
+  - bioconda::minimap2=2.28
+  - bioconda::star-fusion=1.14.0
diff --git a/modules/local/starfusion/detect/main.nf b/modules/local/starfusion/detect/main.nf
@@ -3,7 +3,9 @@ process STARFUSION {
     label 'process_high'
 
     conda "${moduleDir}/environment.yml"
-    container 'community.wave.seqera.io/library/dfam_hmmer_samtools_star-fusion_pruned:5694d82381bf039e'
+    container "${ 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'}"
 
     input:
     tuple val(meta), path(reads), path(junction)

diff --git a/modules/local/starfusion/download/environment.yml b/modules/local/starfusion/download/environment.yml
@@ -4,7 +4,5 @@ channels:
 dependencies:
   - bioconda::dfam=3.7
   - bioconda::hmmer=3.4
-  - bioconda::star-fusion=1.7.0
-  - bioconda::trinity=2.15.2
-  - bioconda::samtools=1.21
-  - bioconda::star=2.7.11b
+  - bioconda::minimap2=2.28
+  - bioconda::star-fusion=1.14.0
diff --git a/modules/local/starfusion/download/main.nf b/modules/local/starfusion/download/main.nf
@@ -2,7 +2,9 @@ process STARFUSION_DOWNLOAD {
     tag 'star-fusion'
 
     conda "${moduleDir}/environment.yml"
-    container 'community.wave.seqera.io/library/dfam_hmmer_samtools_star-fusion_pruned:5694d82381bf039e'
+    container "${ 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'}"
 
     output:
     path "ctat_genome_lib_build_dir/*"            , emit: reference

diff --git a/workflows/build_references.nf b/workflows/build_references.nf
@@ -44,14 +44,14 @@ workflow BUILD_REFERENCES {
     GATK4_CREATESEQUENCEDICTIONARY(ENSEMBL_DOWNLOAD.out.primary_assembly)
 
 
-    RRNATRANSCRIPTS(ENSEMBL_DOWNLOAD.out.gtf.map{ meta, gtf -> [ gtf ] })
+    RRNATRANSCRIPTS(ENSEMBL_DOWNLOAD.out.gtf.map{ it -> [ it[1] ] })
     BEDOPS_CONVERT2BED(RRNATRANSCRIPTS.out.rrna_gtf.map{ it -> [[id:it.Name], it] })
     GATK4_BEDTOINTERVALLIST(BEDOPS_CONVERT2BED.out.bed, GATK4_CREATESEQUENCEDICTIONARY.out.dict)
 
-    GFFREAD(ENSEMBL_DOWNLOAD.out.gtf, ENSEMBL_DOWNLOAD.out.primary_assembly.map { meta, fasta -> [ fasta ] })
+    GFFREAD(ENSEMBL_DOWNLOAD.out.gtf, ENSEMBL_DOWNLOAD.out.primary_assembly.map { it -> [ it[1] ] })
 
     if (!params.skip_salmon_index){
-        SALMON_INDEX(ENSEMBL_DOWNLOAD.out.primary_assembly.map{ meta, fasta -> [ fasta ] }, GFFREAD.out.gffread_fasta.map{ meta, gffread_fasta -> [ gffread_fasta ] })
+        SALMON_INDEX(ENSEMBL_DOWNLOAD.out.primary_assembly.map{ it -> [ it[1] ] }, GFFREAD.out.gffread_fasta.map{ it -> [ it[1] ] })
     }
 
     if (params.starindex || params.all || params.starfusion || params.arriba) {