BioX-Workflow
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example/example1/config.yml view on Meta::CPAN
---
global:
- indir: data/raw
- outdir: data/processed
- file_rule: (.*).csv$
rules:
- backup:
local:
- wait: 0
process: cp {$self->indir}/{$sample}.csv {$self->outdir}/{$sample}.csv
- grep_VARA:
process: |
echo "Working on {$self->{indir}}/{$sample.csv}"
grep -i "VARA" {$self->indir}/{$sample}.csv >> {$self->outdir}/{$sample}.grep_VARA.csv
- grep_VARB:
process: |
grep -i "VARB" {$self->indir}/{$sample}.grep_VARA.csv >> {$self->outdir}/{$sample}.grep_VARA.grep_VARB.csv
example/example1/workflow.sh view on Meta::CPAN
#
# Global Variables:
# indir: data/raw
# outdir: data/processed
# file_rule: (.csv)$
#
#
#
# Starting backup
#
#
# Variables
# Indir: data/raw
# Outdir: data/processed/backup
#
cp data/raw/SAMPLE1.csv data/processed/backup/SAMPLE1.csv
cp data/raw/SAMPLE2.csv data/processed/backup/SAMPLE2.csv
wait
#
# Ending backup
#
#
#
# Starting grep_VARA
#
#
# Variables
# Indir: data/processed/backup
# Outdir: data/processed/grep_VARA
#
echo "Working on data/processed/backup/SAMPLE1csv"
grep -i "VARA" data/processed/backup/SAMPLE1.csv >> data/processed/grep_VARA/SAMPLE1.grep_VARA.csv
echo "Working on data/processed/backup/SAMPLE2csv"
grep -i "VARA" data/processed/backup/SAMPLE2.csv >> data/processed/grep_VARA/SAMPLE2.grep_VARA.csv
wait
#
# Ending grep_VARA
#
example/example3/drake.full.yml view on Meta::CPAN
---
plugins:
- Drake
global:
- indir: data/raw
- outdir: data/processed
- file_rule: (.csv)$
rules:
- backup:
local:
- INPUT: "{$self->indir}/{$sample}.csv"
- OUTPUT: "{$self->outdir}/{$sample}.csv"
- thing: "other thing"
process: |
cp $INPUT $OUTPUT
- grep_VARA:
local:
- OUTPUT: "{$self->outdir}/{$sample}.grep_VARA.csv"
process: |
example/example3/drake.log view on Meta::CPAN
2015-06-21 14:02:47,543 INFO Running 3 steps with concurrence of 1...
2015-06-21 14:02:47,568 INFO
2015-06-21 14:02:47,570 INFO --- 0. Running (timestamped): /home/guests/jir2004/workflow/output/backup/test1.csv <- /home/guests/jir2004/workflow/test1.csv
2015-06-21 14:02:47,592 INFO --- 0: /home/guests/jir2004/workflow/output/backup/test1.csv <- /home/guests/jir2004/workflow/test1.csv -> done in 0.02s
2015-06-21 14:02:47,597 INFO
2015-06-21 14:02:47,598 INFO --- 1. Running (timestamped): /home/guests/jir2004/workflow/output/grep_vara/test1.grep_VARA.csv <- /home/guests/jir2004/workflow/output/backup/test1.csv
2015-06-21 14:02:47,612 INFO --- 1: /home/guests/jir2004/workflow/output/grep_vara/test1.grep_VARA.csv <- /home/guests/jir2004/workflow/output/backup/test1.csv -> done in 0.01s
2015-06-21 14:02:47,614 INFO
2015-06-21 14:02:47,615 INFO --- 2. Running (timestamped): /home/guests/jir2004/workflow/output/grep_varb/test1.grep_VARA.grep_VARB.csv <- /home/guests/jir2004/workflow/output/grep_vara/test1.grep_VARA.csv
2015-06-21 14:02:47,626 INFO --- 2: /home/guests/jir2004/workflow/output/grep_varb/test1.grep_VARA.grep_VARB.csv <- /home/guests/jir2004/workflow/output/grep_vara/test1.grep_VARA.csv -> done in 0.01s
2015-06-21 14:02:47,628 INFO Done (3 steps run).
2015-06-21 14:16:00,147 INFO Running 3 steps with concurrence of 1...
2015-06-21 14:16:00,177 INFO
2015-06-21 14:16:00,181 INFO --- 1. Running (timestamped): /home/guests/jir2004/workflow/output/backup/test2.csv <- /home/guests/jir2004/workflow/test2.csv
2015-06-21 14:16:00,216 INFO --- 1: /home/guests/jir2004/workflow/output/backup/test2.csv <- /home/guests/jir2004/workflow/test2.csv -> done in 0.03s
2015-06-21 14:16:00,221 INFO
2015-06-21 14:16:00,222 INFO --- 3. Running (timestamped): /home/guests/jir2004/workflow/output/grep_vara/test2.grep_VARA.csv <- /home/guests/jir2004/workflow/output/backup/test2.csv
2015-06-21 14:16:00,244 INFO --- 3: /home/guests/jir2004/workflow/output/grep_vara/test2.grep_VARA.csv <- /home/guests/jir2004/workflow/output/backup/test2.csv -> done in 0.02s
2015-06-21 14:16:00,246 INFO
2015-06-21 14:16:00,246 INFO --- 5. Running (timestamped): /home/guests/jir2004/workflow/output/grep_varb/test2.grep_VARA.grep_VARB.csv <- /home/guests/jir2004/workflow/output/grep_vara/test2.grep_VARA.csv
2015-06-21 14:16:00,258 INFO --- 5: /home/guests/jir2004/workflow/output/grep_varb/test2.grep_VARA.grep_VARB.csv <- /home/guests/jir2004/workflow/output/grep_vara/test2.grep_VARA.csv -> done in 0.01s
2015-06-21 14:16:00,259 INFO Done (3 steps run).
