library(ballgown)
library(magrittr)
args <- commandArgs(trailingOnly = TRUE)

sampleids = args[1:length(args)-1]
output = args[length(args)]
print(sampleids)
## generate the  expression table for each sample
bg <-  ballgown(samples = sampleids , meas='FPKM')

print('process sample data')

print(sampleNames(bg))
gene_expression = ballgown::gexpr(bg)
gene_table = tibble::as.tibble(gene_expression)
gene_table$geneid = rownames(gene_expression)

geneID = tibble::tibble(genename = ballgown::geneNames(bg) ,
                        geneid =ballgown::geneIDs(bg) ) %>%
  dplyr::filter(! genename =='.' ) %>% dplyr::distinct()

gene_table <- dplyr::inner_join(gene_table ,geneID )
readr::write_csv(gene_table, path = output)

	shell:
		"""
		cutadapt -e 0.12 -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -j 6 -m 30 \
        -o {output[0]} -p {output[1]} \
        {input.r1} {input.r2} > {log}
        """

shell:
    """
    module load fastqc
    fastqc -o 02_fqc -f fastq --noextract {input}  2> {log}
    """

shell:
	"""
	module load samtools
	samtools sort  -@ {threads} -T {output}.tmp -o {output} {input} 2> {log}
	"""

shell:
	"""
# no window smoothing is done, for paired-end, bamCoverage will extend the length to the fragement length of the paired reads
bamCoverage -b {input[0]}  --binSize 100 --effectiveGenomeSize 2864785220 --skipNonCoveredRegions --normalizeUsing RPKM -p {threads}  -o {output[0]} 2> {log}
	"""

shell:
    """
    multiqc 02_fqc 00_log -o 07_multiQC -d -f -v -n multiQC_log 2> {log}
    """