diff --git a/spsp b/spsp index ba9af8f6b0e43128967c2f7676b1006bbbe6581b..eb891598ae436fbc2401c97b1a17ab49a0bd37c8 100755 --- a/spsp +++ b/spsp @@ -234,7 +234,7 @@ autoMode() { if [ -d "$DIRECTORY" ] && [ "$DIRECTORY" != $OUTBOX ] && [ "$DIRECTORY" != $SENT ] && [ "$DIRECTORY" != $LOGS ]; then for FILE in "$DIRECTORY"/*; do - if [[ -f $FILE && $FILE != *.@(fasta|fa|fasta.gz|fa.gz|fasta.xz|fa.xz|fastq|fastq.gz|cram|bam|cram.gz|bam.gz|csv|tsv|csv.gz|tsv.gz|vcf|xls|xlsx) ]]; then + if [[ -f $FILE && $FILE != *.@(fasta|fa|fasta.gz|fa.gz|fasta.xz|fa.xz|fastq|fastq.gz|cram|bam|cram.gz|bam.gz|csv|tsv|csv.gz|tsv.gz|vcf|xls|xlsx|txt) ]]; then ((ERRORS = ERRORS + 1)) ((STEP_ERRORS = STEP_ERRORS + 1)) echo "[$(date +"%T")] local.ERROR: Unsupported format ($FILE)" >>"../$LOGFILE" @@ -242,7 +242,7 @@ autoMode() { fi done - if ls "$DIRECTORY"/*.fa* 1>/dev/null 2>&1 || ls "$DIRECTORY"/*.*am 1>/dev/null 2>&1 || ls "$DIRECTORY"/*.*sv* 1>/dev/null 2>&1 || ls "$DIRECTORY"/*.vcf 1>/dev/null 2>&1 || ls "$DIRECTORY"/*.xls* 1>/dev/null 2>&1 || ls "$DIRECTORY"/*.*.gz 1>/dev/null 2>&1; then + if ls "$DIRECTORY"/*.fa* 1>/dev/null 2>&1 || ls "$DIRECTORY"/*.*am 1>/dev/null 2>&1 || ls "$DIRECTORY"/*.*sv* 1>/dev/null 2>&1 || ls "$DIRECTORY"/*.vcf 1>/dev/null 2>&1 || ls "$DIRECTORY"/*.xls* 1>/dev/null 2>&1 || ls "$DIRECTORY"/*.*.gz 1>/dev/null 2>&1 || ls "$DIRECTORY"/*.txt 1>/dev/null 2>&1; then if [[ "$*" == *--fake* ]] || [[ "$*" == *-F* ]]; then compressFolder "$DIRECTORY" 2>>"../$ERRORLOGFILE" @@ -297,7 +297,7 @@ autoMode() { if [ -d "$DIRECTORY" ] && [ "$DIRECTORY" != $OUTBOX ] && [ "$DIRECTORY" != $SENT ] && [ "$DIRECTORY" != $LOGS ]; then for FILE in "$DIRECTORY"/*; do - if [[ -f $FILE && $FILE != *.@(fasta|fa|fasta.gz|fa.gz|fasta.xz|fa.xz|fastq|fastq.gz|cram|bam|cram.gz|bam.gz|csv|tsv|csv.gz|tsv.gz|vcf|xls|xlsx) ]]; then + if [[ -f $FILE && $FILE != *.@(fasta|fa|fasta.gz|fa.gz|fasta.xz|fa.xz|fastq|fastq.gz|cram|bam|cram.gz|bam.gz|csv|tsv|csv.gz|tsv.gz|vcf|xls|xlsx|txt) ]]; then ((ERRORS = ERRORS + 1)) ((STEP_ERRORS = STEP_ERRORS + 1)) echo "[$(date +"%T")] local.ERROR: Unsupported format ($FILE)" >>"../$LOGFILE" @@ -305,7 +305,7 @@ autoMode() { fi done - if ls "$DIRECTORY"/*.fa* 1>/dev/null 2>&1 || ls "$DIRECTORY"/*.*am 1>/dev/null 2>&1 || ls "$DIRECTORY"/*.*sv* 1>/dev/null 2>&1 || ls "$DIRECTORY"/*.vcf 1>/dev/null 2>&1 || ls "$DIRECTORY"/*.xls* 1>/dev/null 2>&1 || ls "$DIRECTORY"/*.*.gz 1>/dev/null 2>&1; then + if ls "$DIRECTORY"/*.fa* 1>/dev/null 2>&1 || ls "$DIRECTORY"/*.*am 1>/dev/null 2>&1 || ls "$DIRECTORY"/*.*sv* 1>/dev/null 2>&1 || ls "$DIRECTORY"/*.vcf 1>/dev/null 2>&1 || ls "$DIRECTORY"/*.xls* 1>/dev/null 2>&1 || ls "$DIRECTORY"/*.*.gz 1>/dev/null 2>&1 || ls "$DIRECTORY"/*.txt 1>/dev/null 2>&1; then if [[ "$*" == *--fake* ]] || [[ "$*" == *-F* ]]; then compressFolder "$DIRECTORY" @@ -659,6 +659,14 @@ generateFakeFiles() { truncate -s 100M ./$VIRUSES/fake-viruses-vcf/fake-viruses.vcf + if [ ! -d "$VIRUSES/fake-viruses-txt" ]; then + mkdir -p $VIRUSES/fake-viruses-txt + fi + + rm -rf ./$VIRUSES/fake-viruses-txt/* + + truncate -s 100M ./$VIRUSES/fake-viruses-txt/fake-viruses.txt + if [ ! -d "$BACTERIA/fake-bacteria-xlsx" ]; then mkdir -p $BACTERIA/fake-bacteria-xlsx fi @@ -811,6 +819,14 @@ generateFakeFiles() { truncate -s 100M ./$BACTERIA/fake-bacteria-vcf/fake-bacteria.vcf + if [ ! -d "$BACTERIA/fake-bacteria-txt" ]; then + mkdir -p $BACTERIA/fake-bacteria-txt + fi + + rm -rf ./$BACTERIA/fake-bacteria-txt/* + + truncate -s 100M ./$BACTERIA/fake-bacteria-txt/fake-bacteria.txt + autoMode --fake --no-archive printf "\n${BACK_GREEN} DONE ${COL_RESET} Test completed. Everything went smoothly.\n\n"