diff --git a/subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf index c57ce9f3..7e036228 100644 --- a/subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf @@ -130,7 +130,7 @@ workflow PIPELINE_COMPLETION { plaintext_email, outdir, monochrome_logs, - multiqc_reports.getVal(), + multiqc_reports.getVal() ) } diff --git a/tests/test_cosmic.nf.test b/tests/test_cosmic.nf.test index 9a56e76e..b4f2a363 100644 --- a/tests/test_cosmic.nf.test +++ b/tests/test_cosmic.nf.test @@ -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 @@ -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 @@ -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 diff --git a/tests/test_cosmic.nf.test.snap b/tests/test_cosmic.nf.test.snap index b8e6d4a5..c920e032 100644 --- a/tests/test_cosmic.nf.test.snap +++ b/tests/test_cosmic.nf.test.snap @@ -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": { @@ -29,7 +29,7 @@ "pipeline_info" ], [ - + ] ], "meta": { @@ -46,7 +46,7 @@ "pipeline_info" ], [ - + ] ], "meta": { @@ -55,4 +55,4 @@ }, "timestamp": "2024-12-10T15:09:29.277399" } -} \ No newline at end of file +} diff --git a/tests/test_stub.nf.test b/tests/test_stub.nf.test index b0601a9f..065723e2 100644 --- a/tests/test_stub.nf.test +++ b/tests/test_stub.nf.test @@ -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 @@ -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 diff --git a/tests/test_stub.nf.test.snap b/tests/test_stub.nf.test.snap index c535947e..91d847eb 100644 --- a/tests/test_stub.nf.test.snap +++ b/tests/test_stub.nf.test.snap @@ -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", @@ -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", @@ -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" } } \ No newline at end of file