new module starfusion build

modules/nf-core/abacas/meta.yml

@@ -1,59 +1,65 @@
 name: abacas
 description: contiguate draft genome assembly
 keywords:
-  - genome
-  - assembly
-  - contiguate
+- genome
+- assembly
+- contiguate
 tools:
-  - abacas:
-      description: |
-        ABACAS is intended to rapidly contiguate (align, order, orientate),
-        visualize and design primers to close gaps on shotgun assembled
-        contigs based on a reference sequence.
-      homepage: http://abacas.sourceforge.net/documentation.html
-      documentation: http://abacas.sourceforge.net/documentation.html
-      doi: "10.1093/bioinformatics/btp347"
-      licence: ["GPL v2-or-later"]
-      identifier: biotools:abacas
+- abacas:
+    description: |
+      ABACAS is intended to rapidly contiguate (align, order, orientate),
+      visualize and design primers to close gaps on shotgun assembled
+      contigs based on a reference sequence.
+    homepage: http://abacas.sourceforge.net/documentation.html
+    documentation: http://abacas.sourceforge.net/documentation.html
+    doi: "10.1093/bioinformatics/btp347"
+    licence: ["GPL v2-or-later"]
+    identifier: biotools:abacas
 input:
-  - - meta:
-        type: map
-        description: |
-          Groovy Map containing sample information
-          e.g. [ id:'test', single_end:false ]
-    - scaffold:
-        type: file
-        description: Fasta file containing scaffold
-        pattern: "*.{fasta,fa}"
-  - - fasta:
-        type: file
-        description: FASTA reference file
-        pattern: "*.{fasta,fa}"
+- - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - scaffold:
+      type: file
+      description: Fasta file containing scaffold
+      pattern: "*.{fasta,fa}"
+      ontologies:
+      - edam: http://edamontology.org/format_1929  # FASTA
+- - fasta:
+      type: file
+      description: FASTA reference file
+      pattern: "*.{fasta,fa}"
+      ontologies:
+      - edam: http://edamontology.org/format_1929  # FASTA
 output:
-  - results:
-      - meta:
-          type: map
-          description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-      - "*.abacas*":
-          type: file
-          description: |
-            List containing abacas output files
-            [ 'test.abacas.bin', 'test.abacas.fasta', 'test.abacas.gaps',
-            'test.abacas.gaps.tab', 'test.abacas.nucmer.delta',
-            'test.abacas.nucmer.filtered.delta', 'test.abacas.nucmer.tiling',
-            'test.abacas.tab', 'test.abacas.unused.contigs.out',
-            'test.abacas.MULTIFASTA.fa' ]
-          pattern: "*.{abacas}*"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
+- results:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - "*.abacas*":
+      type: file
+      description: |
+        List containing abacas output files
+        [ 'test.abacas.bin', 'test.abacas.fasta', 'test.abacas.gaps',
+        'test.abacas.gaps.tab', 'test.abacas.nucmer.delta',
+        'test.abacas.nucmer.filtered.delta', 'test.abacas.nucmer.tiling',
+        'test.abacas.tab', 'test.abacas.unused.contigs.out',
+        'test.abacas.MULTIFASTA.fa' ]
+      pattern: "*.{abacas}*"
+      ontologies: []
+- versions:
+  - versions.yml:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+      ontologies: []
 authors:
-  - "@joseespinosa"
-  - "@drpatelh"
+- "@joseespinosa"
+- "@drpatelh"
 maintainers:
-  - "@joseespinosa"
-  - "@drpatelh"
+- "@joseespinosa"
+- "@drpatelh"

modules/nf-core/starfusion/build/environment.yml

@@ -0,0 +1,8 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::dfam=3.7
+  - bioconda::hmmer=3.4
+  - bioconda::minimap2=2.28
+  - bioconda::star-fusion=1.14.0

