diff --git a/.gitignore b/.gitignore index 5124c9ac..792b37f2 100644 --- a/.gitignore +++ b/.gitignore @@ -1,4 +1,5 @@ .nextflow* +.nf-test* work/ data/ results/ diff --git a/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf index a8d7125c..d06230ad 100644 --- a/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf @@ -97,7 +97,7 @@ workflow PIPELINE_INITIALISATION { .map{ meta, fastq_1, fastq_2 -> if (!fastq_2) return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ] else return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ] - }.groupTuple() + } emit: samplesheet = ch_samplesheet diff --git a/tests/annotation.nf.test b/tests/annotation.nf.test index 647d1d47..ca4c0c79 100644 --- a/tests/annotation.nf.test +++ b/tests/annotation.nf.test @@ -9,7 +9,7 @@ nextflow_pipeline { when { params { - modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' outdir = "$outputDir" annotate_tools = 'snpeff' download_cache = true @@ -39,7 +39,7 @@ nextflow_pipeline { when { params { - modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' outdir = "$outputDir" annotate_tools = 'vep' download_cache = true @@ -69,7 +69,7 @@ nextflow_pipeline { when { params { - modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' outdir = "$outputDir" annotate_tools = 'merge' download_cache = true diff --git a/tests/annotation.nf.test.snap b/tests/annotation.nf.test.snap new file mode 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"variant_calling/mills_and_1000G.indels.vcf/mills_and_1000G.indels.vcf.gz.tbi" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.09.0" + }, + "timestamp": "2024-10-11T14:46:10.437216" + } +} \ No newline at end of file diff --git a/tests/bam_csi.nf.test b/tests/bam_csi.nf.test index 02d196e8..64ea8f58 100644 --- a/tests/bam_csi.nf.test +++ b/tests/bam_csi.nf.test @@ -9,7 +9,7 @@ nextflow_pipeline { when { params { - modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' outdir = "$outputDir" bam_csi_index = true } diff --git a/tests/bam_csi.nf.test.snap b/tests/bam_csi.nf.test.snap new file mode 100644 index 00000000..8958e3dc --- /dev/null +++ b/tests/bam_csi.nf.test.snap @@ -0,0 +1,51 @@ +{ + "Run with profile test | bam_csi_index": { + "content": [ + 39, + null, + [ + "pipeline_info", + "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", + "preprocessing", + "preprocessing/GM12878", + "preprocessing/GM12878/GM12878.md.bam", + "preprocessing/GM12878/GM12878.md.bam.csi", + "preprocessing/GM12878/GM12878.recal.bam", + "preprocessing/GM12878/GM12878.recal.bam.csi", + "reports", + "reports/multiqc_data", + "reports/multiqc_data/multiqc.log", + "reports/multiqc_data/multiqc_citations.txt", + "reports/multiqc_data/multiqc_data.json", + "reports/multiqc_data/multiqc_software_versions.txt", + "reports/multiqc_data/multiqc_sources.txt", + "reports/multiqc_report.html", + "reports/stats", + "reports/stats/GM12878", + "reports/stats/GM12878/GM12878.flagstat", + "reports/stats/GM12878/GM12878.stats", + "reports/stats/GM12878/STAR_log", + "reports/stats/GM12878/STAR_log/GM12878.Log.final.out", + "reports/stats/GM12878/STAR_log/GM12878.Log.out", + "reports/stats/GM12878/STAR_log/GM12878.Log.progress.out", + "reports/stats/GM12878/STAR_log/GM12878.SJ.out.tab", + "samtools", + "samtools/GM12878.bam", + "samtools/GM12878.bam.bai", + "variant_calling", + "variant_calling/GM12878", + "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz", + "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz.csi", + "variant_calling/dbsnp_146.hg38.vcf", + "variant_calling/dbsnp_146.hg38.vcf/dbsnp_146.hg38.vcf.gz.csi", + "variant_calling/mills_and_1000G.indels.vcf", + "variant_calling/mills_and_1000G.indels.vcf/mills_and_1000G.indels.vcf.gz.csi" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.09.0" + }, + "timestamp": "2024-10-11T14:57:45.737274" + } +} \ No newline at end of file diff --git a/tests/default.nf.test b/tests/default.nf.test index 217a63a0..18825af0 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -9,7 +9,7 @@ nextflow_pipeline { when { params { - modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' outdir = "$outputDir" } } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap new file mode 100644 index 00000000..b1161f20 --- /dev/null +++ b/tests/default.nf.test.snap @@ -0,0 +1,53 @@ +{ + "Run with profile test": { + "content": [ + 40, + null, + [ + "pipeline_info", + "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", + "preprocessing", + "preprocessing/GM12878", + "preprocessing/GM12878/GM12878.md.bam", + "preprocessing/GM12878/GM12878.md.bam.bai", + "preprocessing/GM12878/GM12878.recal.bam", + "preprocessing/GM12878/GM12878.recal.bam.bai", + "reports", + "reports/multiqc_data", + "reports/multiqc_data/multiqc.log", + "reports/multiqc_data/multiqc_citations.txt", + "reports/multiqc_data/multiqc_data.json", + "reports/multiqc_data/multiqc_software_versions.txt", + "reports/multiqc_data/multiqc_sources.txt", + "reports/multiqc_report.html", + "reports/stats", + "reports/stats/GM12878", + "reports/stats/GM12878/GM12878.flagstat", + "reports/stats/GM12878/GM12878.stats", + "reports/stats/GM12878/STAR_log", + "reports/stats/GM12878/STAR_log/GM12878.Log.final.out", + "reports/stats/GM12878/STAR_log/GM12878.Log.out", + "reports/stats/GM12878/STAR_log/GM12878.Log.progress.out", + "reports/stats/GM12878/STAR_log/GM12878.SJ.out.tab", + "samtools", + "samtools/GM12878.bam", + "samtools/GM12878.bam.bai", + "variant_calling", + "variant_calling/GM12878", + "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz", + "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz.tbi", + "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz", + "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz.tbi", + "variant_calling/dbsnp_146.hg38.vcf", + "variant_calling/dbsnp_146.hg38.vcf/dbsnp_146.hg38.vcf.gz.tbi", + "variant_calling/mills_and_1000G.indels.vcf", + "variant_calling/mills_and_1000G.indels.vcf/mills_and_1000G.indels.vcf.gz.tbi" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.09.0" + }, + "timestamp": "2024-10-11T15:01:04.962148" + } +} \ No newline at end of file diff --git a/tests/removeduplicates.nf.test b/tests/removeduplicates.nf.test index 3b324eed..bac8205b 100644 --- a/tests/removeduplicates.nf.test +++ b/tests/removeduplicates.nf.test @@ -9,7 +9,7 @@ nextflow_pipeline { when { params { - modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' outdir = "$outputDir" remove_duplicates = true } diff --git a/tests/removeduplicates.nf.test.snap b/tests/removeduplicates.nf.test.snap new file mode 100644 index 00000000..6011aff2 --- /dev/null +++ b/tests/removeduplicates.nf.test.snap @@ -0,0 +1,53 @@ +{ + "Run with profile test | remove_duplicates": { + "content": [ + 40, + null, + [ + "pipeline_info", + "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", + "preprocessing", + "preprocessing/GM12878", + "preprocessing/GM12878/GM12878.md.bam", + "preprocessing/GM12878/GM12878.md.bam.bai", + "preprocessing/GM12878/GM12878.recal.bam", + "preprocessing/GM12878/GM12878.recal.bam.bai", + "reports", + "reports/multiqc_data", + "reports/multiqc_data/multiqc.log", + "reports/multiqc_data/multiqc_citations.txt", + "reports/multiqc_data/multiqc_data.json", + "reports/multiqc_data/multiqc_software_versions.txt", + "reports/multiqc_data/multiqc_sources.txt", + "reports/multiqc_report.html", + "reports/stats", + "reports/stats/GM12878", + "reports/stats/GM12878/GM12878.