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update softwareversion file
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@rannick
rannick committed Jan 7, 2025
1 parent 001c415 commit c5c45c0
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Showing 5 changed files with 217 additions and 15 deletions.
2 changes: 1 addition & 1 deletion subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -130,7 +130,7 @@ workflow PIPELINE_COMPLETION {
plaintext_email,
outdir,
monochrome_logs,
multiqc_reports.getVal(),
multiqc_reports.getVal()
)
}

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6 changes: 3 additions & 3 deletions tests/test_cosmic.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@ nextflow_pipeline {
// Number of successful tasks
workflow.trace.succeeded().size(),
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnafusion_software_mqc_versions.yml"),
// All stable path name, with a relative path
stable_name,
// All files with stable contents
Expand Down Expand Up @@ -58,7 +58,7 @@ nextflow_pipeline {
// Number of successful tasks
workflow.trace.succeeded().size(),
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnafusion_software_mqc_versions.yml"),
// All stable path name, with a relative path
stable_name,
// All files with stable contents
Expand Down Expand Up @@ -89,7 +89,7 @@ nextflow_pipeline {
// Number of successful tasks
workflow.trace.succeeded().size(),
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnafusion_software_mqc_versions.yml"),
// All stable path name, with a relative path
stable_name,
// All files with stable contents
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10 changes: 5 additions & 5 deletions tests/test_cosmic.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -9,10 +9,10 @@
},
[
"pipeline_info",
"pipeline_info/nf_core_pipeline_software_mqc_versions.yml"
"pipeline_info/nf_core_rnafusion_software_mqc_versions.yml"
],
[

