def main():
import spiper
from path import Path
from spiper.runner import get_all_files, get_changed_files, cache_run
from pprint import pprint
spiper.rcParams['dir_layout'] = 'flat'
prefix = Path('/tmp/test_import/root')
prefix.dirname().rmtree_p()
print('#### [Note] currently the package change is not recorded')
fs = get_changed_files(test_import, prefix)
pprint(fs)
fs = get_all_files(test_import, prefix)
pprint(fs)
cache_run(test_import, prefix)
pprint(fs)
print('#### [Note] Remote workflow should detect file changes')
fs = get_changed_files(simple_flow, prefix)
pprint(fs)
assert fs != []
print('### run actual workflow')
cache_run(simple_flow, prefix)
fs = get_changed_files(simple_flow, prefix)
pprint(fs)
#### The Flow() execution will never be skipped
#### hence The self.output.log will always be changed
assert fs == [
File('/tmp/test_import/root.workflow.log'),
File('/tmp/test_import/root_backup.output..log')
]
def job_stringtie_count(
self,
prefix,
BAM_FILE=File,
GTF_FILE=File,
THREADS_=int,
_IMAGE=Depend(
'docker://quay.io/biocontainers/stringtie:2.1.1--hc900ff6_0'),
_output=['count', 'cmd']):
_ = '''
Example run:
stringtie
-p 4
--rf 809_S1.bam
-G /home/feng/ref/Arabidopsis_thaliana_TAIR10/annotation/genes.gtf
-o 809_S1.stringtie.gtf
-A 809_S1.stringtie.count &> 809_S1.stringtie.log
'''
CMD = [
'stringtie',
'-p',
str(THREADS_),
File(BAM_FILE),
'--rf',
'-G',
File(GTF_FILE),
'-A',
File(self.output.count),
]
res = SingularityShellCommand(CMD, _IMAGE, self.output.cmd)
def job_picard_dedup(
self,
prefix,
bam_file=File,
THREADS_=int,
_IMAGE=Depend('docker://quay.io/biocontainers/picard:2.21.9--0'),
_IMAGE_SAMTOOLS=Depend(
"docker://quay.io/biocontainers/samtools:1.10--h9402c20_2"),
_output=['bam', 'log', 'cmd_log'],
):
CMD = [
'picard',
'MarkDuplicates',
Concat('I=', File(bam_file)),
Concat('O=', File(self.output.bam)),
Concat('M=', File(self.output.log)),
# Concat('TMP_DIR=',File(self.output.bam+'.picard_temp').makedirs_p().check_writable()),
'REMOVE_DUPLICATES=true',
]
res = LoggedSingularityCommand(
self.prefix_named,
CMD,
_IMAGE,
self.output.cmd_log,
)
res = LoggedSingularityCommand(
self.prefix_named,
# prefix,
['samtools', 'index', self.output.bam],
_IMAGE_SAMTOOLS,
self.output.cmd_log,
mode='a',
extra_files=[self.output.bam + '.bai'])
def job_hisat2_index(
self,
prefix,
FASTA_FILE=File,
THREADS_=int,
_IMAGE=Depend(
"docker://quay.io/biocontainers/hisat2:2.1.0--py36hc9558a2_4"),
_output=[
Prefix('index_prefix'),
File('log'),
File('cmd'),
],
):
CMD = [
'hisat2-build',
'-p',
str(THREADS_),
File(FASTA_FILE),
Prefix(self.output.index_prefix),
'&>',
File(self.output.log),
]
res = LoggedSingularityCommand(self.prefix_named, CMD, _IMAGE,
self.output.cmd)
return self
def tarball_dangerous_cache(self,prefix,
input_prefix = File,
_output=[
File('tar_gz'),
File('cmd')]):
with input_prefix.dirname():
stdout = LoggedShellCommand([
'tar', '-cvzf', self.output.tar_gz, input_prefix.basename()+'*',
],
self.output.cmd)
return self
def gen_files(self, prefix,
_seq = 'AGCTTCGTC',
_output=[
File('out_txt')]):
with open(self.output.out_txt,'w') as f:
f.write( _seq * 10 )
return self
def workflow(self, prefix, seed =int , L=int,
_output = [
File('log'),
]):
print('\n[Flow running] mock=%s'%getattr(self.runner.func,'__name__','None'))
