Mercurial > repos > pjbriggs > pal_finder
annotate pal_finder_wrapper.sh @ 9:b3ca3ece8a8b draft
WIP detect/trap "bad primer product range" errors.
| author | pjbriggs |
|---|---|
| date | Fri, 16 Jun 2017 09:12:09 -0400 |
| parents | 67ab365c29a7 |
| children | 84613d5f1713 |
| rev | line source |
|---|---|
| 0 | 1 #!/bin/sh |
| 2 # | |
| 3 # pal_finder_wrapper.sh: run pal_finder perl script as a Galaxy tool | |
| 4 # | |
| 5 # Usage: run_palfinder.sh FASTQ_R1 FASTQ_R2 MICROSAT_SUMMARY PAL_SUMMARY FILTERED_MICROSATS [OPTIONS] | |
| 6 # run_palfinder.sh --454 FASTA MICROSAT_SUMMARY PAL_SUMMARY [OPTIONS] | |
| 7 # | |
| 8 # Options: | |
| 9 # | |
| 10 # --primer-prefix PREFIX: prefix added to the beginning of all primer names (prPrefixName) | |
| 11 # --2merMinReps N: miniumum number of 2-mer repeat units to detect (0=ignore units of this size) | |
| 12 # --3merMinReps N | |
| 13 # --4merMinReps N | |
| 14 # --5merMinReps N | |
| 15 # --6merMinReps N | |
| 16 # --primer-mispriming-library FASTA: specify a Fasta file with sequences to avoid amplifying | |
| 17 # --primer-opt-size VALUE: optimum primer length | |
| 18 # --primer-min-size VALUE: minimum acceptable primer length | |
| 19 # --primer-max-size VALUE: maximum acceptable primer length | |
| 20 # --primer-min-gc VALUE: minimum allowable percentage of Gs and Cs in any primer | |
| 21 # --primer-max-gc VALUE: maximum allowable percentage of Gs and Cs | |
| 22 # --primer-gc-clamp VALUE: number of consecutive Gs and Cs at 3' end of both left and right primer | |
| 23 # --primer-max-end-gc VALUE: max number of Gs or Cs in last five 3' bases of left or right primer | |
| 24 # --primer-min-tm VALUE: minimum acceptable melting temperature (Celsius) for a primer oligo | |
| 25 # --primer-max-tm VALUE: maximum acceptable melting temperature (Celsius) | |
| 26 # --primer-opt-tm VALUE: optimum melting temperature (Celsius) | |
| 27 # --primer-pair-max-diff-tm VALUE: max difference between melting temps of left & right primers | |
| 28 # --output_config_file FNAME: write a copy of the config.txt file to FNAME | |
| 3 | 29 # --filter_microsats FNAME: write output of filter options FNAME |
| 30 # -assembly FNAME: run the 'assembly' filter option and write to FNAME | |
| 31 # -primers: run the 'primers' filter option | |
| 32 # -occurrences: run the 'occurrences' filter option | |
| 33 # -rankmotifs: run the 'rankmotifs' filter option | |
| 0 | 34 # |
| 35 # pal_finder is available from http://sourceforge.net/projects/palfinder/ | |
| 36 # | |
| 37 # primer3 is available from http://primer3.sourceforge.net/releases.php | |
| 38 # (nb needs version 2.0.0-alpha) | |
| 39 # | |
| 40 # Explicitly set the locations of the pal_finder script, data files and the primer3 | |
| 41 # executable by setting the following variables in the environment: | |
| 42 # | |
| 43 # * PALFINDER_SCRIPT_DIR: location of the pal_finder Perl script (defaults to | |
| 44 # /usr/bin) | |
| 45 # * PALFINDER_DATA_DIR: location of the pal_finder data files (specifically | |
| 46 # config.txt and simple.ref; defaults to /usr/share/pal_finder_v0.02.04) | |
| 47 # * PRIMER3_CORE_EXE: name of the primer3_core program, which should include the | |
| 48 # full path if it's not on the Galaxy user's PATH (defaults to primer3_core) | |
| 49 # | |
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50 echo "### $(basename $0) ###" |
| 0 | 51 echo $* |
| 52 # | |
| 8 | 53 # Maximum size reporting log file contents |
| 54 MAX_LINES=500 | |
| 55 # | |
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56 # Get helper functions |
