Samplesheet preprocess

modules/preprocess.R

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+# code for preprocessing of the samplesheets
+
+# At the very beginning of the pipeline, we need to verify that the samplesheet makes sense, and sanitize it.
+# For instance, the samplesheet used by nf-core/rnaseq can contain multiple rows for the same sample 
+# (in case multiple fastq files need to be merged).
+
+# Input: samplesheet as provided by user
+# Output: cleaned samplesheet with one row per sample.
+
+library (dplyr)
+
+# load input files, e.g. test data
+
+sampleAnnotation <- read_csv("https://raw.githubusercontent.com/icbi-lab/nf-deseq2/main/tests/testdata/example_nfcore/rnaseq_samplesheet_nfcore-3.1.csv", show_col_types = FALSE)
+geneCounts <- read_tsv("https://raw.githubusercontent.com/icbi-lab/nf-deseq2/main/tests/testdata/example_nfcore/salmon.merged.gene_counts.subset.tsv", show_col_types = F)
+
+sampleAnnotation2 <- sampleAnnotation %>%
+  select(-fastq_1, -fastq_2) %>%
+  distinct()      # filter distinct rows
+
+# another approach
+geneCounts2 <- select(geneCounts, -gene_id, -gene_name) %>%
+  colnames()
+outputSheet <- filter(sampleAnnotation, sample==geneCounts2) # this preserves two more columns
+
+
+# output cleaned samplesheets
+print(sampleAnnotation2)
+print(outputSheet)