Interconnecting 2 to 3 shell scripts

[AnushaC]

Hi All,
I have 3 to 4 working shell scripts
for SRA to FASTQ
FASTQ to BAM
BAM to BEDGRAPH
can I write single shell script interconnecting these shell which are working individually fine . If so it is creating me several problem like I am writing fastq files to a temporary folder which is not able is recognize by second shell . If there any online links to these kind of problems I would appreciate help. What are kinds of issues to consider while merging several shell programs .

Thanks in advance,
Anusha.Ch

[TiborNagy]

Yes, you can write a single shell script wich is contains only other shell scripts. You need to set the command line parameters to each script get a proper input files. For example:
#!/bin/bash

./first.sh input.sra >/tmp/out.fastq
./second.sh /tmp/out.fastq >/tmp/out.bam

Even better, if you use variables, because there is less chance to misstype. For example:
FASTQ=/tmp/out.fastq
./fist.sh input.sh >$FASTQ
./second.sh $FASTQ ...

[gringer]

If you want to conserve space and get something close to pipe-like functionality, you can use FIFO buffers:

$ mkfifo test.txt
$ cat test.txt &
[1] 21854
$ echo -e "blah\nblah\nblah" > test.txt
$ blah
blah
blah

[1]+  Fertig                  cat test.txt