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57 . $(dirname $0)/pal_finder_wrapper_utils.sh |
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58 # |
| 0 | 59 # Initialise locations of scripts, data and executables |
| 60 # | |
| 61 # Set these in the environment to overide at execution time | |
| 62 : ${PALFINDER_SCRIPT_DIR:=/usr/bin} | |
| 63 : ${PALFINDER_DATA_DIR:=/usr/share/pal_finder_v0.02.04} | |
| 64 : ${PRIMER3_CORE_EXE:=primer3_core} | |
| 65 # | |
| 66 # Filter script is in the same directory as this script | |
| 5 | 67 PALFINDER_FILTER=$(dirname $0)/pal_filter.py |
| 3 | 68 if [ ! -f $PALFINDER_FILTER ] ; then |
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69 fatal No $PALFINDER_FILTER script |
| 0 | 70 fi |
| 71 # | |
| 72 # Check that we have all the components | |
| 73 if [ "$(have_program $PRIMER3_CORE_EXE)" == "no" ] ; then | |
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74 fatal "primer3_core missing: ${PRIMER3_CORE_EXE} not found" |
| 0 | 75 fi |
| 76 if [ ! -f "${PALFINDER_DATA_DIR}/config.txt" ] ; then | |
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77 fatal "pal_finder config.txt not found in ${PALFINDER_DATA_DIR}" |
| 0 | 78 fi |
| 79 if [ ! -f "${PALFINDER_SCRIPT_DIR}/pal_finder_v0.02.04.pl" ] ; then | |
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80 fatal "pal_finder_v0.02.04.pl not found in ${PALFINDER_SCRIPT_DIR}" |
| 0 | 81 fi |
| 82 # | |
| 83 # Initialise parameters used in the config.txt file | |
| 84 PRIMER_PREFIX="test" | |
| 85 MIN_2_MER_REPS=6 | |
| 86 MIN_3_MER_REPS=0 | |
| 87 MIN_4_MER_REPS=0 | |
| 88 MIN_5_MER_REPS=0 | |
| 89 MIN_6_MER_REPS=0 | |
| 90 PRIMER_MISPRIMING_LIBRARY=$PALFINDER_DATA_DIR/simple.ref | |
| 91 PRIMER_OPT_SIZE= | |
| 92 PRIMER_MAX_SIZE= | |
| 93 PRIMER_MIN_SIZE= | |
| 94 PRIMER_MAX_GC= | |
| 95 PRIMER_MIN_GC= | |
| 96 PRIMER_GC_CLAMP= | |
| 97 PRIMER_MAX_END_GC= | |
| 98 PRIMER_OPT_TM= | |
| 99 PRIMER_MAX_TM= | |
| 100 PRIMER_MIN_TM= | |
| 101 PRIMER_PAIR_MAX_DIFF_TM= | |
| 102 OUTPUT_CONFIG_FILE= | |
| 3 | 103 OUTPUT_ASSEMBLY= |
| 0 | 104 FILTERED_MICROSATS= |
| 3 | 105 FILTER_OPTIONS= |
| 0 | 106 # |
| 107 # Collect command line arguments | |
| 108 if [ $# -lt 2 ] ; then | |
| 109 echo "Usage: $0 FASTQ_R1 FASTQ_R2 MICROSAT_SUMMARY PAL_SUMMARY [OPTIONS]" | |
| 110 echo " $0 --454 FASTA MICROSAT_SUMMARY PAL_SUMMARY [OPTIONS]" | |
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111 fatal "Bad command line" |
| 0 | 112 fi |
| 113 if [ "$1" == "--454" ] ; then | |
| 114 PLATFORM="454" | |
| 115 FNA=$2 | |
| 116 else | |
| 117 PLATFORM="Illumina" | |
| 118 FASTQ_R1=$1 | |
| 119 FASTQ_R2=$2 | |
| 120 fi | |
| 121 MICROSAT_SUMMARY=$3 | |
| 122 PAL_SUMMARY=$4 | |
| 123 shift; shift; shift; shift | |
| 124 # | |
| 125 # Collect command line options | |
| 126 while [ ! -z "$1" ] ; do | |
| 127 case "$1" in | |
| 128 --primer-prefix) | |
| 129 shift | |
| 3 | 130 # Convert all non-alphanumeric characters to underscores in prefix |
| 131 PRIMER_PREFIX=$(echo -n $1 | tr -s -c "[:alnum:]" "_") | |
| 0 | 132 ;; |
| 133 --2merMinReps) | |
| 134 shift | |
| 135 MIN_2_MER_REPS=$1 | |
| 136 ;; | |
| 137 --3merMinReps) | |
| 138 shift | |
| 139 MIN_3_MER_REPS=$1 | |
| 140 ;; | |
| 141 --4merMinReps) | |
| 142 shift | |
| 143 MIN_4_MER_REPS=$1 | |
| 144 ;; | |
| 145 --5merMinReps) | |
| 146 shift | |
| 147 MIN_5_MER_REPS=$1 | |
| 148 ;; | |
| 149 --6merMinReps) | |
| 150 shift | |
| 151 MIN_6_MER_REPS=$1 | |
| 152 ;; | |
| 153 --primer-mispriming-library) | |
