Merge pull request #1270 from scwatts/oncoanalyser

[oncoanalyser] Add simulated test read data and samplesheets
nf-core · Jul 31, 2024 · a9a7c25 · a9a7c25
2 parents 4aa23a5 + eafe1d2
commit a9a7c25
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diff --git a/...simulated_reads/targeted/fastq/single_lane_single_library/subject_a.tumor.dna.R1.fastq.gz b/...simulated_reads/targeted/fastq/single_lane_single_library/subject_a.tumor.dna.R1.fastq.gz
diff --git a/...simulated_reads/targeted/fastq/single_lane_single_library/subject_a.tumor.dna.R2.fastq.gz b/...simulated_reads/targeted/fastq/single_lane_single_library/subject_a.tumor.dna.R2.fastq.gz
diff --git a/...simulated_reads/targeted/fastq/single_lane_single_library/subject_a.tumor.rna.R1.fastq.gz b/...simulated_reads/targeted/fastq/single_lane_single_library/subject_a.tumor.rna.R1.fastq.gz
diff --git a/...simulated_reads/targeted/fastq/single_lane_single_library/subject_a.tumor.rna.R2.fastq.gz b/...simulated_reads/targeted/fastq/single_lane_single_library/subject_a.tumor.rna.R2.fastq.gz
diff --git a/...ta/simulated_reads/wgts/fastq/single_lane_single_library/subject_a.normal.dna.R1.fastq.gz b/...ta/simulated_reads/wgts/fastq/single_lane_single_library/subject_a.normal.dna.R1.fastq.gz
diff --git a/...ta/simulated_reads/wgts/fastq/single_lane_single_library/subject_a.normal.dna.R2.fastq.gz b/...ta/simulated_reads/wgts/fastq/single_lane_single_library/subject_a.normal.dna.R2.fastq.gz
diff --git a/...ata/simulated_reads/wgts/fastq/single_lane_single_library/subject_a.tumor.dna.R1.fastq.gz b/...ata/simulated_reads/wgts/fastq/single_lane_single_library/subject_a.tumor.dna.R1.fastq.gz
diff --git a/...ata/simulated_reads/wgts/fastq/single_lane_single_library/subject_a.tumor.dna.R2.fastq.gz b/...ata/simulated_reads/wgts/fastq/single_lane_single_library/subject_a.tumor.dna.R2.fastq.gz
diff --git a/...ata/simulated_reads/wgts/fastq/single_lane_single_library/subject_a.tumor.rna.R1.fastq.gz b/...ata/simulated_reads/wgts/fastq/single_lane_single_library/subject_a.tumor.rna.R1.fastq.gz
diff --git a/...ata/simulated_reads/wgts/fastq/single_lane_single_library/subject_a.tumor.rna.R2.fastq.gz b/...ata/simulated_reads/wgts/fastq/single_lane_single_library/subject_a.tumor.rna.R2.fastq.gz
diff --git a/samplesheet/fastq_eval.subject_a.targeted.todna_trna.minimal.csv b/samplesheet/fastq_eval.subject_a.targeted.todna_trna.minimal.csv
@@ -0,0 +1,3 @@
+group_id,subject_id,sample_id,sample_type,sequence_type,filetype,info,filepath
+subject_a,subject_a,subject_a.tumor,tumor,dna,fastq,library_id:library_1;lane:001,https://github.com/nf-core/test-datasets/raw/oncoanalyser/sample_data/simulated_reads/targeted/fastq/single_lane_single_library/subject_a.tumor.dna.R1.fastq.gz;https://github.com/nf-core/test-datasets/raw/oncoanalyser/sample_data/simulated_reads/targeted/fastq/single_lane_single_library/subject_a.tumor.dna.R2.fastq.gz
+subject_a,subject_a,subject_a.tumor_rna,tumor,rna,fastq,library_id:library_1;lane:001,https://github.com/nf-core/test-datasets/raw/oncoanalyser/sample_data/simulated_reads/targeted/fastq/single_lane_single_library/subject_a.tumor.rna.R1.fastq.gz;https://github.com/nf-core/test-datasets/raw/oncoanalyser/sample_data/simulated_reads/targeted/fastq/single_lane_single_library/subject_a.tumor.rna.R2.fastq.gz
diff --git a/samplesheet/fastq_eval.subject_a.wgts.tndna_trna.minimal.csv b/samplesheet/fastq_eval.subject_a.wgts.tndna_trna.minimal.csv
@@ -0,0 +1,4 @@
+group_id,subject_id,sample_id,sample_type,sequence_type,filetype,info,filepath
+subject_a,subject_a,subject_a.tumor,tumor,dna,fastq,library_id:library_1;lane:001,https://github.com/nf-core/test-datasets/raw/oncoanalyser/sample_data/simulated_reads/wgts/fastq/single_lane_single_library/subject_a.tumor.dna.R1.fastq.gz;https://github.com/nf-core/test-datasets/raw/oncoanalyser/sample_data/simulated_reads/wgts/fastq/single_lane_single_library/subject_a.tumor.dna.R2.fastq.gz
+subject_a,subject_a,subject_a.normal,normal,dna,fastq,library_id:library_1;lane:001,https://github.com/nf-core/test-datasets/raw/oncoanalyser/sample_data/simulated_reads/wgts/fastq/single_lane_single_library/subject_a.normal.dna.R1.fastq.gz;https://github.com/nf-core/test-datasets/raw/oncoanalyser/sample_data/simulated_reads/wgts/fastq/single_lane_single_library/subject_a.normal.dna.R2.fastq.gz
+subject_a,subject_a,subject_a.tumor_rna,tumor,rna,fastq,library_id:library_1;lane:001,https://github.com/nf-core/test-datasets/raw/oncoanalyser/sample_data/simulated_reads/wgts/fastq/single_lane_single_library/subject_a.tumor.rna.R1.fastq.gz;https://github.com/nf-core/test-datasets/raw/oncoanalyser/sample_data/simulated_reads/wgts/fastq/single_lane_single_library/subject_a.tumor.rna.R2.fastq.gz