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@rannick
rannick committed Dec 20, 2024
1 parent 60f0da6 commit ab65540
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Showing 2 changed files with 70 additions and 14 deletions.
78 changes: 67 additions & 11 deletions tests/test_stub.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,14 +1,17 @@
{
"stub test no fastp trim": {
"content": [
29,
31,
{
"ARRIBA_ARRIBA": {
"arriba": "2.4.0"
},
"ARRIBA_DOWNLOAD": {
"arriba_download": "2.4.0"
},
"CTATSPLICING_STARTOCANCERINTRONS": {
"ctat-splicing": "0.0.2"
},
"FASTQC": {
"fastqc": "0.12.1"
},
Expand Down Expand Up @@ -74,17 +77,17 @@
"STAR-Fusion": "1.14.0"
},
"STAR_FOR_ARRIBA": {
"star": null,
"star": "2.7.11b",
"samtools": 1.2,
"gawk": "5.1.0"
},
"STAR_FOR_STARFUSION": {
"star": null,
"star": "2.7.11b",
"samtools": 1.2,
"gawk": "5.1.0"
},
"STAR_GENOMEGENERATE": {
"star": null,
"star": "2.7.11b",
"samtools": 1.2,
"gawk": "5.1.0"
},
Expand All @@ -102,6 +105,31 @@
"arriba",
"arriba/test.arriba.fusions.discarded.tsv",
"arriba/test.arriba.fusions.tsv",
"ctatsplicing",
"ctatsplicing/arriba",
"ctatsplicing/arriba/test.cancer.introns",
"ctatsplicing/arriba/test.cancer.introns.prelim",
"ctatsplicing/arriba/test.cancer_intron_reads.sorted.bam",
"ctatsplicing/arriba/test.cancer_intron_reads.sorted.bam.bai",
"ctatsplicing/arriba/test.chckpts",
"ctatsplicing/arriba/test.ctat-splicing.igv.html",
"ctatsplicing/arriba/test.gene_reads.sorted.sifted.bam",
"ctatsplicing/arriba/test.gene_reads.sorted.sifted.bam.bai",
"ctatsplicing/arriba/test.igv.tracks",
"ctatsplicing/arriba/test.introns",
"ctatsplicing/arriba/test.introns.for_IGV.bed",
"ctatsplicing/starfusion",
"ctatsplicing/starfusion/test.cancer.introns",
"ctatsplicing/starfusion/test.cancer.introns.prelim",
"ctatsplicing/starfusion/test.cancer_intron_reads.sorted.bam",
"ctatsplicing/starfusion/test.cancer_intron_reads.sorted.bam.bai",
"ctatsplicing/starfusion/test.chckpts",
"ctatsplicing/starfusion/test.ctat-splicing.igv.html",
"ctatsplicing/starfusion/test.gene_reads.sorted.sifted.bam",
"ctatsplicing/starfusion/test.gene_reads.sorted.sifted.bam.bai",
"ctatsplicing/starfusion/test.igv.tracks",
"ctatsplicing/starfusion/test.introns",
"ctatsplicing/starfusion/test.introns.for_IGV.bed",
"fastqc",
"fastqc/test.html",
"fastqc/test.zip",
Expand Down Expand Up @@ -329,18 +357,21 @@
"nf-test": "0.9.0",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-20T13:17:20.018293"
"timestamp": "2024-12-20T14:00:19.311265"
},
"stub test with fastp trim": {
"content": [
31,
33,
{
"ARRIBA_ARRIBA": {
"arriba": "2.4.0"
},
"ARRIBA_DOWNLOAD": {
"arriba_download": "2.4.0"
},
"CTATSPLICING_STARTOCANCERINTRONS": {
"ctat-splicing": "0.0.2"
},
"FASTP": {
"fastp": "0.23.4"
},
Expand Down Expand Up @@ -412,17 +443,17 @@
"STAR-Fusion": "1.14.0"
},
"STAR_FOR_ARRIBA": {
"star": null,
"star": "2.7.11b",
"samtools": 1.2,
"gawk": "5.1.0"
},
"STAR_FOR_STARFUSION": {
"star": null,
"star": "2.7.11b",
"samtools": 1.2,
"gawk": "5.1.0"
},
"STAR_GENOMEGENERATE": {
"star": null,
"star": "2.7.11b",
"samtools": 1.2,
"gawk": "5.1.0"
},
Expand All @@ -440,6 +471,31 @@
"arriba",
"arriba/test.arriba.fusions.discarded.tsv",
"arriba/test.arriba.fusions.tsv",
"ctatsplicing",
"ctatsplicing/arriba",
"ctatsplicing/arriba/test.cancer.introns",
"ctatsplicing/arriba/test.cancer.introns.prelim",
"ctatsplicing/arriba/test.cancer_intron_reads.sorted.bam",
"ctatsplicing/arriba/test.cancer_intron_reads.sorted.bam.bai",
"ctatsplicing/arriba/test.chckpts",
"ctatsplicing/arriba/test.ctat-splicing.igv.html",
"ctatsplicing/arriba/test.gene_reads.sorted.sifted.bam",
"ctatsplicing/arriba/test.gene_reads.sorted.sifted.bam.bai",
"ctatsplicing/arriba/test.igv.tracks",
"ctatsplicing/arriba/test.introns",
"ctatsplicing/arriba/test.introns.for_IGV.bed",
"ctatsplicing/starfusion",
"ctatsplicing/starfusion/test.cancer.introns",
"ctatsplicing/starfusion/test.cancer.introns.prelim",
"ctatsplicing/starfusion/test.cancer_intron_reads.sorted.bam",
"ctatsplicing/starfusion/test.cancer_intron_reads.sorted.bam.bai",
"ctatsplicing/starfusion/test.chckpts",
"ctatsplicing/starfusion/test.ctat-splicing.igv.html",
"ctatsplicing/starfusion/test.gene_reads.sorted.sifted.bam",
"ctatsplicing/starfusion/test.gene_reads.sorted.sifted.bam.bai",
"ctatsplicing/starfusion/test.igv.tracks",
"ctatsplicing/starfusion/test.introns",
"ctatsplicing/starfusion/test.introns.for_IGV.bed",
"fastp",
"fastp/test.fastp.html",
"fastp/test.fastp.json",
Expand Down Expand Up @@ -676,6 +732,6 @@
"nf-test": "0.9.0",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-20T13:15:06.974011"
"timestamp": "2024-12-20T13:57:10.179877"
}
}
}
6 changes: 3 additions & 3 deletions workflows/rnafusion.nf
View file
Original file line number Diff line number Diff line change
Expand Up @@ -92,7 +92,7 @@ workflow RNAFUSION {
BUILD_REFERENCES.out.ch_arriba_ref_cytobands,
BUILD_REFERENCES.out.ch_arriba_ref_known_fusions,
BUILD_REFERENCES.out.ch_arriba_ref_protein_domains,
ch_starfusion_ref,
BUILD_REFERENCES.out.ch_starfusion_ref,
params.arriba, // boolean
params.all, // boolean
params.fusioninspector_only, // boolean
Expand All @@ -110,8 +110,8 @@ workflow RNAFUSION {
ch_reads,
BUILD_REFERENCES.out.ch_gtf,
BUILD_REFERENCES.out.ch_starindex_ref,
BUILD_REFERENCES.out.ch_fasta
ch_starfusion_ref
BUILD_REFERENCES.out.ch_fasta,
BUILD_REFERENCES.out.ch_starfusion_ref
)
ch_versions = ch_versions.mix(STARFUSION_WORKFLOW.out.versions)

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