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Add singularity containers #588

Merged
merged 16 commits into from
Dec 19, 2024
Merged
4 changes: 3 additions & 1 deletion CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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

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3 changes: 1 addition & 2 deletions modules/local/fusioncatcher/detect/main.nf
Original file line number Diff line number Diff line change
Expand Up @@ -2,8 +2,7 @@ process FUSIONCATCHER {
tag "$meta.id"
label 'process_high'

conda "${moduleDir}/environment.yml"
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container "community.wave.seqera.io/library/fusioncatcher:1.33--4733482b637ef92f"
container "docker.io/rannickscilifelab/fusioncatcher:1.34"
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input:
tuple val(meta), path(fasta)
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3 changes: 1 addition & 2 deletions modules/local/fusioncatcher/download/main.nf
Original file line number Diff line number Diff line change
Expand Up @@ -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"
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output:
path "*" , emit: reference
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6 changes: 2 additions & 4 deletions modules/local/fusioninspector/environment.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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
4 changes: 3 additions & 1 deletion modules/local/fusioninspector/main.nf
Original file line number Diff line number Diff line change
Expand Up @@ -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)
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6 changes: 2 additions & 4 deletions modules/local/starfusion/build/environment.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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
7 changes: 4 additions & 3 deletions modules/local/starfusion/build/main.nf
Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand All @@ -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
Expand All @@ -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 \\
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6 changes: 2 additions & 4 deletions modules/local/starfusion/detect/environment.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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
4 changes: 3 additions & 1 deletion modules/local/starfusion/detect/main.nf
Original file line number Diff line number Diff line change
Expand Up @@ -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)
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6 changes: 2 additions & 4 deletions modules/local/starfusion/download/environment.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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
4 changes: 3 additions & 1 deletion modules/local/starfusion/download/main.nf
Original file line number Diff line number Diff line change
Expand Up @@ -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
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6 changes: 3 additions & 3 deletions workflows/build_references.nf
Original file line number Diff line number Diff line change
Expand Up @@ -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) {
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