Nextflow workflow report

blastp -db /nfs/db/ncbi/202010/blastdb/db/nr -query input.1 -num_threads 8 -evalue 0.00001 -out blastXmlinput.1 -outfmt 5

exec_annotation --cpu 8 -p /nfs/db/kegg/profiles -k /nfs/db/kegg/ko_list -o koala_input.1 input.1

sed 's/*//g' input.1 > tmp4ipscn
    interproscan.sh -i tmp4ipscn --goterms --iprlookup --pathways -o out_interpro_input.1 -f TSV -T /users/bi/thermoso/projects/Adorsata/ipscantmp

touch out_hit_input.1

signalp  input.1 > out_signalp_input.1

touch out_hit_input.1

targetp -P -c  input.1 > out_targetp_input.1

mkdir -p /users/bi/thermoso/projects/Adorsata/results/
sed 's/^\s*params\s*{\s*$//gi' params.debug.blast.conf | sed 's/^\s*}\s*$//gi' | sed '/^\s*$/d' | sed 's/\s\=\s/:/gi' > configt
export escaped=$(echo '/nfs/users2/bi/thermoso/projects/Adorsata/FA-nf')
export basedirvar=$(echo '\$\{baseDir\}')
perl -lae '$_=~s/$ENV{'basedirvar'}/$ENV{'escaped'}/g; print;' configt > config
echo "$(cat config)
 dbhost:172.21.11.75" > configIn ;
fa_main.v1.pl init -conf configIn -gff annot.gff -fasta input.3

blast-annotator.pl -in blastXmlinput.1 -out blastAnnot --hits 30 --url http://gogo.test.crg.eu/api -t common -q --format blastxml

blast-annotator.pl -in blastXmlinput.1 -out blastAnnot --hits 30 --url http://gogo.test.crg.eu/api -t common -q --format blastxml

DBHOST="dbhost:'`cat /users/bi/thermoso/projects/Adorsata/mysqllog/DBHOST`'"; echo "$(cat config)
 $DBHOST" > configIn ;
config=configIn ;    cat def* > allDef;    upload_go_definitions.pl -i allDef -conf $config -mode def -param 'blast_def' > def_done

DBHOST="dbhost:'`cat /users/bi/thermoso/projects/Adorsata/mysqllog/DBHOST`'"; echo "$(cat config)
 $DBHOST" > configIn ;
config=configIn ;    cat out_targetp* > allTarget ;    load_CBSpredictions.signalP.pl -i allTarget -conf $config -type t > upload_targetp ;