shell:
		"""
		mkdir -p  output/{wildcards.project_accession}/{wildcards.experiment_accession}/ 

                #Grabs meta data, fetches in table format, and saves to csv
                esearch -db sra -query '{wildcards.experiment_accession}' |efetch -format runinfo \
			> {params.metadata_out_dir}/run_metadata.csv

                #same thing, but save only SRRs, one per line, to use with nstall -c bioconda perl-xml-xpathpprefetch or fasterqdump
                #First column (-f1) holds SRRs, delim is ",", egrep gets rid of the heading and returns just SRRs
		esearch -db sra -query '{wildcards.experiment_accession}' | efetch -format runinfo | cut -f1 -d, \
			| egrep 'SRR' > {output.run_accession_list}

		"""

	shell:
		"""


		#Use this section if you want to use prefetch and validate the downloads. Necessary with
		#fastq dump but not neccesary with fasterq-dump
		#prefetch SRR6854061
		cat {input.run_accession_list} | while IFS= read -r run_accession; do
            		prefetch $run_accession && fasterq-dump $run_accession {params.fasterq_flags} \
				-O {params.fastq_out_dir}/{wildcards.project_accession}/{wildcards.experiment_accession}
			done > {log} 2>&1

		#feeds each line of SRR accession numbers list to fasterq command
		#flags: --split-files separates paired reads
		#xargs operates on each line with "-l"
		#-I appends a unique "1" or "2" to pairs
		#-O output directory, -t temp directory
		##Tags project accession and exp accession to general fastq location, to be processed togtherr
#		cat {input.run_accession_list} | xargs -l fasterq-dump {params.fasterq_flags} \
#-O {params.fastq_out_dir}/{wildcards.project_accession}/{wildcards.experiment_accession} \
#2> {log}

		echo 'fastqs for {wildcards.experiment_accession} were obtained on:' > {output.status}
		date >> {output.status}

		"""