flagstat", + "reports/stats/GM12878/GM12878.stats", + "reports/stats/GM12878/STAR_log", + "reports/stats/GM12878/STAR_log/GM12878.Log.final.out", + "reports/stats/GM12878/STAR_log/GM12878.Log.out", + "reports/stats/GM12878/STAR_log/GM12878.Log.progress.out", + "reports/stats/GM12878/STAR_log/GM12878.SJ.out.tab", + "samtools", + "samtools/GM12878.bam", + "samtools/GM12878.bam.bai", + "variant_calling", + "variant_calling/GM12878", + "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz", + "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz.tbi", + "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz", + "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz.tbi", + "variant_calling/dbsnp_146.hg38.vcf", + "variant_calling/dbsnp_146.hg38.vcf/dbsnp_146.hg38.vcf.gz.tbi", + "variant_calling/mills_and_1000G.indels.vcf", + "variant_calling/mills_and_1000G.indels.vcf/mills_and_1000G.indels.vcf.gz.tbi" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.09.0" + }, + "timestamp": "2024-10-11T15:05:33.998547" + } +} \ No newline at end of file diff --git a/tests/skip_baserecalibration.nf.test b/tests/skip_baserecalibration.nf.test index dbafa2b9..78982da0 100644 --- a/tests/skip_baserecalibration.nf.test +++ b/tests/skip_baserecalibration.nf.test @@ -9,7 +9,7 @@ nextflow_pipeline { when { params { - modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' outdir = "$outputDir" skip_baserecalibration = true } diff --git a/tests/skip_baserecalibration.nf.test.snap b/tests/skip_baserecalibration.nf.test.snap new file mode 100644 index 00000000..2b3cefbe --- /dev/null +++ b/tests/skip_baserecalibration.nf.test.snap @@ -0,0 +1,51 @@ +{ + "Run with profile test | skip_baserecalibration": { + "content": [ + 36, + null, + [ + "pipeline_info", + "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", + "preprocessing", + "preprocessing/GM12878", + "preprocessing/GM12878/GM12878.md.bam", + "preprocessing/GM12878/GM12878.md.bam.bai", + "reports", + "reports/multiqc_data", + "reports/multiqc_data/multiqc.log", + "reports/multiqc_data/multiqc_citations.txt", + "reports/multiqc_data/multiqc_data.json", + "reports/multiqc_data/multiqc_software_versions.txt", + "reports/multiqc_data/multiqc_sources.txt", + "reports/multiqc_report.html", + "reports/stats", + "reports/stats/GM12878", + "reports/stats/GM12878/GM12878.flagstat", + "reports/stats/GM12878/GM12878.stats", + "reports/stats/GM12878/STAR_log", + "reports/stats/GM12878/STAR_log/GM12878.Log.final.out", + "reports/stats/GM12878/STAR_log/GM12878.Log.out", + "reports/stats/GM12878/STAR_log/GM12878.Log.progress.out", + "reports/stats/GM12878/STAR_log/GM12878.SJ.out.tab", + "samtools", + "samtools/GM12878.bam", + "samtools/GM12878.bam.bai", + "variant_calling", + "variant_calling/GM12878", + "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz", + "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz.tbi", + "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz", + "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz.tbi", + "variant_calling/dbsnp_146.hg38.vcf", + "variant_calling/dbsnp_146.hg38.vcf/dbsnp_146.hg38.vcf.gz.tbi", + "variant_calling/mills_and_1000G.indels.vcf", + "variant_calling/mills_and_1000G.indels.vcf/mills_and_1000G.indels.vcf.gz.tbi" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.09.0" + }, + "timestamp": "2024-10-11T15:10:25.387052" + } +} \ No newline at end of file diff --git a/workflows/rnavar/main.nf b/workflows/rnavar/main.nf index 09456978..3deaa578 100755 --- a/workflows/rnavar/main.nf +++ b/workflows/rnavar/main.nf @@ -88,7 +88,6 @@ workflow RNAVAR { return [ meta, fastqs.flatten() ] } - CAT_FASTQ(ch_fastq.multiple) ch_cat_fastq = CAT_FASTQ.out.reads.mix(ch_fastq.single)