added custom music modules test data

Author: Baksic-Ivan

genomics/homo_sapiens/genome/ensembl_v113_chr6.gtf.gz

@@ -0,0 +1,22 @@
+# Program:featureCounts v2.0.6, generated by RustQC v0.2.1
+Geneid	Chr	Start	End	Strand	Length	SAMPLE1.markdup.bam
+ENSG00000000001	chr1	100	200	+	100	10
+ENSG00000000002	chr1	300	400	+	100	25
+ENSG00000000003	chr1	500	600	-	100	5
+ENSG00000000004	chr2	100	200	+	100	0
+ENSG00000000005	chr2	300	400	-	100	18
+ENSG00000000006	chr2	500	600	+	100	42
+ENSG00000000007	chr3	100	200	+	100	7
+ENSG00000000008	chr3	300	400	-	100	3
+ENSG00000000009	chr3	500	600	+	100	11
+ENSG00000000010	chr3	700	800	-	100	22
+ENSG00000000011	chr4	100	200	+	100	9
+ENSG00000000012	chr4	300	400	+	100	14
+ENSG00000000013	chr4	500	600	-	100	6
+ENSG00000000014	chr4	700	800	+	100	31
+ENSG00000000015	chr5	100	200	-	100	2
+ENSG00000000016	chr5	300	400	+	100	17
+ENSG00000000017	chr5	500	600	-	100	8
+ENSG00000000018	chr5	700	800	+	100	4
+ENSG00000000019	chr5	900	1000	+	100	20
+ENSG00000000020	chr5	1100	1200	-	100	13

modules/music/SAMPLE1.featureCounts.tsv

@@ -0,0 +1,7 @@
+##description: minimal GTF for nf-test stubs
+chr1	HAVANA	gene	65419	71585	.	+	.	gene_id "ENSG00000186092"; gene_name "OR4F5"; gene_biotype "protein_coding";
+chr1	HAVANA	transcript	65419	71585	.	+	.	gene_id "ENSG00000186092"; transcript_id "ENST00000641515"; gene_name "OR4F5";
+chr1	HAVANA	exon	65419	65433	.	+	.	gene_id "ENSG00000186092"; transcript_id "ENST00000641515"; gene_name "OR4F5";
+chr1	HAVANA	gene	923923	944581	.	+	.	gene_id "ENSG00000187634"; gene_name "SAMD11"; gene_biotype "protein_coding";
+chr1	HAVANA	transcript	923923	944581	.	+	.	gene_id "ENSG00000187634"; transcript_id "ENST00000420190"; gene_name "SAMD11";
+chr1	HAVANA	exon	923923	924948	.	+	.	gene_id "ENSG00000187634"; transcript_id "ENST00000420190"; gene_name "SAMD11";

modules/music/genome.gtf

@@ -0,0 +1,3 @@
+sample	liver	lung	kidney
+SAMPLE1	0.45	0.35	0.20
+SAMPLE2	0.10	0.60	0.30

modules/music_analysis/test_proportions.tsv

@@ -0,0 +1,2 @@
+sample,type,bam,bai
+RNA_FULL,RNA,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam.bai

samplesheet/samplesheet_full.csv

@@ -0,0 +1,3 @@
+sample,type,bam,bai
+RNA_TEST,RNA,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam.bai
+DNA_TEST,DNA,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai

samplesheet/samplesheet_test.csv

@@ -0,0 +1,27 @@
+#!/usr/bin/env Rscript
+# Generates a minimal SingleCellExperiment RDS for use in module tests.
+# Run once: Rscript make_test_sce.R
+suppressPackageStartupMessages({
+    library(SingleCellExperiment)
+})
+
+set.seed(42)
+genes   <- paste0("ENSG0000000", seq_len(20))
+cells   <- paste0("cell_", seq_len(30))
+tissues <- rep(c("liver", "lung", "kidney"), each = 10)
+samples <- rep(paste0("donor", seq_len(3)), 10)
+
+counts_mat <- matrix(
+    rpois(length(genes) * length(cells), lambda = 5),
+    nrow = length(genes),
+    ncol = length(cells),
+    dimnames = list(genes, cells)
+)
+
+sce <- SingleCellExperiment(
+    assays  = list(counts = counts_mat),
+    colData = DataFrame(tissue = tissues, sample_id = samples)
+)
+
+saveRDS(sce, "test_sc_reference.rds")
+message("Written: test_sc_reference.rds")