2015-06-21 14:16:15,961 INFO Running 6 steps with concurrence of 1...
2015-06-21 14:16:15,992 INFO
2015-06-21 14:16:15,993 INFO --- 0. Running (timestamped): /home/guests/jir2004/workflow/output/backup/test1.csv <- /home/guests/jir2004/workflow/test1.csv
2015-06-21 14:16:16,016 INFO --- 0: /home/guests/jir2004/workflow/output/backup/test1.csv <- /home/guests/jir2004/workflow/test1.csv -> done in 0.02s
2015-06-21 14:16:16,021 INFO
2015-06-21 14:16:16,022 INFO --- 1. Running (timestamped): /home/guests/jir2004/workflow/output/backup/test2.csv <- /home/guests/jir2004/workflow/test2.csv
2015-06-21 14:16:16,035 INFO --- 1: /home/guests/jir2004/workflow/output/backup/test2.csv <- /home/guests/jir2004/workflow/test2.csv -> done in 0.01s
2015-06-21 14:16:16,037 INFO
2015-06-21 14:16:16,037 INFO --- 2. Running (timestamped): /home/guests/jir2004/workflow/output/grep_vara/test1.grep_VARA.csv <- /home/guests/jir2004/workflow/output/backup/test1.csv
2015-06-21 14:16:16,051 INFO --- 2: /home/guests/jir2004/workflow/output/grep_vara/test1.grep_VARA.csv <- /home/guests/jir2004/workflow/output/backup/test1.csv -> done in 0.01s
2015-06-21 14:16:16,053 INFO
2015-06-21 14:16:16,053 INFO --- 3. Running (timestamped): /home/guests/jir2004/workflow/output/grep_vara/test2.grep_VARA.csv <- /home/guests/jir2004/workflow/output/backup/test2.csv
2015-06-21 14:16:16,066 INFO --- 3: /home/guests/jir2004/workflow/output/grep_vara/test2.grep_VARA.csv <- /home/guests/jir2004/workflow/output/backup/test2.csv -> done in 0.01s
2015-06-21 14:16:16,068 INFO
2015-06-21 14:16:16,069 INFO --- 4. Running (timestamped): /home/guests/jir2004/workflow/output/grep_varb/test1.grep_VARA.grep_VARB.csv <- /home/guests/jir2004/workflow/output/grep_vara/test1.grep_VARA.csv
2015-06-21 14:16:16,080 INFO --- 4: /home/guests/jir2004/workflow/output/grep_varb/test1.grep_VARA.grep_VARB.csv <- /home/guests/jir2004/workflow/output/grep_vara/test1.grep_VARA.csv -> done in 0.01s
2015-06-21 14:16:16,082 INFO
2015-06-21 14:16:16,082 INFO --- 5. Running (timestamped): /home/guests/jir2004/workflow/output/grep_varb/test2.grep_VARA.grep_VARB.csv <- /home/guests/jir2004/workflow/output/grep_vara/test2.grep_VARA.csv
2015-06-21 14:16:16,160 INFO --- 5: /home/guests/jir2004/workflow/output/grep_varb/test2.grep_VARA.grep_VARB.csv <- /home/guests/jir2004/workflow/output/grep_vara/test2.grep_VARA.csv -> done in 0.08s
2015-06-21 14:16:16,163 INFO Done (6 steps run).
example/example3/drake.min.yml view on Meta::CPAN
---
plugins:
- Drake
global:
- indir: data/raw
- outdir: data/processed
- file_rule: (.csv)$
- min: 1
rules:
- backup:
local:
- INPUT: "{$self->indir}/{$sample}.csv"
- OUTPUT: "{$self->outdir}/{$sample}.csv"
- thing: "other thing"
process: |
cp $INPUT $OUTPUT
- grep_VARA:
local:
- OUTPUT: "{$self->outdir}/{$sample}.grep_VARA.csv"
process: |
example/example3/drake.yml view on Meta::CPAN
---
plugins:
- Drake
global:
- indir: data/raw
- outdir: data/processed
- file_rule: (.csv)$
rules:
- backup:
local:
- INPUT: "{$self->indir}/{$sample}.csv"
- OUTPUT: "{$self->outdir}/{$sample}.csv"
- thing: "other thing"
process: |
cp $INPUT $OUTPUT
- grep_VARA:
local:
- OUTPUT: "{$self->outdir}/{$sample}.grep_VARA.csv"
process: |
example/example3/workflow.full.drake view on Meta::CPAN
;
;
; Samples: test1, test2
;
;
; Starting Workflow
;
;
; Starting backup
;
;
; Variables
; Indir: /home/guests/jir2004/workflow
; Outdir: /home/guests/jir2004/workflow/output/backup
; Local Variables:
; INPUT: {$self->indir}/{$sample}.csv
; OUTPUT: {$self->outdir}/{$sample}.csv
; thing: other thing
;
/home/guests/jir2004/workflow/output/backup/test1.csv <- /home/guests/jir2004/workflow/test1.csv
cp $INPUT $OUTPUT
/home/guests/jir2004/workflow/output/backup/test2.csv <- /home/guests/jir2004/workflow/test2.csv
cp $INPUT $OUTPUT
;
; Ending backup
;
;
; Starting grep_VARA
;
;
; Variables
; Indir: /home/guests/jir2004/workflow/output/backup
; Outdir: /home/guests/jir2004/workflow/output/grep_vara
; Local Variables:
; OUTPUT: {$self->outdir}/{$sample}.grep_VARA.csv
; INPUT: {$self->indir}/{$sample}.csv
;
