Mercurial > repos > petr-novak > re_utils
diff single_fastq_filtering_wrapper.sh @ 32:628b235d76c7 draft
planemo upload commit 39094a128ea3dd2c39f4997c6de739c33c07e5f3-dirty
| author | petr-novak |
|---|---|
| date | Fri, 04 Aug 2023 07:37:49 +0000 |
| parents | a4cd8608ef6b |
| children |
line wrap: on
line diff
--- a/single_fastq_filtering_wrapper.sh Thu Aug 03 10:54:34 2023 +0000 +++ b/single_fastq_filtering_wrapper.sh Fri Aug 04 07:37:49 2023 +0000 @@ -47,10 +47,10 @@ if [ -z "$CUTADAPT" ] # test if $CUTADAPT is empty then - ${WD}/single_fastq_filtering.R -a $FASTAA -x $OUTPUT ${SAMPLING[@]} -c $CUT_OFF\ + Rscript ${WD}/single_fastq_filtering.R -a $FASTAA -x $OUTPUT ${SAMPLING[@]} -c $CUT_OFF\ -p $PERCENT_ABOVE ${TRIM_START[@]} ${TRIM_END[@]} -N $MAX_N -G $PNG_OUTPUT ${FILTER_SEQ[@]} else - ${WD}/single_fastq_filtering.R -a $FASTAA -x $OUTPUT ${SAMPLING[@]} -c $CUT_OFF -G $PNG_OUTPUT\ + Rscript ${WD}/single_fastq_filtering.R -a $FASTAA -x $OUTPUT ${SAMPLING[@]} -c $CUT_OFF -G $PNG_OUTPUT\ -p $PERCENT_ABOVE ${TRIM_START[@]} ${TRIM_END[@]} -N $MAX_N "${CUTADAPT[@]}" ${FILTER_SEQ[@]} fi