Mercurial > repos > petr-novak > re_utils
annotate single_fastq_filtering_wrapper.sh @ 34:91996b991991 draft default tip
Uploaded
author | petr-novak |
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date | Fri, 16 Feb 2024 15:22:21 +0000 |
parents | 628b235d76c7 |
children |
rev | line source |
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0 | 1 #!/bin/bash |
2 | |
3 #set -euo pipefail # this is something like string in perl | |
4 IFS=$'\n\t' | |
5 | |
6 # run filtering | |
7 WD="`dirname $0`" | |
8 ORIDIR=$PWD | |
9 cd $WD | |
10 WD=$PWD # absolute path to this script | |
11 cd $ORIDIR | |
12 SAMPLING="" | |
13 TRIM_END="" | |
14 TRIM_START="" | |
15 PERCENT_ABOVE="95" | |
16 CUTADAPT="" | |
17 FILTER_SEQ="" | |
18 while getopts "a:o:n:c:p:e:s:N:C:G:F:" OPTION | |
19 do | |
20 case $OPTION in | |
21 a) | |
22 FASTAA=$OPTARG;; | |
23 o) | |
24 OUTPUT=$OPTARG;; | |
25 n) | |
26 SAMPLING=( -n ${OPTARG} );; | |
27 c) | |
28 CUT_OFF=$OPTARG;; | |
29 p) | |
30 PERCENT_ABOVE=$OPTARG;; | |
31 e) | |
32 TRIM_END=( -e ${OPTARG} );; | |
33 s) | |
34 TRIM_START=( -s ${OPTARG} );; | |
35 N) | |
36 MAX_N=${OPTARG};; | |
37 C) | |
38 CUTADAPT=(-C " "${OPTARG}" " );; | |
39 G) | |
40 PNG_OUTPUT=${OPTARG};; | |
41 F) | |
42 FILTER_SEQ=( -F ${OPTARG} );; | |
43 esac | |
44 done | |
45 | |
46 | |
47 | |
48 if [ -z "$CUTADAPT" ] # test if $CUTADAPT is empty | |
49 then | |
32
628b235d76c7
planemo upload commit 39094a128ea3dd2c39f4997c6de739c33c07e5f3-dirty
petr-novak
parents:
0
diff
changeset
|
50 Rscript ${WD}/single_fastq_filtering.R -a $FASTAA -x $OUTPUT ${SAMPLING[@]} -c $CUT_OFF\ |
0 | 51 -p $PERCENT_ABOVE ${TRIM_START[@]} ${TRIM_END[@]} -N $MAX_N -G $PNG_OUTPUT ${FILTER_SEQ[@]} |
52 else | |
32
628b235d76c7
planemo upload commit 39094a128ea3dd2c39f4997c6de739c33c07e5f3-dirty
petr-novak
parents:
0
diff
changeset
|
53 Rscript ${WD}/single_fastq_filtering.R -a $FASTAA -x $OUTPUT ${SAMPLING[@]} -c $CUT_OFF -G $PNG_OUTPUT\ |
0 | 54 -p $PERCENT_ABOVE ${TRIM_START[@]} ${TRIM_END[@]} -N $MAX_N "${CUTADAPT[@]}" ${FILTER_SEQ[@]} |
55 fi | |
56 | |
57 | |
58 | |
59 |