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Added additional file formats support (txt)

Merged Added additional file formats support (txt)
txt into master
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Trinidad Martin Camposrequested to merge
txt into master
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spsp
+ 20
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@@ -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"