/home/guests/jir2004/workflow/output/grep_vara/test1.grep_VARA.csv <- /home/guests/jir2004/workflow/output/backup/test1.csv
echo "Working on /home/guests/jir2004/workflow/output/backup/test1csv"
grep -i "VARA" /home/guests/jir2004/workflow/output/backup/test1.csv >> /home/guests/jir2004/workflow/output/grep_vara/test1.grep_VARA.csv \
|| touch /home/guests/jir2004/workflow/output/grep_vara/test1.grep_VARA.csv
/home/guests/jir2004/workflow/output/grep_vara/test2.grep_VARA.csv <- /home/guests/jir2004/workflow/output/backup/test2.csv
echo "Working on /home/guests/jir2004/workflow/output/backup/test2csv"
grep -i "VARA" /home/guests/jir2004/workflow/output/backup/test2.csv >> /home/guests/jir2004/workflow/output/grep_vara/test2.grep_VARA.csv \
|| touch /home/guests/jir2004/workflow/output/grep_vara/test2.grep_VARA.csv
;
; Ending grep_VARA
;
;
; Starting grep_VARB
example/example3/workflow.min.drake view on Meta::CPAN
;
;
; Samples: test1, test2
;
;
; Starting Workflow
;
;
; Starting backup
;
;
; Variables
; Indir: /home/guests/jir2004/workflow
; Outdir: /home/guests/jir2004/workflow/output/backup
; Local Variables:
; INPUT: {$self->indir}/{$sample}.csv
; OUTPUT: {$self->outdir}/{$sample}.csv
; thing: other thing
;
/home/guests/jir2004/workflow/output/backup/$[SAMPLE].csv <- /home/guests/jir2004/workflow/$[SAMPLE].csv
cp $INPUT $OUTPUT
;
; Ending backup
;
;
; Starting grep_VARA
;
;
; Variables
; Indir: /home/guests/jir2004/workflow/output/backup
; Outdir: /home/guests/jir2004/workflow/output/grep_vara
; Local Variables:
; OUTPUT: {$self->outdir}/{$sample}.grep_VARA.csv
; INPUT: {$self->indir}/{$sample}.csv
;
/home/guests/jir2004/workflow/output/grep_vara/$[SAMPLE].grep_VARA.csv <- /home/guests/jir2004/workflow/output/backup/$[SAMPLE].csv
echo "Working on /home/guests/jir2004/workflow/output/backup/$SAMPLEcsv"
grep -i "VARA" /home/guests/jir2004/workflow/output/backup/$SAMPLE.csv >> /home/guests/jir2004/workflow/output/grep_vara/$SAMPLE.grep_VARA.csv \
|| touch /home/guests/jir2004/workflow/output/grep_vara/$SAMPLE.grep_VARA.csv
;
; Ending grep_VARA
;
;
; Starting grep_VARB
lib/BioX/Workflow/Example002.pod view on Meta::CPAN
Create the /home/user/workflow/workflow.yml
yaml
---
global:
- indir: /home/user/workflow/workflow
- outdir: /home/user/workflow/workflow/output
- file_rule: (.*).csv$
rules:
- backup:
process: cp {$self->indir}/{$sample}.csv {$self->outdir}/{$sample}.csv
- grep_VARA:
process: |
echo "Working on {$self->{indir}}/{$sample.csv}"
grep -i "VARA" {$self->indir}/{$sample}.csv >> {$self->outdir}/{$sample}.grep_VARA.csv
- grep_VARB:
process: |
grep -i "VARB" {$self->indir}/{$sample}.grep_VARA.csv >> {$self->outdir}/{$sample}.grep_VARA.grep_VARB.csv
lib/BioX/Workflow/Example002.pod view on Meta::CPAN
biox-workflow.pl --workflow workflow.yml > workflow.sh
=head2 Look at the directory structure
/home/user/workflow/
test1.csv
test2.csv
/output
/backup
/grep_vara
/grep_varb
=head2 Run the workflow
Assuming you saved your output to workflow.sh if you run ./workflow.sh you will get the following.
yaml
/home/user/workflow/
test1.csv
test2.csv
/output
/backup
test1.csv
test2.csv
/grep_vara
test1.grep_VARA.csv
test2.grep_VARA.csv
/grep_varb
test1.grep_VARA.grep_VARB.csv
test2.grep_VARA.grep_VARB.csv
lib/BioX/Workflow/Example002.pod view on Meta::CPAN
# --workflow workflow.yml
#
If --verbose is enabled, and it is by default, you'll see some variables printed out for your benefit
bash
#
# Variables
# Indir: /home/user/workflow
# Outdir: /home/user/workflow/output/backup
# Samples: test1 test2
#
Here is out first rule, named backup. As you can see our $self->outdir is automatically named 'backup', relative to the globally defined outdir.
```bash
#
# Starting backup
#
cp /home/user/workflow/test1.csv /home/user/workflow/output/backup/test1.csv
cp /home/user/workflow/test2.csv /home/user/workflow/output/backup/test2.csv
wait
#
# Ending backup
#
```
Notice the 'wait' command. If running your outputted workflow through any of the HPC::Runner scripts, the wait signals to wait until all previous processes have ended before beginning the next one.
Basically, wait builds a linear dependency tree.