| 154 shift | |
| 155 PRIMER_MISPRIMING_LIBRARY=$1 | |
| 156 ;; | |
| 157 --primer-opt-size) | |
| 158 shift | |
| 159 PRIMER_OPT_SIZE=$1 | |
| 160 ;; | |
| 161 --primer-max-size) | |
| 162 shift | |
| 163 PRIMER_MAX_SIZE=$1 | |
| 164 ;; | |
| 165 --primer-min-size) | |
| 166 shift | |
| 167 PRIMER_MIN_SIZE=$1 | |
| 168 ;; | |
| 169 --primer-max-gc) | |
| 170 shift | |
| 171 PRIMER_MAX_GC=$1 | |
| 172 ;; | |
| 173 --primer-min-gc) | |
| 174 shift | |
| 175 PRIMER_MIN_GC=$1 | |
| 176 ;; | |
| 177 --primer-gc-clamp) | |
| 178 shift | |
| 179 PRIMER_GC_CLAMP=$1 | |
| 180 ;; | |
| 181 --primer-max-end-gc) | |
| 182 shift | |
| 183 PRIMER_MAX_END_GC=$1 | |
| 184 ;; | |
| 185 --primer-opt-tm) | |
| 186 shift | |
| 187 PRIMER_OPT_TM=$1 | |
| 188 ;; | |
| 189 --primer-max-tm) | |
| 190 shift | |
| 191 PRIMER_MAX_TM=$1 | |
| 192 ;; | |
| 193 --primer-min-tm) | |
| 194 shift | |
| 195 PRIMER_MIN_TM=$1 | |
| 196 ;; | |
| 197 --primer-pair-max-diff-tm) | |
| 198 shift | |
| 199 PRIMER_PAIR_MAX_DIFF_TM=$1 | |
| 200 ;; | |
| 201 --output_config_file) | |
| 202 shift | |
| 203 OUTPUT_CONFIG_FILE=$1 | |
| 204 ;; | |
| 205 --filter_microsats) | |
| 206 shift | |
| 207 FILTERED_MICROSATS=$1 | |
| 208 ;; | |
| 3 | 209 -primers|-occurrences|-rankmotifs) |
| 210 FILTER_OPTIONS="$FILTER_OPTIONS $1" | |
| 211 ;; | |
| 212 -assembly) | |
| 213 FILTER_OPTIONS="$FILTER_OPTIONS $1" | |
| 214 shift | |
| 215 OUTPUT_ASSEMBLY=$1 | |
| 216 ;; | |
| 0 | 217 *) |
| 218 echo Unknown option: $1 >&2 | |
| 219 exit 1 | |
| 220 ;; | |
| 221 esac | |
| 222 shift | |
| 223 done | |
| 224 # | |
| 225 # Check that primer3_core is available | |
| 226 got_primer3=`which $PRIMER3_CORE_EXE 2>&1 | grep -v "no primer3_core in"` | |
| 227 if [ -z "$got_primer3" ] ; then | |
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228 fatal "primer3_core not found" |
| 0 | 229 fi |
| 230 # | |
| 231 # Set up the working dir | |
| 232 if [ "$PLATFORM" == "Illumina" ] ; then | |
| 233 # Paired end Illumina data as input | |
| 234 if [ $FASTQ_R1 == $FASTQ_R2 ] ; then | |
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235 fatal ERROR R1 and R2 fastqs are the same file |
| 0 | 236 fi |
| 237 ln -s $FASTQ_R1 | |
| 238 ln -s $FASTQ_R2 | |
| 239 fastq_r1=$(basename $FASTQ_R1) | |
| 240 fastq_r2=$(basename $FASTQ_R2) | |
| 241 else | |
| 242 # 454 data as input | |
| 243 ln -s $FNA | |
| 244 fna=$(basename $FNA) | |
| 245 fi | |
| 246 ln -s $PRIMER_MISPRIMING_LIBRARY | |
| 247 PRIMER_MISPRIMING_LIBRARY=$(basename $PRIMER_MISPRIMING_LIBRARY) | |
| 248 mkdir Output | |
| 249 # | |
| 250 # Copy in the default config.txt file | |
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251 echo "### Creating config.txt file for pal_finder run ###" |
| 0 | 252 /bin/cp $PALFINDER_DATA_DIR/config.txt . |
| 253 # | |
| 254 # Update the config.txt file with new values | |
| 255 # Input files | |
| 256 set_config_value platform $PLATFORM config.txt | |
| 257 if [ "$PLATFORM" == "Illumina" ] ; then | |
| 258 set_config_value inputFormat fastq config.txt | |
| 259 set_config_value pairedEnd 1 config.txt | |
| 260 set_config_value inputReadFile $fastq_r1 config.txt | |
| 261 set_config_value pairedReadFile $fastq_r2 config.txt | |
| 262 else | |
| 263 set_config_value inputFormat fasta config.txt | |
| 264 set_config_value pairedEnd 0 config.txt | |
| 265 set_config_value input454reads $fna config.txt | |
| 266 fi | |
| 267 # Output files | |
| 268 set_config_value MicrosatSumOut Output/microsat_summary.txt config.txt | |
| 269 set_config_value PALsummaryOut Output/PAL_summary.txt config.txt | |