modules/nf-core/starfusion/build/main.nf

@@ -0,0 +1,135 @@
+process STARFUSION_BUILD {
+    tag "$meta.id"
+    label 'process_high'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/be/bed86145102fdf7e381e1a506a4723676f98b4bbe1db5085d02213cef18525c9/data' :
+        'community.wave.seqera.io/library/dfam_hmmer_minimap2_star-fusion:aa3a8e3951498552'}"
+
+    input:
+    tuple val(meta), path(fasta)
+    tuple val(meta2), path(gtf)
+    path fusion_annot_lib
+    val dfam_species
+
+    output:
+    tuple val(meta), path("${prefix}_genome_lib_build_dir"), emit: reference
+    path "versions.yml", emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    prep_genome_lib.pl \\
+        --genome_fa $fasta \\
+        --gtf $gtf \\
+        --dfam_db ${dfam_species} \\
+        --pfam_db current \\
+        --fusion_annot_lib $fusion_annot_lib \\
+        --CPU $task.cpus \\
+        --output_dir ${prefix}_genome_lib_build_dir \\
+        ${args}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        STAR-Fusion: \$(STAR-Fusion --version 2>&1 | grep -i 'version' | sed 's/STAR-Fusion version: //')
+    END_VERSIONS
+    """
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir -p ${prefix}_genome_lib_build_dir
+
+    touch ${prefix}_genome_lib_build_dir/AnnotFilterRule.pm
+    echo | gzip > ${prefix}_genome_lib_build_dir/blast_pairs.dat.gz
+    touch ${prefix}_genome_lib_build_dir/blast_pairs.idx
+
+    mkdir -p ${prefix}_genome_lib_build_dir/__chkpts
+    touch ${prefix}_genome_lib_build_dir/__chkpts/annotfiltrule_cp.ok
+    touch ${prefix}_genome_lib_build_dir/__chkpts/blast_pairs.idx.ok
+    touch ${prefix}_genome_lib_build_dir/__chkpts/cp_gene_blast_pairs.ok
+    touch ${prefix}_genome_lib_build_dir/__chkpts/cp_pfam_dat.ok
+    touch ${prefix}_genome_lib_build_dir/__chkpts/cp_ref_annot_cdna.ok
+    touch ${prefix}_genome_lib_build_dir/__chkpts/fusion_annot_lib.cp.ok
+    touch ${prefix}_genome_lib_build_dir/__chkpts/_fusion_annot_lib.idx.ok
+    touch ${prefix}_genome_lib_build_dir/__chkpts/index_pfam_hits.ok
+    touch ${prefix}_genome_lib_build_dir/__chkpts/index_ref_annot_cdna.ok
+    touch ${prefix}_genome_lib_build_dir/__chkpts/makeblastdb.ok
+    touch ${prefix}_genome_lib_build_dir/__chkpts/mm2_genome_idx.ok
+    touch ${prefix}_genome_lib_build_dir/__chkpts/mm2.splice_bed.ok
+    touch ${prefix}_genome_lib_build_dir/__chkpts/_prot_info_db.ok
+    touch ${prefix}_genome_lib_build_dir/__chkpts/ref_annot.cdsplus.dfam_masked.fa.cp.ok
+    touch ${prefix}_genome_lib_build_dir/__chkpts/ref_annot.cdsplus.dfam_masked.fa.idx.ok
+    touch ${prefix}_genome_lib_build_dir/__chkpts/ref_annot.gtf.gene_spans.ok
+    touch ${prefix}_genome_lib_build_dir/__chkpts/ref_annot.gtf.mini.sortu.ok
+    touch ${prefix}_genome_lib_build_dir/__chkpts/ref_annot.gtf.ok
+    touch ${prefix}_genome_lib_build_dir/__chkpts/ref_genome_fai.ok
+    touch ${prefix}_genome_lib_build_dir/__chkpts/ref_genome.fa.ok
+    touch ${prefix}_genome_lib_build_dir/__chkpts/trans.blast.dat.cp.ok
+    touch ${prefix}_genome_lib_build_dir/__chkpts/trans.blast.dat.index.ok
+    touch ${prefix}_genome_lib_build_dir/__chkpts/validate_ctat_genome_lib.ok
+
+    echo | gzip > ${prefix}_genome_lib_build_dir/fusion_annot_lib.gz
+    touch ${prefix}_genome_lib_build_dir/fusion_annot_lib.idx
+    touch ${prefix}_genome_lib_build_dir/pfam_domains.dbm
+    echo | gzip > ${prefix}_genome_lib_build_dir/PFAM.domtblout.dat.gz
+
+    touch ${prefix}_genome_lib_build_dir/ref_annot.cdna.fa
+    touch ${prefix}_genome_lib_build_dir/ref_annot.cdna.fa.idx
+    touch ${prefix}_genome_lib_build_dir/ref_annot.cds
+    touch ${prefix}_genome_lib_build_dir/ref_annot.cdsplus.fa
+    touch ${prefix}_genome_lib_build_dir/ref_annot.cdsplus.fa.idx
+    touch ${prefix}_genome_lib_build_dir/ref_annot.gtf
+    touch ${prefix}_genome_lib_build_dir/ref_annot.gtf.gene_spans
+    touch ${prefix}_genome_lib_build_dir/ref_annot.gtf.mini.sortu
+    touch ${prefix}_genome_lib_build_dir/ref_annot.gtf.mm2.splice.bed
+    touch ${prefix}_genome_lib_build_dir/ref_annot.pep
+    touch ${prefix}_genome_lib_build_dir/ref_annot.prot_info.dbm
+
+    touch ${prefix}_genome_lib_build_dir/ref_genome.fa
+    touch ${prefix}_genome_lib_build_dir/ref_genome.fa.fai
+    touch ${prefix}_genome_lib_build_dir/ref_genome.fa.mm2
+    touch ${prefix}_genome_lib_build_dir/ref_genome.fa.ndb
+    touch ${prefix}_genome_lib_build_dir/ref_genome.fa.nhr
+    touch ${prefix}_genome_lib_build_dir/ref_genome.fa.nin
+    touch ${prefix}_genome_lib_build_dir/ref_genome.fa.njs
+    touch ${prefix}_genome_lib_build_dir/ref_genome.fa.not
+    touch ${prefix}_genome_lib_build_dir/ref_genome.fa.nsq
+    touch ${prefix}_genome_lib_build_dir/ref_genome.fa.ntf
+    touch ${prefix}_genome_lib_build_dir/ref_genome.fa.nto
+
+    mkdir -p ${prefix}_genome_lib_build_dir/ref_genome.fa.star.idx
+    touch ${prefix}_genome_lib_build_dir/ref_genome.fa.star.idx/build.ok
+    touch ${prefix}_genome_lib_build_dir/ref_genome.fa.star.idx/chrLength.txt
+    touch ${prefix}_genome_lib_build_dir/ref_genome.fa.star.idx/chrNameLength.txt
+    touch ${prefix}_genome_lib_build_dir/ref_genome.fa.star.idx/chrName.txt
+    touch ${prefix}_genome_lib_build_dir/ref_genome.fa.star.idx/chrStart.txt
+    touch ${prefix}_genome_lib_build_dir/ref_genome.fa.star.idx/exonGeTrInfo.tab
+    touch ${prefix}_genome_lib_build_dir/ref_genome.fa.star.idx/exonInfo.tab
+    touch ${prefix}_genome_lib_build_dir/ref_genome.fa.star.idx/geneInfo.tab
+    touch ${prefix}_genome_lib_build_dir/ref_genome.fa.star.idx/Genome
+    touch ${prefix}_genome_lib_build_dir/ref_genome.fa.star.idx/genomeParameters.txt
+    touch ${prefix}_genome_lib_build_dir/ref_genome.fa.star.idx/Log.out
+    touch ${prefix}_genome_lib_build_dir/ref_genome.fa.star.idx/SA
+    touch ${prefix}_genome_lib_build_dir/ref_genome.fa.star.idx/SAindex
+    touch ${prefix}_genome_lib_build_dir/ref_genome.fa.star.idx/sjdbInfo.txt
+    touch ${prefix}_genome_lib_build_dir/ref_genome.fa.star.idx/sjdbList.fromGTF.out.tab
+    touch ${prefix}_genome_lib_build_dir/ref_genome.fa.star.idx/sjdbList.out.tab
+    touch ${prefix}_genome_lib_build_dir/ref_genome.fa.star.idx/transcriptInfo.tab
+
+    touch ${prefix}_genome_lib_build_dir/trans.blast.align_coords.align_coords.dat
+    touch ${prefix}_genome_lib_build_dir/trans.blast.align_coords.align_coords.dbm
+    echo | gzip > ${prefix}_genome_lib_build_dir/trans.blast.dat.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        STAR-Fusion: \$(STAR-Fusion --version 2>&1 | grep -i 'version' | sed 's/STAR-Fusion version: //')
+    END_VERSIONS
+    """
+
+}