curr = self.runner(random_seq, prefix, seed, L)
curr1 = self.config_runner(tag='const')(random_seq, prefix, 0, 100)
curr = self.runner(transcribe, prefix, curr.output.seq,)
curr = self.runner(mutate, prefix, curr.output.fasta)
stdout = LoggedShellCommand(['ls -lhtr',prefix.dirname()], self.output.log).rstrip()
self.runner(copy_file, prefix+'.source.py', __file__)
return self
def workflow(self, prefix, seed =int , L=int,
_output = [
File('log'),
]):
_ = '''
A workflow is not a Node()
'''
print('\n[Flow running] mock=%s'%getattr(self.runner.func,'__name__','None'))
### [ToDo] (func, prefix) must be unique within each workflow
# self.data = {}
curr = self.runner(random_seq, prefix, seed, L)
curr1 = self.config_runner(tag='temp')(random_seq, prefix, 0, 100)
curr = self.runner(transcribe, prefix, curr.output.seq,)
curr = self.runner(mutate, prefix, curr.output.fasta)
stdout = LoggedShellCommand(['ls -lhtr',prefix.dirname()],).rstrip()
return self
def test_mock_overwrite(self):
# assert 0
prefix = None
if prefix is None:
prefix = File('/tmp/spiper.symbolic/root')
prefix.dirname().rmtree_p()
_d = spiper.rcParams.copy()
spiper.rcParams['dir_layout'] = 'clean'
tarball_main( mock_run, prefix)
fs = sorted(prefix.fileglob('*',0,0)); print(pprint(fs))
assert fs == [
File('/tmp/spiper.symbolic/root.gen_files.out_txt'),
File('/tmp/spiper.symbolic/root.gen_files.out_txt.empty.mock'),
File('/tmp/spiper.symbolic/root.gen_files.out_txt.old.mock'),
File('/tmp/spiper.symbolic/root.tarball_dangerous_cache.cmd'),
File('/tmp/spiper.symbolic/root.tarball_dangerous_cache.cmd.empty.mock'),
File('/tmp/spiper.symbolic/root.tarball_dangerous_cache.cmd.old.mock'),
File('/tmp/spiper.symbolic/root.tarball_dangerous_cache.tar_gz'),
File('/tmp/spiper.symbolic/root.tarball_dangerous_cache.tar_gz.empty.mock'),
File('/tmp/spiper.symbolic/root.tarball_dangerous_cache.tar_gz.old.mock'),
File('/tmp/spiper.symbolic/root.tarball_prefix_cache.cmd'),
File('/tmp/spiper.symbolic/root.tarball_prefix_cache.cmd.empty.mock'),
File('/tmp/spiper.symbolic/root.tarball_prefix_cache.cmd.old.mock'),
File('/tmp/spiper.symbolic/root.tarball_prefix_cache.tar_gz'),
File('/tmp/spiper.symbolic/root.tarball_prefix_cache.tar_gz.empty.mock'),
File('/tmp/spiper.symbolic/root.tarball_prefix_cache.tar_gz.old.mock')]
# tarball_main( lambda *a:cache_run(*a,check_changed=2), prefix)
tarball_main( cache_run, prefix)
fs = sorted(prefix.fileglob('*',0,0)); print(pprint(fs))
assert fs == [
File('/tmp/spiper.symbolic/root.gen_files.out_txt'),
File('/tmp/spiper.symbolic/root.tarball_dangerous_cache.cmd'),
File('/tmp/spiper.symbolic/root.tarball_dangerous_cache.tar_gz'),
File('/tmp/spiper.symbolic/root.tarball_prefix_cache.cmd'),
File('/tmp/spiper.symbolic/root.tarball_prefix_cache.tar_gz')]
tarball_main( mock_run , prefix)
fs = sorted(prefix.fileglob('*',0,0)); print(pprint(fs))
assert fs == [
File('/tmp/spiper.symbolic/root.gen_files.out_txt'),
File('/tmp/spiper.symbolic/root.tarball_dangerous_cache.cmd'),
File('/tmp/spiper.symbolic/root.tarball_dangerous_cache.tar_gz'),
File('/tmp/spiper.symbolic/root.tarball_prefix_cache.cmd'),
File('/tmp/spiper.symbolic/root.tarball_prefix_cache.tar_gz')]
with open((prefix + '.gen_files.out_txt'),'w') as f:
f.write('100'*2000)
tarball_main( mock_run , prefix)