| 270 # Microsat info | |
| 271 set_config_value 2merMinReps $MIN_2_MER_REPS config.txt | |
| 272 set_config_value 3merMinReps $MIN_3_MER_REPS config.txt | |
| 273 set_config_value 4merMinReps $MIN_4_MER_REPS config.txt | |
| 274 set_config_value 5merMinReps $MIN_5_MER_REPS config.txt | |
| 275 set_config_value 6merMinReps $MIN_6_MER_REPS config.txt | |
| 276 # Primer3 settings | |
| 277 set_config_value primer3input Output/pr3in.txt config.txt | |
| 278 set_config_value primer3output Output/pr3out.txt config.txt | |
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279 set_config_value keepPrimer3files 1 config.txt |
| 0 | 280 set_config_value primer3executable $PRIMER3_CORE_EXE config.txt |
| 281 set_config_value prNamePrefix ${PRIMER_PREFIX}_ config.txt | |
| 282 set_config_value PRIMER_MISPRIMING_LIBRARY "$PRIMER_MISPRIMING_LIBRARY" config.txt | |
| 283 set_config_value PRIMER_OPT_SIZE "$PRIMER_OPT_SIZE" config.txt | |
| 284 set_config_value PRIMER_MIN_SIZE "$PRIMER_MIN_SIZE" config.txt | |
| 285 set_config_value PRIMER_MAX_SIZE "$PRIMER_MAX_SIZE" config.txt | |
| 286 set_config_value PRIMER_MIN_GC "$PRIMER_MIN_GC" config.txt | |
| 287 set_config_value PRIMER_MAX_GC "$PRIMER_MAX_GC" config.txt | |
| 288 set_config_value PRIMER_GC_CLAMP "$PRIMER_GC_CLAMP" config.txt | |
| 289 set_config_value PRIMER_MAX_END_GC "$PRIMER_MAX_END_GC" config.txt | |
| 290 set_config_value PRIMER_MIN_TM "$PRIMER_MIN_TM" config.txt | |
| 291 set_config_value PRIMER_MAX_TM "$PRIMER_MAX_TM" config.txt | |
| 292 set_config_value PRIMER_OPT_TM "$PRIMER_OPT_TM" config.txt | |
| 293 set_config_value PRIMER_PAIR_MAX_DIFF_TM "$PRIMER_PAIR_MAX_DIFF_TM" config.txt | |
| 294 # | |
| 295 # Run pal_finder | |
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296 echo "### Running pal_finder ###" |
| 8 | 297 perl $PALFINDER_SCRIPT_DIR/pal_finder_v0.02.04.pl config.txt 1>pal_finder.log 2>&1 |
| 298 echo "### pal_finder finished ###" | |
| 299 # | |
| 300 # Handlers the pal_finder log file | |
| 301 echo "### Output from pal_finder ###" | |
| 302 if [ $(wc -l pal_finder.log | cut -d" " -f1) -gt $MAX_LINES ] ; then | |
| 303 echo WARNING output too long, truncated to last $MAX_LINES lines: | |
| 304 echo ... | |
| 305 fi | |
| 306 tail -$MAX_LINES pal_finder.log | |
| 0 | 307 # |
| 308 # Check that log ends with "Done!!" message | |
| 309 if [ -z "$(tail -n 1 pal_finder.log | grep Done!!)" ] ; then | |
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310 fatal ERROR pal_finder failed to complete successfully |
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311 fi |
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312 echo "### pal_finder finished ###" |
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313 # |
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314 # Check for errors in pal_finder output |
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315 echo "### Checking for errors ###" |
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316 if [ ! -z "$(grep 'primer3_core: Illegal element in PRIMER_PRODUCT_SIZE_RANGE' pal_finder.log)" ] ; then |
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317 echo ERROR primer3 terminated prematurely due to bad product size ranges |
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318 cat >&2 <<EOF |
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319 ERROR primer3 terminated prematurely due to bad product size ranges |
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320 |