modules/nf-core/starfusion/build/meta.yml

@@ -0,0 +1,74 @@
+name: starfusion_build
+description: Download STAR-fusion genome resource required to run STAR-Fusion caller
+keywords:
+  - download
+  - starfusion
+  - build
+
+tools:
+  - star-fusion:
+      description: Fusion calling algorithm for RNAseq data
+      homepage: https://github.com/STAR-Fusion/
+      documentation: https://github.com/STAR-Fusion/STAR-Fusion/wiki/installing-star-fusion
+      tool_dev_url: https://github.com/STAR-Fusion/STAR-Fusion
+      doi: "10.1186/s13059-019-1842-9"
+      licence: ["GPL v3"]
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: Metadata map
+        required: true
+    - fasta:
+        type: file
+        description: Input FASTA file
+        pattern: "*.{fa,fasta}"
+        required: true
+        ontologies:
+          - edam: http://edamontology.org/format_1929 # FASTA
+  - - meta2:
+        type: map
+        description: Second metadata map
+        required: true
+    - gtf:
+        type: file
+        description: Input GTF (Gene Transfer Format) file
+        pattern: "*.gtf"
+        required: true
+        ontologies:
+          - edam: "http://edamontology.org/format_2306" # GTF
+  - - fusion_annot_lib:
+        type: file
+        description: Fusion annotation library file containing known fusion genes
+        required: true
+        ontologies:
+          - edam: "http://edamontology.org/topic_0203" # Gene fusion
+  - - dfam_species:
+        type: string
+        description: Dfam species name
+output:
+  - reference:
+      - meta:
+          type: map
+          description: Metadata map
+      - ${prefix}_genome_lib_build_dir:
+          type: directory
+          description: Genome library build directory
+          pattern: "*_genome_lib_build_dir"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+          ontologies:
+            - edam: http://edamontology.org/format_3750 # YAML
+authors:
+  - "@praveenraj2018"
+  - "@martings"
+  - "@alanmmobbs93"
+  - "@delfiterradas"
+  - "@sofiromano"
+
+maintainers:
+  - "@praveenraj2018"