From a285e9a70eb8ed785d097b81f4c11851415a3ec3 Mon Sep 17 00:00:00 2001
From: tmartin <trinidad.martincampos@sib.swiss>
Date: Fri, 1 Jul 2022 13:14:32 +0200
Subject: [PATCH] txt available

---
 spsp | 24 ++++++++++++++++++++----
 1 file changed, 20 insertions(+), 4 deletions(-)

diff --git a/spsp b/spsp
index ba9af8f..eb89159 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"
-- 
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