fs = sorted(prefix.fileglob('*',0,0)); print(pprint(fs))
assert fs == [
File('/tmp/spiper.symbolic/root.gen_files.out_txt'),
File('/tmp/spiper.symbolic/root.gen_files.out_txt.old.mock'),
File('/tmp/spiper.symbolic/root.tarball_dangerous_cache.cmd'),
File('/tmp/spiper.symbolic/root.tarball_dangerous_cache.tar_gz'),
File('/tmp/spiper.symbolic/root.tarball_prefix_cache.cmd'),
File('/tmp/spiper.symbolic/root.tarball_prefix_cache.cmd.old.mock'),
File('/tmp/spiper.symbolic/root.tarball_prefix_cache.tar_gz'),
File('/tmp/spiper.symbolic/root.tarball_prefix_cache.tar_gz.old.mock')]
tarball_main( cache_run, prefix)
fs = sorted(prefix.fileglob('*',0,0)); print(pprint(fs))
assert fs == [
File('/tmp/spiper.symbolic/root.gen_files.out_txt'),
File('/tmp/spiper.symbolic/root.tarball_dangerous_cache.cmd'),
File('/tmp/spiper.symbolic/root.tarball_dangerous_cache.tar_gz'),
File('/tmp/spiper.symbolic/root.tarball_prefix_cache.cmd'),
File('/tmp/spiper.symbolic/root.tarball_prefix_cache.tar_gz')]
# res = LoggedShellCommand(['ls -lhtr',prefix+'*'])
# .fileglob('*'),])
# print(res)
# prefix
# tarball_main( mock_run , prefix)
# assert 0
# (prefix.dirname()/'root.tarball_dangerous_cache.tar_gz').touch()
# self.assertRaises(spiper._types.OverwriteError, tarball_main, mock_run, prefix)
spiper.rcParams.update(_d)
def main(self=None,
prefix = None):
from spiper.runner import cache_run, mock_run, get_changed_files, get_all_files
from spiper.shell import LoggedShellCommand
from spiper.types import File,CacheFile
from pprint import pprint
spiper.rcParams['dir_layout']='clean'
# if prefix is None:
prefix = Path('/tmp/spiper.symbolic/root')
# backup_prefix = File('/home/user/.temp/backup_03_mock_flow/root')
backup_prefix = File('~/.temp/backup_03_mock_flow/root').expand()
prefix.dirname().rmtree_p()
backup_prefix.dirname().rmtree_p()
print('\n...[start]%r'%prefix)
#### once a workflow is defined, we can view the proposed file changes
fs = get_changed_files(workflow, prefix, 1, 100, verbose=0)
pprint(fs)
assert fs ==[
File('/tmp/spiper.symbolic/root.workflow.log'),
File('/tmp/spiper.symbolic/root.random_seq.seq'),
File('/tmp/spiper.symbolic/root.random_seq_const.seq'),
File('/tmp/spiper.symbolic/root.transcribe.fasta'),
File('/tmp/spiper.symbolic/root.mutate.fasta'),
File('/tmp/spiper.symbolic/root.source.py'),
# File('/home/user/.temp/backup_03_mock_flow/root.source.py')
]
### backup is conveniently defined as a workflow taking an executed workflow as an input.
### To check the proposed backup, mock_run() the workflow first.
workflow_out = mock_run(workflow, prefix, 1, 100)
fs = get_changed_files(backup, backup_prefix, workflow_out)
pprint(fs)
assert fs == [
File('/home/user/.temp/backup_03_mock_flow/root.subflow.random_seq.output.seq'),
File('/home/user/.temp/backup_03_mock_flow/root.subflow.random_seq_const.output.seq'),
File('/home/user/.temp/backup_03_mock_flow/root.subflow.transcribe.output.fasta'),
File('/home/user/.temp/backup_03_mock_flow/root.subflow.mutate.output.fasta'),
File('/home/user/.temp/backup_03_mock_flow/root.output.log'),
# File('/tmp/spiper.symbolic/root.source.py')
File('/home/user/.temp/backup_03_mock_flow/root.source.py')
]
### a convenient Flow may be defined to execute the two in chain
### If there is certain change to the workflow,
### the backup can also be runned
fs = get_changed_files (run_and_backup, prefix, 1, 100, backup_prefix, verbose=0)
