Mercurial > repos > petr-novak > re_utils

comparison single_fastq_filtering_wrapper.sh @ 32:628b235d76c7 draft

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planemo upload commit 39094a128ea3dd2c39f4997c6de739c33c07e5f3-dirty
author petr-novak
date Fri, 04 Aug 2023 07:37:49 +0000
parents a4cd8608ef6b
children
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31:be1f407e1018 32:628b235d76c7
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48 if [ -z "$CUTADAPT" ] # test if $CUTADAPT is empty 48 if [ -z "$CUTADAPT" ] # test if $CUTADAPT is empty
49 then 49 then
50 ${WD}/single_fastq_filtering.R -a $FASTAA -x $OUTPUT ${SAMPLING[@]} -c $CUT_OFF\ 50 Rscript ${WD}/single_fastq_filtering.R -a $FASTAA -x $OUTPUT ${SAMPLING[@]} -c $CUT_OFF\
51 -p $PERCENT_ABOVE ${TRIM_START[@]} ${TRIM_END[@]} -N $MAX_N -G $PNG_OUTPUT ${FILTER_SEQ[@]} 51 -p $PERCENT_ABOVE ${TRIM_START[@]} ${TRIM_END[@]} -N $MAX_N -G $PNG_OUTPUT ${FILTER_SEQ[@]}
52 else 52 else
53 ${WD}/single_fastq_filtering.R -a $FASTAA -x $OUTPUT ${SAMPLING[@]} -c $CUT_OFF -G $PNG_OUTPUT\ 53 Rscript ${WD}/single_fastq_filtering.R -a $FASTAA -x $OUTPUT ${SAMPLING[@]} -c $CUT_OFF -G $PNG_OUTPUT\
54 -p $PERCENT_ABOVE ${TRIM_START[@]} ${TRIM_END[@]} -N $MAX_N "${CUTADAPT[@]}" ${FILTER_SEQ[@]} 54 -p $PERCENT_ABOVE ${TRIM_START[@]} ${TRIM_END[@]} -N $MAX_N "${CUTADAPT[@]}" ${FILTER_SEQ[@]}
55 fi 55 fi
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