For instance, if running this as
lib/BioX/Workflow/Example003.pod view on Meta::CPAN
yaml
---
global:
- indir: /home/user/workflow/workflow/input
- outdir: /home/user/workflow/workflow/output
- file_rule: (.*)
- find_by_dir: 1
- by_sample_outdir: 1
rules:
- backup:
process: cp {$self->indir}/{$sample}.csv {$self->outdir}/{$sample}.csv
- grep_VARA:
process: |
echo "Working on {$self->{indir}}/{$sample.csv}"
grep -i "VARA" {$self->indir}/{$sample}.csv >> {$self->outdir}/{$sample}.grep_VARA.csv
- grep_VARB:
process: |
grep -i "VARB" {$self->indir}/{$sample}.grep_VARA.csv >> {$self->outdir}/{$sample}.grep_VARA.grep_VARB.csv
lib/BioX/Workflow/Example003.pod view on Meta::CPAN
=head2 Look at the directory structure
bash
/home/user/workflow/input
test1/test1.csv
test2/test2.csv
/output
/test1
/backup
/grep_vara
/grep_varb
/test2
/backup
/grep_vara
/grep_varb
=head2 Run the workflow
Assuming you saved your output to workflow.sh if you run ./workflow.sh you will get the following.
yaml
/home/user/workflow/input
test1/test1.csv
test2/test2.csv
/output
/test1
/backup
test1.csv
/grep_vara
test1.grep_VARA.csv
/grep_varb
test1.grep_VARA.grep_VARB.csv
/test2
/backup
test2.csv
/grep_vara
test2.grep_VARA.csv
/grep_varb
test2.grep_VARA.grep_VARB.csv
lib/BioX/Workflow/SpecialVariables.pod view on Meta::CPAN
code. These are special variables that are also used in Drake. Please see L<BioX::Workflow::Plugin::Drake|https://metacpan.org/pod/BioX::Workflow::Plugin::Drake>
for more details.
yaml
---
global:
- ROOT: /home/user/workflow
- indir: {$self->ROOT}
- outdir: {$self->indir}/output
rules:
- backup:
local:
- INPUT: {$self->indir}/{$sample}.in
- OUTPUT: {$self->outdir}/{$sample}.out
lib/BioX/Workflow/Usage.pod view on Meta::CPAN
variables contained in your rules.
---
global:
- indir: /home/user/example-workflow
- outdir: /home/user/example-workflow/gemini-wrapper
- file_rule: (.vcf)$|(.vcf.gz)$
- some_variable: {$self->indir}/file_to_keep_handy
- ext: txt
rules:
- backup:
local:
- ext: "backup"
process: cp {$self->indir}/{$sample}.csv {$self->outdir}/{$sample}.{$self->ext}.csv
- rule2:
process: cp {$self->indir}/{$sample}.csv {$self->outdir}/{$sample}.{$self->ext}.csv
=head2 Rules
Rules are processed in the order they appear.
Before any rules are processed, first the samples are found. These are grepped using File::Basename, the indir, and the file_rule variable. The
default is to get rid of the everything after the final '.' .
lib/BioX/Workflow/Usage.pod view on Meta::CPAN
By default your process is evaluated as
foreach my $sample (@{$self->samples}){
#Get the value from the process key.
}
If instead you would like to use the infiles, or some other random process that has nothing to do with your samples, you can override the process
template. Make sure to use the previously defined $OUT. For more information see the L<Text::Template> man page.
rules:
- backup:
outdir: {$self->ROOT}/datafiles
override_process: 1
process: |
$OUT .= wget {$self->some_globally_defined_parameter}
{
foreach my $infile (@{$self->infiles}){
$OUT .= "dostuff $infile";
}
}
lib/BioX/Workflow/Usage.pod view on Meta::CPAN
code. These are special variables that are also used in Drake. Please see L<BioX::Workflow::Plugin::Drake|https://metacpan.org/pod/BioX::Workflow::Plugin::Drake>
for more details.
yaml
---
global:
- ROOT: /home/user/workflow
- indir: {$self->ROOT}
- outdir: {$self->indir}/output
rules:
- backup:
local:
- INPUT: {$self->indir}/{$sample}.in
- OUTPUT: {$self->outdir}/{$sample}.out
=encoding utf8
=head1 Example001
Here is a very simple example that searches a directory for *.csv files and creates an outdir /home/user/workflow/output if one doesn't exist.
lib/BioX/Workflow/Usage.pod view on Meta::CPAN
Create the /home/user/workflow/workflow.yml
yaml
---
global:
- indir: /home/user/workflow/workflow
- outdir: /home/user/workflow/workflow/output
- file_rule: (.*).csv$
rules:
- backup:
process: cp {$self->indir}/{$sample}.csv {$self->outdir}/{$sample}.csv
- grep_VARA:
process: |
echo "Working on {$self->{indir}}/{$sample.csv}"
grep -i "VARA" {$self->indir}/{$sample}.csv >> {$self->outdir}/{$sample}.grep_VARA.csv
- grep_VARB:
process: |
grep -i "VARB" {$self->indir}/{$sample}.grep_VARA.csv >> {$self->outdir}/{$sample}.grep_VARA.grep_VARB.csv
lib/BioX/Workflow/Usage.pod view on Meta::CPAN
biox-workflow.pl --workflow workflow.yml > workflow.sh
=head2 Look at the directory structure
/home/user/workflow/
test1.csv
test2.csv
/output
/backup
/grep_vara
/grep_varb
=head2 Run the workflow
Assuming you saved your output to workflow.sh if you run ./workflow.sh you will get the following.
yaml
/home/user/workflow/
test1.csv
test2.csv
/output
/backup
test1.csv
test2.csv
/grep_vara
test1.grep_VARA.csv
test2.grep_VARA.csv
/grep_varb
test1.grep_VARA.grep_VARB.csv
test2.grep_VARA.grep_VARB.csv
lib/BioX/Workflow/Usage.pod view on Meta::CPAN
# --workflow workflow.yml
#
If --verbose is enabled, and it is by default, you'll see some variables printed out for your benefit
bash
#
# Variables
# Indir: /home/user/workflow
# Outdir: /home/user/workflow/output/backup
# Samples: test1 test2
#
Here is out first rule, named backup. As you can see our $self->outdir is automatically named 'backup', relative to the globally defined outdir.
