add arguments in r script and run the hpc job with oneliners

scripts/isd_crete_dada2_taxonomy.R

@@ -17,8 +17,10 @@ library(dada2, lib.loc="/home1/s.paragkamian/software/R/4.1.1")
 
 # Working Environment
 # path of the sequences as retrieved from ENA
-path <- "/home1/s.paragkamian/isd-crete/ena_data"
-output_path <- "/home1/s.paragkamian/isd-crete/dada2_output"
+args = commandArgs(trailingOnly=TRUE)
+
+path <- args[1] #"/home1/s.paragkamian/isd-crete/ena_data"
+output_path <- args[2]# "/home1/s.paragkamian/isd-crete/dada2_output"
 
 setwd(output_path)
 

scripts/isd_crete_hpc_job_dada2.sh

@@ -2,7 +2,7 @@
 
 #SBATCH --partition=fat
 #SBATCH --nodes=1
-#SBATCH --ntasks-per-node=20
+#SBATCH --ntasks-per-node=30
 #SBATCH --mem=400G
 #SBATCH --job-name="isd-species"
 #SBATCH [email protected]
@@ -12,10 +12,28 @@
 
 start=`date +%s`
 
+data_path="/home1/s.paragkamian/isd-crete/ena_data"
+output_path="/home1/s.paragkamian/isd-crete/dada2_output"
 module purge # unloads all previous loads
 
 module load  R/4.1.1 #loads  R/4.1.1
-/home1/s.paragkamian/isd-crete/scripts/isd_crete_dada2_taxonomy.R
+/home1/s.paragkamian/isd-crete/scripts/isd_crete_dada2_taxonomy.R $data_path $output_path
+
+
+dada2=`date +%s`
+runtime_dada2=$((dada2-start))
+echo $((runtime_dada2/60)) " minutes for the DADA2 pipeline" 
+echo "start the helper oneliners"
+
+cd $output_path
+cd taxonomy
+
+gawk -F"\t" 'BEGIN{print "file" "\t" "asv_id" "\t" "abundance"}(NR==1){split($0,asv,"\t")}(NR>1){split($0, data, "\t"); for (i=2; i<=length(data); ++i){print data[1] "\t" "asv"i-1 "\t" data[i]}}' seqtab_nochim.tsv > seqtab_nochim_long.tsv
+
+gawk -F"\t" 'BEGIN{print "asv_id" "\t" "asv"}(NR==1){split($0,asv,"\t"); for (i in asv){print "asv"i "\t" asv[i]}}' seqtab_nochim.tsv > asv_fasta_ids.tsv
+
+cd ../
+/home1/s.paragkamian/isd-crete/scripts/isd_crete_reads_summary.sh -i filtered -o .
 
 module purge