pprint(fs)
assert fs == [
File('/tmp/spiper.symbolic/root.workflow.log'),
File('/tmp/spiper.symbolic/root.random_seq.seq'),
File('/tmp/spiper.symbolic/root.random_seq_const.seq'),
File('/tmp/spiper.symbolic/root.transcribe.fasta'),
File('/tmp/spiper.symbolic/root.mutate.fasta'),
File('/tmp/spiper.symbolic/root.source.py'),
File('/home/user/.temp/backup_03_mock_flow/root.subflow.random_seq.output.seq'),
File('/home/user/.temp/backup_03_mock_flow/root.subflow.random_seq_const.output.seq'),
File('/home/user/.temp/backup_03_mock_flow/root.subflow.transcribe.output.fasta'),
File('/home/user/.temp/backup_03_mock_flow/root.subflow.mutate.output.fasta'),
File('/home/user/.temp/backup_03_mock_flow/root.output.log'),
File('/home/user/.temp/backup_03_mock_flow/root.source.py'),
File('/home/user/.temp/backup_03_mock_flow/root.plot_graph.deptree_json'),
File('/home/user/.temp/backup_03_mock_flow/root.plot_graph.deptree_dot_txt'),
]
###### constants that are preserved between runs should be detected unchanged
_ = cache_run (run_and_backup, prefix, 1, 100, backup_prefix, verbose=0)
fs = get_changed_files (run_and_backup, prefix, 2, 200, backup_prefix, verbose=0)
pprint(fs)
assert fs == [File('/tmp/spiper.symbolic/root.workflow.log'),
File('/tmp/spiper.symbolic/root.random_seq.seq'),
# File('/tmp/spiper.symbolic/root.random_seq_const.seq'),
File('/tmp/spiper.symbolic/root.transcribe.fasta'),
File('/tmp/spiper.symbolic/root.mutate.fasta'),
# File('/tmp/spiper.symbolic/root.source.py'),
File('/home/user/.temp/backup_03_mock_flow/root.subflow.random_seq.output.seq'),
# File('/home/user/.temp/backup_03_mock_flow/root.subflow.random_seq_const.output.seq'),
File('/home/user/.temp/backup_03_mock_flow/root.subflow.transcribe.output.fasta'),
File('/home/user/.temp/backup_03_mock_flow/root.subflow.mutate.output.fasta'),
File('/home/user/.temp/backup_03_mock_flow/root.output.log'),
# File('/home/user/.temp/backup_03_mock_flow/root.source.py'),
File('/home/user/.temp/backup_03_mock_flow/root.plot_graph.deptree_json'),
File('/home/user/.temp/backup_03_mock_flow/root.plot_graph.deptree_dot_txt'),
]
##### get_all_files() return a leaf file regardless of whether is is changed
fs = get_all_files (run_and_backup, prefix, 2, 200, backup_prefix, verbose=0)
pprint(fs)
assert fs == [
File('/tmp/spiper.symbolic/root.workflow.log'),
File('/tmp/spiper.symbolic/root.random_seq.seq'),
File('/tmp/spiper.symbolic/root.random_seq_const.seq'),
File('/tmp/spiper.symbolic/root.transcribe.fasta'),
File('/tmp/spiper.symbolic/root.mutate.fasta'),
File('/tmp/spiper.symbolic/root.source.py'),
File('/home/user/.temp/backup_03_mock_flow/root.subflow.random_seq.output.seq'),
File('/home/user/.temp/backup_03_mock_flow/root.subflow.random_seq_const.output.seq'),
File('/home/user/.temp/backup_03_mock_flow/root.subflow.transcribe.output.fasta'),
File('/home/user/.temp/backup_03_mock_flow/root.subflow.mutate.output.fasta'),
File('/home/user/.temp/backup_03_mock_flow/root.output.log'),
File('/home/user/.temp/backup_03_mock_flow/root.source.py'),
File('/home/user/.temp/backup_03_mock_flow/root.plot_graph.deptree_json'),
File('/home/user/.temp/backup_03_mock_flow/root.plot_graph.deptree_dot_txt'),