```bash
#
# Starting backup
#
cp /home/user/workflow/test1.csv /home/user/workflow/output/backup/test1.csv
cp /home/user/workflow/test2.csv /home/user/workflow/output/backup/test2.csv
wait
#
# Ending backup
#
```
Notice the 'wait' command. If running your outputted workflow through any of the HPC::Runner scripts, the wait signals to wait until all previous processes have ended before beginning the next one.
Basically, wait builds a linear dependency tree.
For instance, if running this as
lib/BioX/Workflow/Usage.pod view on Meta::CPAN
yaml
---
global:
- indir: /home/user/workflow/workflow/input
- outdir: /home/user/workflow/workflow/output
- file_rule: (.*)
- find_by_dir: 1
- by_sample_outdir: 1
rules:
- backup:
process: cp {$self->indir}/{$sample}.csv {$self->outdir}/{$sample}.csv
- grep_VARA:
process: |
echo "Working on {$self->{indir}}/{$sample.csv}"
grep -i "VARA" {$self->indir}/{$sample}.csv >> {$self->outdir}/{$sample}.grep_VARA.csv
- grep_VARB:
process: |
grep -i "VARB" {$self->indir}/{$sample}.grep_VARA.csv >> {$self->outdir}/{$sample}.grep_VARA.grep_VARB.csv
lib/BioX/Workflow/Usage.pod view on Meta::CPAN
=head2 Look at the directory structure
bash
/home/user/workflow/input
test1/test1.csv
test2/test2.csv
/output
/test1
/backup
/grep_vara
/grep_varb
/test2
/backup
/grep_vara
/grep_varb
=head2 Run the workflow
Assuming you saved your output to workflow.sh if you run ./workflow.sh you will get the following.
yaml
/home/user/workflow/input
test1/test1.csv
test2/test2.csv
/output
/test1
/backup
test1.csv
/grep_vara
test1.grep_VARA.csv
/grep_varb
test1.grep_VARA.grep_VARB.csv
/test2
/backup
test2.csv
/grep_vara
test2.grep_VARA.csv
/grep_varb
test2.grep_VARA.grep_VARB.csv
=head1 Acknowledgements
Before version 0.03
lib/BioX/Workflow/Workflow.pod view on Meta::CPAN
variables contained in your rules.
---
global:
- indir: /home/user/example-workflow
- outdir: /home/user/example-workflow/gemini-wrapper
- file_rule: (.vcf)$|(.vcf.gz)$
- some_variable: {$self->indir}/file_to_keep_handy
- ext: txt
rules:
- backup:
local:
- ext: "backup"
process: cp {$self->indir}/{$sample}.csv {$self->outdir}/{$sample}.{$self->ext}.csv
- rule2:
process: cp {$self->indir}/{$sample}.csv {$self->outdir}/{$sample}.{$self->ext}.csv
=head2 Rules
Rules are processed in the order they appear.
Before any rules are processed, first the samples are found. These are grepped using File::Basename, the indir, and the file_rule variable. The
default is to get rid of the everything after the final '.' .
lib/BioX/Workflow/Workflow.pod view on Meta::CPAN
By default your process is evaluated as
foreach my $sample (@{$self->samples}){
#Get the value from the process key.
}
If instead you would like to use the infiles, or some other random process that has nothing to do with your samples, you can override the process
template. Make sure to use the previously defined $OUT. For more information see the L<Text::Template> man page.
rules:
- backup:
outdir: {$self->ROOT}/datafiles
override_process: 1
process: |
$OUT .= wget {$self->some_globally_defined_parameter}
{
foreach my $infile (@{$self->infiles}){
$OUT .= "dostuff $infile";
}
}
t/example/test001.sh view on Meta::CPAN
# override_process: 0
# rule_based: 1
# verbose: 1
# create_outdir: 1
# file_rule: (.*).csv$
#
#
#
# Starting backup
#
#
# Variables
# Indir: $Bin/example/data/raw/test001
# Outdir: $Bin/example/data/processed/test001/backup
#
cp $Bin/example/data/raw/test001/sample1.csv $Bin/example/data/processed/test001/backup/sample1.csv
cp $Bin/example/data/raw/test001/sample2.csv $Bin/example/data/processed/test001/backup/sample2.csv
cp $Bin/example/data/raw/test001/sample3.csv $Bin/example/data/processed/test001/backup/sample3.csv
cp $Bin/example/data/raw/test001/sample4.csv $Bin/example/data/processed/test001/backup/sample4.csv
cp $Bin/example/data/raw/test001/sample5.csv $Bin/example/data/processed/test001/backup/sample5.csv
wait
#
# Ending backup
#
#
#
# Starting grep_VARA
#
#
# Variables
# Indir: $Bin/example/data/processed/test001/backup
# Outdir: $Bin/example/data/processed/test001/grep_VARA
#
echo "Working on $Bin/example/data/processed/test001/backup/sample1.csv"
grep -i "VARA" $Bin/example/data/processed/test001/backup/sample1.csv >> $Bin/example/data/processed/test001/grep_VARA/sample1.grep_VARA.csv
echo "Working on $Bin/example/data/processed/test001/backup/sample2.csv"
