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The tools/alighment.py
file is first created in the tutorial 1.
# File: tools/alignment.py
from janis_core import WorkflowBuilder, String
from janis_bioinformatics.data_types import FastqGzPairedEnd, FastaWithDict
from janis_bioinformatics.tools.bwa import BwaMemLatest
from janis_bioinformatics.tools.samtools import SamToolsView_1_9
from janis_bioinformatics.tools.gatk4 import Gatk4SortSam_4_1_2
w = WorkflowBuilder("alignmentWorkflow")
# Inputs
w.input("sample_name", String)
w.input("read_group", String)
w.input("fastq", FastqGzPairedEnd)
w.input("reference", FastaWithDict)
# Steps
w.step(
"bwamem",
BwaMemLatest(
reads=w.fastq,
readGroupHeaderLine=w.read_group,
reference=w.reference
)
)
w.step(
"samtoolsview",
SamToolsView_1_9(
sam=w.bwamem.out
)
)
w.step(
"sortsam",
Gatk4SortSam_4_1_2(
bam=w.samtoolsview.out,
sortOrder="coordinate",
createIndex=True
)
)
# Outputs
w.output("out", source=w.sortsam.out)
In tutorial 3, there's a paragraph that says
I think tools/alignment.py
has only out
output, while tools/samtoolsflagstat.py
has the stats
output?
# File: tools/samtoolsflagstat.py
from janis_core import CommandToolBuilder, ToolInput, ToolOutput, Int, Stdout
from janis_unix.data_types import TextFile
from janis_bioinformatics.data_types import Bam
SamtoolsFlagstat = CommandToolBuilder(
tool="samtoolsflagstat",
base_command=["samtools", "flagstat"],
container="quay.io/biocontainers/samtools:1.9--h8571acd_11",
version="v1.9.0",
inputs=[
# 1. Positional bam input
ToolInput("bam", Bam, position=1),
# 2. `threads` inputs
ToolInput("threads", Int(optional=True), prefix="--threads"),
],
outputs=[ToolOutput("stats", Stdout(TextFile))],
)
Not really a user of these tools, and just getting started with Janis, so maybe I missed something? Or is there an error in that paragraph? Found while reading tutorials and preparing #51
Thanks!
Bruno
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