]
_ = cache_run (run_and_backup, prefix, 2, 200, backup_prefix, verbose=0)
def job_trimmomatic(
self,
prefix,
FASTQ_FILE_1=InputFile,
FASTQ_FILE_2=InputFile,
THREADS_=int,
_IMAGE=Depend('docker://quay.io/biocontainers/trimmomatic:0.35--6'),
_output=[
File('fastq1'),
File('fastq2'),
File('log'),
File('cmd'),
],
):
_ = '''
trimmomatic PE -threads 4 -phred33
/home/feng/temp/187R/187R-S1-2018_06_27_14:02:08/809_S1_R1_raw.fastq
/home/feng/temp
/187R/187R-S1-2018_06_27_14:02:08/809_S1_R2_raw.fastq
809_S1_R1_raw_pass.fastq
809_S1_R1_raw_fail.fastq
809_S1_R2_raw_pass.fastq
809_S1_R2_raw_fail.fastq
ILLUMINACLIP:/home/Program_NGS_sl-pw-srv01/Trimmomatic-0.32/adapters/TruSeq3-PE-2.fa
:6:30:10 LEADING:3 TRAILING:3 MINLEN:36 SLIDINGWINDOW:4:15
'''
# _out = get_output_files(self, prefix, _output)
CMD = [
'trimmomatic', 'PE', '-threads',
str(THREADS_), '-phred33',
File(FASTQ_FILE_1),
File(FASTQ_FILE_2),
File(self.output.fastq1),
File(self.output.fastq1 + '.fail'),
File(self.output.fastq2),
File(self.output.fastq2 + '.fail'), 'ILLUMINACLIP:'
'/usr/local/share/trimmomatic-0.35-6/adapters/TruSeq3-PE-2.fa'
':6:30:10', 'LEADING:3', 'TRAILING:3', 'MINLEN:36',
'SLIDINGWINDOW:4:15', '&>',
File(self.output.log)
]
res = SingularityShellCommand(CMD, _IMAGE, self.output.cmd)
return self
def job_hisat2_align(
self,
prefix,
INDEX_PREFIX=Prefix,
FASTQ_FILE_1=InputFile,
FASTQ_FILE_2=InputFile,
THREADS_=int,
_IMAGE=Depend(
"docker://quay.io/biocontainers/hisat2:2.1.0--py36hc9558a2_4"),
_IMAGE_SAMTOOLS=Depend(
"docker://quay.io/biocontainers/samtools:1.10--h9402c20_2"),
_output=[
File('bam'),
File('log'),
File('cmd'),
]):
# _out = get_output_files(self,prefix,_output)
results = []
CMD = [
'hisat2',
'-x',
Prefix(INDEX_PREFIX),
'-1',
File(FASTQ_FILE_1),
'-2',
File(FASTQ_FILE_2),
# '-U', InputFile( FASTQ_FILE_1),
# ['-2',InputFile( FASTQ_FILE_2) ] if FASTQ_FILE_2 else [],
'-S',
File(self.output.bam + '.sam'),
'--threads',
str(THREADS_),
'--no-mixed',
'--rna-strandness',
'RF',
'--dta',
'--fr',
'&>',
File(self.output.log),
]
res = SingularityShellCommand(CMD, _IMAGE, self.output.cmd)
# results.append(job_result( None, CMD, self.output))
_ = '''
samtools view /home/feng/temp/187R/187R-S1-2018_06_27_14:02:08/809_S1.sam -b --threads 4 -o 809_S1.bam
'''
CMD = [
'samtools',
'view',
File(self.output.bam + '.sam'),
'--threads',
str(THREADS_),
'-o',
File(self.output.bam + '.unsorted'),
]
res = SingularityShellCommand(CMD, _IMAGE_SAMTOOLS, self.output.cmd)
CMD = [
'samtools',
'sort',
File(self.output.bam + '.unsorted'),
'--threads',
str(THREADS_),
'-o',
File(self.output.bam),
]
res = SingularityShellCommand(CMD, _IMAGE_SAMTOOLS, self.output.cmd)
return self
def workflow(self,
prefix,
hisat2_cache_prefix=str,
genome_fasta=File,
genome_gtf_file=File,
fastq1=File,
fastq2=File,
THREADS_=int,
_output=[]):
# print
# assert 0,repr((hisat2_cache_prefix))
# self.data = {}
# self.data['index'] =
curr = self.runner(
job_hisat2_index,
hisat2_cache_prefix,
genome_fasta,
THREADS_,
)
# self.data['trimmed'] =
curr = self.runner(
job_trimmomatic,
prefix,
fastq1,
fastq2,
THREADS_,
)
curr = self.runner(
job_hisat2_align,
prefix,
self.subflow['job_hisat2_index'].output.index_prefix,
self.subflow['job_trimmomatic'].output.fastq1,
self.subflow['job_trimmomatic'].output.fastq2,
[],