grep -i "VARA" $Bin/example/data/processed/test001/backup/sample2.csv >> $Bin/example/data/processed/test001/grep_VARA/sample2.grep_VARA.csv
echo "Working on $Bin/example/data/processed/test001/backup/sample3.csv"
grep -i "VARA" $Bin/example/data/processed/test001/backup/sample3.csv >> $Bin/example/data/processed/test001/grep_VARA/sample3.grep_VARA.csv
echo "Working on $Bin/example/data/processed/test001/backup/sample4.csv"
grep -i "VARA" $Bin/example/data/processed/test001/backup/sample4.csv >> $Bin/example/data/processed/test001/grep_VARA/sample4.grep_VARA.csv
echo "Working on $Bin/example/data/processed/test001/backup/sample5.csv"
grep -i "VARA" $Bin/example/data/processed/test001/backup/sample5.csv >> $Bin/example/data/processed/test001/grep_VARA/sample5.grep_VARA.csv
wait
#
# Ending grep_VARA
#
t/example/test001.yml view on Meta::CPAN
---
global:
- indir: t/example/data/raw/test001
- outdir: t/example/data/processed/test001
- file_rule: (.*).csv$
rules:
- backup:
process: cp {$self->indir}/{$sample}.csv {$self->outdir}/{$sample}.csv
- grep_VARA:
process: |
echo "Working on {$self->{indir}}/{$sample}.csv"
grep -i "VARA" {$self->indir}/{$sample}.csv >> {$self->outdir}/{$sample}.grep_VARA.csv
- grep_VARB:
process: |
grep -i "VARB" {$self->indir}/{$sample}.grep_VARA.csv >> {$self->outdir}/{$sample}.grep_VARA.grep_VARB.csv
t/example/test002.sh view on Meta::CPAN
# verbose: 1
# create_outdir: 1
# file_rule: (sample.*)$
# by_sample_outdir: 1
# find_by_dir: 1
#
#
#
# Starting backup
#
#
# Variables
# Indir: $Bin/example/data/raw/test002
# Outdir: $Bin/example/data/processed/test002/backup
#
cp $Bin/example/data/raw/test002/sample1/sample1.csv $Bin/example/data/processed/test002/sample1/backup/sample1.csv
cp $Bin/example/data/raw/test002/sample2/sample2.csv $Bin/example/data/processed/test002/sample2/backup/sample2.csv
cp $Bin/example/data/raw/test002/sample3/sample3.csv $Bin/example/data/processed/test002/sample3/backup/sample3.csv
cp $Bin/example/data/raw/test002/sample4/sample4.csv $Bin/example/data/processed/test002/sample4/backup/sample4.csv
cp $Bin/example/data/raw/test002/sample5/sample5.csv $Bin/example/data/processed/test002/sample5/backup/sample5.csv
wait
#
# Ending backup
#
#
#
# Starting grep_VARA
#
#
# Variables
# Indir: $Bin/example/data/processed/test002/backup
# Outdir: $Bin/example/data/processed/test002/grep_VARA
#
echo "Working on $Bin/example/data/processed/test002/sample1/backup/sample1.csv"
grep -i "VARA" $Bin/example/data/processed/test002/sample1/backup/sample1.csv >> $Bin/example/data/processed/test002/sample1/grep_VARA/sample1.grep_VARA.csv
echo "Working on $Bin/example/data/processed/test002/sample2/backup/sample2.csv"
grep -i "VARA" $Bin/example/data/processed/test002/sample2/backup/sample2.csv >> $Bin/example/data/processed/test002/sample2/grep_VARA/sample2.grep_VARA.csv
echo "Working on $Bin/example/data/processed/test002/sample3/backup/sample3.csv"
grep -i "VARA" $Bin/example/data/processed/test002/sample3/backup/sample3.csv >> $Bin/example/data/processed/test002/sample3/grep_VARA/sample3.grep_VARA.csv
echo "Working on $Bin/example/data/processed/test002/sample4/backup/sample4.csv"
grep -i "VARA" $Bin/example/data/processed/test002/sample4/backup/sample4.csv >> $Bin/example/data/processed/test002/sample4/grep_VARA/sample4.grep_VARA.csv
echo "Working on $Bin/example/data/processed/test002/sample5/backup/sample5.csv"
grep -i "VARA" $Bin/example/data/processed/test002/sample5/backup/sample5.csv >> $Bin/example/data/processed/test002/sample5/grep_VARA/sample5.grep_VARA.csv
wait
#
# Ending grep_VARA
#
t/example/test002.yml view on Meta::CPAN
---
global:
- indir: t/example/data/raw/test002
- outdir: t/example/data/processed/test002
- file_rule: (sample.*)$
- by_sample_outdir: 1
- find_by_dir: 1
rules:
- backup:
process: cp {$self->indir}/{$sample}.csv {$self->outdir}/{$sample}.csv
- grep_VARA:
process: |
echo "Working on {$self->{indir}}/{$sample}.csv"
grep -i "VARA" {$self->indir}/{$sample}.csv >> {$self->outdir}/{$sample}.grep_VARA.csv
- grep_VARB:
process: |
grep -i "VARB" {$self->indir}/{$sample}.grep_VARA.csv >> {$self->outdir}/{$sample}.grep_VARA.grep_VARB.csv
t/example/test003.sh view on Meta::CPAN
# ROOT: t/example/data/processed/test003
# file_rule: (sample.*)$
# by_sample_outdir: 1
# find_by_dir: 1
# LOCAL_VAR: This should be overwritten
#
#
#
# Starting backup
#
#
# Variables
# Indir: $Bin/example/data/raw/test003
# Outdir: $Bin/example/data/processed/test003/backup
# Local Variables:
# LOCAL_VAR: my_local_var
# analysis_dir: {$self->ROOT}/analysis
# outdir: $Bin/example/data/processed/test003/backup
# indir: $Bin/example/data/raw/test003
#
echo "my_local_var" && \