]
],
"meta": {
Expand All @@ -29,7 +29,7 @@
"pipeline_info"
],
[

]
],
"meta": {
Expand All @@ -46,7 +46,7 @@
"pipeline_info"
],
[

]
],
"meta": {
Expand All @@ -55,4 +55,4 @@
},
"timestamp": "2024-12-10T15:09:29.277399"
}
}
}
4 changes: 2 additions & 2 deletions tests/test_stub.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ nextflow_pipeline {
// Number of successful tasks
workflow.trace.succeeded().size(),
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnafusion_software_mqc_versions.yml"),
// All stable path name, with a relative path
stable_name,
// All files with stable contents
Expand Down Expand Up @@ -61,7 +61,7 @@ nextflow_pipeline {
// Number of successful tasks
workflow.trace.succeeded().size(),
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnafusion_software_mqc_versions.yml"),
// All stable path name, with a relative path
stable_name,
// All files with stable contents
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210 changes: 206 additions & 4 deletions tests/test_stub.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,105 @@
"stub test no fastp trim": {
"content": [
31,
null,
{
"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"
},
"FUSIONCATCHER": {
"fusioncatcher": 1.35
},
"FUSIONCATCHER_BUILD": {
"fusioncatcher": "fusioncatcher.py 1.35"
},
"FUSIONREPORT": {
"fusion_report": "2.1.5"
},
"FUSIONREPORT_DOWNLOAD": {
"fusion_report": "2.1.5"
},
"GATK4_BEDTOINTERVALLIST": {
"gatk4": "4.6.1.0"
},
"GATK4_CREATESEQUENCEDICTIONARY": {
"gatk4": "4.6.1.0"
},
"GATK4_MARKDUPLICATES": {
"gatk4": "4.5.0.0",
"samtools": "1.19.2"
},
"GENCODE_DOWNLOAD": {
"wget": null
},
"GET_RRNA_TRANSCRIPTS": {
"get_rrna_transcripts": "v1.0"
},
"GFFREAD": {
"gffread": "0.12.7"
},
"GTF_TO_REFFLAT": {
"gtfToGenePred": 377
},
"HGNC_DOWNLOAD": {
"wget": null
},
"PICARD_COLLECTINSERTSIZEMETRICS": {
"picard": "3.3.0"
},
"PICARD_COLLECTRNASEQMETRICS": {
"picard": "3.3.0"
},
"SALMON_INDEX": {
"salmon": "1.10.3"
},
"SALMON_QUANT": {
"salmon": "1.10.3"
},
"SAMTOOLS_FAIDX": {
"samtools": 1.21
},
"SAMTOOLS_INDEX_FOR_STARFUSION": {
"samtools": 1.21
},
"STARFUSION": {
"STAR-Fusion": "1.14.0"
},
"STARFUSION_BUILD": {
"STAR-Fusion": "1.14.0"
},
"STAR_FOR_ARRIBA": {
"star": null,
"samtools": 1.2,
"gawk": "5.1.0"
},
"STAR_FOR_STARFUSION": {
"star": null,
"samtools": 1.2,
"gawk": "5.1.0"
},
"STAR_GENOMEGENERATE": {
"star": null,
"samtools": 1.2,
"gawk": "5.1.0"
},
"STRINGTIE_MERGE": {
"stringtie": "2.2.1"
},
"STRINGTIE_STRINGTIE": {
"stringtie": "2.2.3"
},
"Workflow": {
"nf-core/rnafusion": "v4.0.0dev"
}
},
[
"arriba",
"arriba/test.arriba.fusions.discarded.tsv",
Expand Down Expand Up @@ -259,12 +357,116 @@
"nf-test": "0.9.0",
"nextflow": "24.10.2"
},
"timestamp": "2025-01-07T10:53:09.572584"
"timestamp": "2025-01-07T13:16:02.754052"
},
"stub test with fastp trim": {
"content": [
33,
null,
{
"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"
},
"FASTQC": {
"fastqc": "0.12.1"
},
"FASTQC_FOR_FASTP": {
"fastqc": "0.12.1"
},
"FUSIONCATCHER": {
"fusioncatcher": 1.35
},
"FUSIONCATCHER_BUILD": {
"fusioncatcher": "fusioncatcher.py 1.35"
},
"FUSIONREPORT": {
"fusion_report": "2.1.5"
},
"FUSIONREPORT_DOWNLOAD": {
"fusion_report": "2.1.5"
},
"GATK4_BEDTOINTERVALLIST": {
"gatk4": "4.6.1.0"
},
"GATK4_CREATESEQUENCEDICTIONARY": {
"gatk4": "4.6.1.0"
},
"GATK4_MARKDUPLICATES": {
"gatk4": "4.5.0.0",
"samtools": "1.19.2"
},
"GENCODE_DOWNLOAD": {
"wget": null
},
"GET_RRNA_TRANSCRIPTS": {
"get_rrna_transcripts": "v1.0"
},
"GFFREAD": {
"gffread": "0.12.7"
},
"GTF_TO_REFFLAT": {
"gtfToGenePred": 377
},
"HGNC_DOWNLOAD": {
"wget": null
},
"PICARD_COLLECTINSERTSIZEMETRICS": {
"picard": "3.3.0"
},
"PICARD_COLLECTRNASEQMETRICS": {
"picard": "3.3.0"
},
"SALMON_INDEX": {
"salmon": "1.10.3"
},
"SALMON_QUANT": {
"salmon": "1.10.3"
},
"SAMTOOLS_FAIDX": {
"samtools": 1.21
},
"SAMTOOLS_INDEX_FOR_STARFUSION": {
"samtools": 1.21
},
"STARFUSION": {
"STAR-Fusion": "1.14.0"
},
"STARFUSION_BUILD": {
"STAR-Fusion": "1.14.0"
},
"STAR_FOR_ARRIBA": {
"star": null,
"samtools": 1.2,
"gawk": "5.1.0"
},
"STAR_FOR_STARFUSION": {
"star": null,
"samtools": 1.2,
"gawk": "5.1.0"
},
"STAR_GENOMEGENERATE": {
"star": null,
"samtools": 1.2,
"gawk": "5.1.0"
},
"STRINGTIE_MERGE": {
"stringtie": "2.2.1"
},
"STRINGTIE_STRINGTIE": {
"stringtie": "2.2.3"
},
"Workflow": {
"nf-core/rnafusion": "v4.0.0dev"
}
},
[
"arriba",
"arriba/test.arriba.fusions.discarded.tsv",
Expand Down Expand Up @@ -530,6 +732,6 @@
"nf-test": "0.9.0",
"nextflow": "24.10.2"
},
"timestamp": "2025-01-07T10:50:24.959026"
"timestamp": "2025-01-07T13:13:38.690939"
}
}

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