snakemake script access to stdin / stdout for stream processing - snakemake

Question

For a Snakemake workflow, I need to manipulate tags in many BAM files, and would like to process these by piping them through a script (using the Snakemake script: directive). The specific way I'm doing this is with pysam stream processing.
infile = pysam.AlignmentFile("-", "rb")
outfile = pysam.AlignmentFile("-", "wb", template=infile)
for s in infile:
(flowcell, lane) = s.query_name.split(':')[0:2]
rg_id = ".".join([flowcell, lane])
s.set_tag('RG',rg_id,'Z')
outfile.write(s)
This script works well standalone, but I haven't been able to figure out how to integrate it via the snakemake script directive.
I prefer this way to minimize IO and RAM usage.
Edit: Resorted to direct loading to fix the RG tag.
# parameters passed from snakemake
bam_file = snakemake.input[0]
fixed_bam_file = snakemake.output[0]
bamfile = pysam.AlignmentFile(bam_file, "rb")
fixed_bamfile = pysam.AlignmentFile(fixed_bam_file, "wb", template = bamfile)
for i, read in enumerate(bamfile.fetch()):
(flowcell, lane) = read.query_name.split(':')[0:2]
rg_id = ".".join([flowcell, lane])
read.set_tag('RG',rg_id,'Z')
fixed_bamfile.write(read)
if not (i % 100000):
print("Updated the read group for {} reads to {}".format(i, rg_id))
bamfile.close()
fixed_bamfile.close()
EDIT: Snakemakes run: and shell: directives set the workdir: directory, while the script: directive operates relative to the directory where the Snakefile was executed (keeping everything nice and tidy). Hence the problem of putting a stream processor under script:.

Answer 1

Using shell instead of script directive:
rule all:
input:
expand('{sample}_edited.bam'), sample=['a', 'b', 'c']
rule somename:
input:
'{sample}.bam'
output:
'{sample}_edited.bam'
shell:
'''
cat {input} > python edit_bam.py > {output}
'''

Answer 2

#Krischan it seems you found a solution already and if so maybe good to post it as an answer.
Alternatively, you can use the object {workflow} to get the directory of the Snakefile and from there construct the path to your python script. If your directory structure is:
./
├── Snakefile
├── data
│   └── sample.bam
└── scripts
└── edit_bam.py
The Snakefile may look like:
rule all:
input:
'test.tmp',
rule one:
input:
'sample.bam',
output:
'test.tmp',
shell:
r"""
cat {input} \
| {workflow.basedir}/scripts/edit_bam.py > {output}
"""
Executed with snakemake -d data ...
It seems the workflow object is not documented but check this thread Any way to get the full path of the Snakefile within the Snakefile?