echo $Bin/example/data/processed/test003/analysis && \
cp $Bin/example/data/raw/test003/sample1/sample1.csv $Bin/example/data/processed/test003/sample1/backup/sample1.csv
echo "my_local_var" && \
echo $Bin/example/data/processed/test003/analysis && \
cp $Bin/example/data/raw/test003/sample2/sample2.csv $Bin/example/data/processed/test003/sample2/backup/sample2.csv
echo "my_local_var" && \
echo $Bin/example/data/processed/test003/analysis && \
cp $Bin/example/data/raw/test003/sample3/sample3.csv $Bin/example/data/processed/test003/sample3/backup/sample3.csv
echo "my_local_var" && \
echo $Bin/example/data/processed/test003/analysis && \
cp $Bin/example/data/raw/test003/sample4/sample4.csv $Bin/example/data/processed/test003/sample4/backup/sample4.csv
echo "my_local_var" && \
echo $Bin/example/data/processed/test003/analysis && \
cp $Bin/example/data/raw/test003/sample5/sample5.csv $Bin/example/data/processed/test003/sample5/backup/sample5.csv
wait
#
# Ending backup
#
#
#
# Starting grep_VARA
#
#
# Variables
# Indir: $Bin/example/data/processed/test003/backup
# Outdir: $Bin/example/data/processed/test003/grep_VARA
# Local Variables:
# LOCAL_VAR: my_local_new_var
# outdir: $Bin/example/data/processed/test003/grep_VARA
# indir: $Bin/example/data/processed/test003/backup
#
echo "my_local_new_var" && \
echo "Working on $Bin/example/data/processed/test003/sample1/backup/sample1.csv"
grep -i "VARA" $Bin/example/data/processed/test003/sample1/backup/sample1.csv >> $Bin/example/data/processed/test003/sample1/grep_VARA/sample1.grep_VARA.csv
echo "my_local_new_var" && \
echo "Working on $Bin/example/data/processed/test003/sample2/backup/sample2.csv"
grep -i "VARA" $Bin/example/data/processed/test003/sample2/backup/sample2.csv >> $Bin/example/data/processed/test003/sample2/grep_VARA/sample2.grep_VARA.csv
echo "my_local_new_var" && \
echo "Working on $Bin/example/data/processed/test003/sample3/backup/sample3.csv"
grep -i "VARA" $Bin/example/data/processed/test003/sample3/backup/sample3.csv >> $Bin/example/data/processed/test003/sample3/grep_VARA/sample3.grep_VARA.csv
echo "my_local_new_var" && \
echo "Working on $Bin/example/data/processed/test003/sample4/backup/sample4.csv"
grep -i "VARA" $Bin/example/data/processed/test003/sample4/backup/sample4.csv >> $Bin/example/data/processed/test003/sample4/grep_VARA/sample4.grep_VARA.csv
echo "my_local_new_var" && \
echo "Working on $Bin/example/data/processed/test003/sample5/backup/sample5.csv"
grep -i "VARA" $Bin/example/data/processed/test003/sample5/backup/sample5.csv >> $Bin/example/data/processed/test003/sample5/grep_VARA/sample5.grep_VARA.csv
wait
#
# Ending grep_VARA
#
t/example/test003.yml view on Meta::CPAN
---
global:
- indir: t/example/data/raw/test003
- outdir: t/example/data/processed/test003
- ROOT: t/example/data/processed/test003
- file_rule: (sample.*)$
- by_sample_outdir: 1
- find_by_dir: 1
- LOCAL_VAR: "This should be overwritten"
rules:
- backup:
local:
- LOCAL_VAR: "my_local_var"
- analysis_dir: "{$self->ROOT}/analysis"
process: |
echo "{$self->LOCAL_VAR}" && \
echo {$self->analysis_dir} && \
cp {$self->indir}/{$sample}.csv {$self->outdir}/{$sample}.csv
- grep_VARA:
local:
- LOCAL_VAR: "my_local_new_var"
t/example/test004.sh view on Meta::CPAN
# override_process: 0
# rule_based: 1
# verbose: 1
# create_outdir: 1
# file_rule: (.csv)$
#
#
#
# Starting backup
#
#
# Variables
# Indir: $Bin/example/data/raw/test004
# Outdir: $Bin/example/data/processed/test004/backup
#
cp $Bin/example/data/raw/test004/.csv.csv $Bin/example/data/processed/test004/backup/.csv.csv
wait
#
# Ending backup
#
#
#
# Starting grep_VARA
#
#
# Variables
# Indir: $Bin/example/data/processed/test004/backup
# Outdir: $Bin/example/data/processed/test004/grep_VARA
#
echo "Working on $Bin/example/data/processed/test004/backup/.csv.csv"
grep -i "VARA" $Bin/example/data/processed/test004/backup/.csv.csv >> $Bin/example/data/processed/test004/grep_VARA/.csv.grep_VARA.csv
wait
#
# Ending grep_VARA
#
t/example/test004.yml view on Meta::CPAN
---
global:
- indir: t/example/data/raw/test004
- outdir: t/example/data/processed/test004
- file_rule: (.csv)$
rules:
- backup:
process: cp {$self->indir}/{$sample}.csv {$self->outdir}/{$sample}.csv