THREADS_,
)
self.runner(
job_picard_dedup,
prefix,
self.subflow['job_hisat2_align'].output.bam,
THREADS_,
)
self.config_runner(tag='picard_dedup_bam')(
job_bam_qc,
prefix,
self.subflow['job_picard_dedup'].output.bam,
THREADS_,
)
last = self.config_runner(tag='picard_dedup_bam')(
job_bam2bw_cpm,
prefix,
self.subflow['job_picard_dedup'].output.bam,
self.subflow['job_bam_qc-picard_dedup_bam'].output.data_json,
1,
)
self.runner(
LinkFile,
# last.output.output.bw[:-len('.bw')] + '.cpm_bw',
# last.output.bw,
# )
self.subflow['job_bam2bw_cpm-picard_dedup_bam'].output.bw[:-len('.bw')]
+ '.cpm_bw',
self.subflow['job_bam2bw_cpm-picard_dedup_bam'].output.bw)
self.runner(
job_stringtie_count,
prefix,
self.subflow['job_picard_dedup'].output.bam,
genome_gtf_file,
THREADS_,
)
assert File(__file__).isfile(
), 'Cannot find source file using __file__:%r' % __file__
self.runner(CopyFile, self.prefix_named + '.source.py', __file__)
return self
def job_hisat2_align(
self,
prefix,
INDEX_PREFIX=Prefix,
FASTQ_FILE_1=File,
FASTQ_FILE_2=File,
hisat2_args=list,
THREADS_=int,
_IMAGE=Depend(
"docker://quay.io/biocontainers/hisat2:2.1.0--py36hc9558a2_4"),
_IMAGE_SAMTOOLS=Depend(
"docker://quay.io/biocontainers/samtools:1.10--h9402c20_2"),
_output=[
File('bam'),
File('log'),
File('cmd'),
]):
# _out = get_output_files(self,prefix,_output)
results = []
cmd1 = CMD = [
'hisat2',
# hisat2_args,
'-x',
Prefix(INDEX_PREFIX),
'-1',
File(FASTQ_FILE_1),
'-2',
File(FASTQ_FILE_2),
# '-U', File( FASTQ_FILE_1),
# ['-2',File( FASTQ_FILE_2) ] if FASTQ_FILE_2 else [],
'-S',
'/dev/stdout',
'--threads',
str(max(1, THREADS_ - 1)),
hisat2_args
or ['--no-mixed', '--rna-strandness', 'RF', '--dta', '--fr'],
'2>',
File(self.output.log),
]
'''
singularity --verbose --debug exec docker://python:2.7.17-alpine python -V
singularity shell docker://python:2.7.17-alpine python -V
'''
# res = LoggedSingularityCommand(CMD, _IMAGE, self.output.cmd)
# results.append(job_result( None, CMD, self.output))
# _ = '''
# samtools view /home/feng/temp/187R/187R-S1-2018_06_27_14:02:08/809_S1.sam -b --threads 4 -o 809_S1.bam
# '''
cmd2 = CMD = [
'samtools',
'view',
'-bS',
'/dev/stdin',
'--threads',
str(1),
'-o',
(self.output.bam + '.unsorted'),
]
# res = LoggedSingularityCommand(CMD, _IMAGE_SAMTOOLS, self.output.cmd)
cmd3 = CMD = [
'samtools',
'sort',
(self.output.bam + '.unsorted'),
'--threads',
str(THREADS_),
'-o',
(self.output.bam),
'-T',
File(self.output.bam + '.sort_temp/').makedirs_p().check_writable(),
]
CMD = [
# 'PIPE=$(mktemp -u);mkfifo $PIPE;exec 3<>$PIPE ;rm $PIPE;',
LoggedSingularityCommandList(
self.prefix_named,
cmd1,
_IMAGE,
),
'|',
LoggedSingularityCommandList(self.prefix_named, cmd2, _IMAGE_SAMTOOLS),
'&&',
LoggedSingularityCommandList(self.prefix_named, cmd3, _IMAGE_SAMTOOLS),
# extra_files = [File(self.output.bam.dirname())]),
# LoggedSingularityCommandList(cmd3, _IMAGE_SAMTOOLS, extra_files = [File(self.output.bam.dirname())]),
# LoggedSingularityCommandList([cmd3,'&&','df',File(self.output.bam.dirname())], _IMAGE_SAMTOOLS,
# extra_files = [File(self.output.bam.dirname())]),
]
res = LoggedShellCommand(CMD, self.output.cmd)
# (self.output.bam+'.sam').unlink_p()
# (self.output.bam+'.unsorted').unlink_p()
# res = LoggedSingularityCommand(CMD, _IMAGE_SAMTOOLS, self.output.cmd)
return self