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321 Pal_finder generated bad ranges for the following read IDs: |
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322 EOF |
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323 $(find_bad_primer_ranges Output/pr3in.txt) >&2 |
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324 cat >&2 <<EOF |
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325 |
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326 This error can occur when input data contains short R1 reads and has |
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327 has not been properly trimmed and filtered. |
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328 |
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329 EOF |
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330 fatal pal_finder failed to complete successfully |
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331 EOF |
| 0 | 332 fi |
| 333 # | |
| 3 | 334 # Sort outputs into a consistent order regardless of Perl version |
| 335 echo "### Sorting outputs ###" | |
| 336 head -1 Output/PAL_summary.txt > Output/PAL_summary.sorted.txt | |
| 337 if [ "$PLATFORM" == "Illumina" ] ; then | |
| 338 grep -v "^readPairID" Output/PAL_summary.txt | sort -k 1 >> Output/PAL_summary.sorted.txt | |
| 339 else | |
| 340 grep -v "^SequenceID" Output/PAL_summary.txt | sort -k 1 >> Output/PAL_summary.sorted.txt | |
| 341 fi | |
| 342 mv Output/PAL_summary.sorted.txt Output/PAL_summary.txt | |
| 343 # | |
| 344 # Run the filtering & assembly script | |
| 345 if [ ! -z "$FILTERED_MICROSATS" ] || [ ! -z "$OUTPUT_ASSEMBLY" ] ; then | |
| 346 echo "### Running filtering & assembly script ###" | |
| 8 | 347 python $PALFINDER_FILTER -i $fastq_r1 -j $fastq_r2 -p Output/PAL_summary.txt $FILTER_OPTIONS 1>pal_filter.log 2>&1 |
| 348 echo "### Output from pal_filter ###" | |
| 349 if [ $(wc -l pal_filter.log | cut -d" " -f1) -gt $MAX_LINES ] ; then | |
| 350 echo WARNING output too long, truncated to last $MAX_LINES lines: | |
| 351 echo ... | |
| 352 fi | |
| 353 tail -$MAX_LINES pal_filter.log | |
| 0 | 354 if [ $? -ne 0 ] ; then |
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355 fatal $PALFINDER_FILTER exited with non-zero status |
| 3 | 356 elif [ ! -f PAL_summary.filtered ] ; then |
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357 fatal no output from $PALFINDER_FILTER |
| 0 | 358 fi |
| 359 fi | |
| 360 # | |
| 361 # Clean up | |
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362 echo "### Handling output files ###" |
| 0 | 363 if [ -f Output/microsat_summary.txt ] ; then |
| 364 /bin/mv Output/microsat_summary.txt $MICROSAT_SUMMARY | |
| 365 fi | |
| 366 if [ -f Output/PAL_summary.txt ] ; then | |
| 367 /bin/mv Output/PAL_summary.txt $PAL_SUMMARY | |
| 368 fi | |
| 3 | 369 if [ ! -z "$FILTERED_MICROSATS" ] && [ -f PAL_summary.filtered ] ; then |
| 370 /bin/mv PAL_summary.filtered $FILTERED_MICROSATS | |
| 371 fi | |
| 372 if [ ! -z "$OUTPUT_ASSEMBLY" ] ; then | |
| 5 | 373 assembly=${fastq_r1%.*}_pal_filter_assembly_output.txt |
| 3 | 374 if [ -f "$assembly" ] ; then |
| 375 /bin/mv $assembly "$OUTPUT_ASSEMBLY" | |
| 5 | 376 else |
|
9
b3ca3ece8a8b
WIP detect/trap "bad primer product range" errors.
pjbriggs
parents:
8
diff
changeset
|
377 fatal no assembly output found |
| 3 | 378 fi |
| 0 | 379 fi |
| 380 if [ ! -z "$OUTPUT_CONFIG_FILE" ] && [ -f config.txt ] ; then | |
| 381 /bin/mv config.txt $OUTPUT_CONFIG_FILE | |
| 382 fi | |
| 8 | 383 # |
| 384 echo "### Pal_finder tool completed ###" | |
| 0 | 385 ## |
| 386 # |