- grep_VARA:
process: |
echo "Working on {$self->{indir}}/{$sample}.csv"
grep -i "VARA" {$self->indir}/{$sample}.csv >> {$self->outdir}/{$sample}.grep_VARA.csv
- grep_VARB:
process: |
grep -i "VARB" {$self->indir}/{$sample}.grep_VARA.csv >> {$self->outdir}/{$sample}.grep_VARA.grep_VARB.csv
t/example/test005.sh view on Meta::CPAN
# override_process: 0
# rule_based: 1
# verbose: 1
# create_outdir: 1
# file_rule: (.*).csv
#
#
#
# Starting backup
#
#
# Variables
# Indir: $Bin/example/data/raw/test005
# Outdir: $Bin/example/data/processed/test005/backup
#
cp $Bin/example/data/raw/test005/${SAMPLE}.csv $Bin/example/data/processed/test005/backup/${SAMPLE}.csv
wait
#
# Ending backup
#
#
#
# Starting grep_VARA
#
#
# Variables
# Indir: $Bin/example/data/processed/test005/backup
# Outdir: $Bin/example/data/processed/test005/grep_VARA
#
echo "Working on $Bin/example/data/processed/test005/backup/${SAMPLE}.csv"
grep -i "VARA" $Bin/example/data/processed/test005/backup/${SAMPLE}.csv >> $Bin/example/data/processed/test005/grep_VARA/${SAMPLE}.grep_VARA.csv
wait
#
# Ending grep_VARA
#
t/example/test005.yml view on Meta::CPAN
---
global:
- indir: t/example/data/raw/test005
- outdir: t/example/data/processed/test005
- file_rule: (.*).csv
- min: 1
rules:
- backup:
process: cp {$self->indir}/{$sample}.csv {$self->outdir}/{$sample}.csv
- grep_VARA:
process: |
echo "Working on {$self->{indir}}/{$sample}.csv"
grep -i "VARA" {$self->indir}/{$sample}.csv >> {$self->outdir}/{$sample}.grep_VARA.csv
- grep_VARB:
process: |
grep -i "VARB" {$self->indir}/{$sample}.grep_VARA.csv >> {$self->outdir}/{$sample}.grep_VARA.grep_VARB.csv
t/lib/TestsFor/BioX/Workflow/Test001.pm view on Meta::CPAN
#TODO to keep or not to keep?
open( my $fh, ">$Bin/example/test001.yml" );
print $fh <<EOF;
---
global:
- indir: t/example/data/raw/test001
- outdir: t/example/data/processed/test001
- file_rule: (.*).csv\$
rules:
- backup:
process: cp {\$self->indir}/{\$sample}.csv {\$self->outdir}/{\$sample}.csv
- grep_VARA:
process: |
echo "Working on {\$self->{indir}}/{\$sample}.csv"
grep -i "VARA" {\$self->indir}/{\$sample}.csv >> {\$self->outdir}/{\$sample}.grep_VARA.csv
- grep_VARB:
process: |
grep -i "VARB" {\$self->indir}/{\$sample}.grep_VARA.csv >> {\$self->outdir}/{\$sample}.grep_VARA.grep_VARB.csv
EOF
t/lib/TestsFor/BioX/Workflow/Test001.pm view on Meta::CPAN
my $cmd2 = <<EOF;
echo "Working on {\$self->{indir}}/{\$sample}.csv"
grep -i "VARA" {\$self->indir}/{\$sample}.csv >> {\$self->outdir}/{\$sample}.grep_VARA.csv
EOF
my $cmd3 = <<EOF;
grep -i "VARB" {\$self->indir}/{\$sample}.grep_VARA.csv >> {\$self->outdir}/{\$sample}.grep_VARA.grep_VARB.csv
EOF
my $process_exp = [
{ backup => {
process =>
'cp {$self->indir}/{$sample}.csv {$self->outdir}/{$sample}.csv'
}
},
{ grep_VARA => { process => $cmd2 } },
{ grep_VARB => { process => $cmd3 } }
];
for ( my $i = 0; $i < @{$process_got}; $i++ ) {
is_deeply( $process_got->[$i], $process_exp->[$i],
t/lib/TestsFor/BioX/Workflow/Test001.pm view on Meta::CPAN
#use Text::Diff;
#my $diff = diff \$got, \$expected;
#diag("Diff is ".$diff);
#return;
is( $got, $expected, "Got expected output!" );
ok( -d "$Bin/example/data/processed/test001" );
my @processes = qw(backup grep_VARA grep_VARB);
foreach my $process (@processes) {
ok( -d "$Bin/example/data/processed/test001/$process" );
}
}
1;
t/lib/TestsFor/BioX/Workflow/Test002.pm view on Meta::CPAN
$obj->write_workflow_meta('end');
};
#use Text::Diff;
#my $diff = diff \$got, \$expected;
#diag("Diff is ".$diff);
#return;
is($got, $expected, "Got expected output!" );
ok(-d "$Bin/example/data/processed/test002");
my @processes = qw(backup grep_VARA grep_VARB);
foreach my $sample (@{$obj->samples}){
foreach my $process (@processes){
ok(-d "$Bin/example/data/processed/test002/$sample/$process", "Sample $sample Process $process dir exists");
}
}
my $cwd = cwd();
}
1;
t/lib/TestsFor/BioX/Workflow/Test003.pm view on Meta::CPAN
};
#use Text::Diff;
#my $diff = diff \$got, \$expected;
#diag("Diff is ".$diff);
#return;
is($got, $expected, "Got expected output!" );
ok(-d "$Bin/example/data/processed/test003");
#my @processes = qw(backup grep_VARA grep_VARB);
#foreach my $sample (@{$obj->samples}){
#foreach my $process (@processes){
#ok(-d "$Bin/example/data/processed/test003/$sample/$process", "Sample $sample Process $process dir exists");
#}
#}
}
1;
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