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Revert AMR assembly to using short-read-mngs docker image #344

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merged 3 commits into from
Apr 8, 2024
Merged

Revert AMR assembly to using short-read-mngs docker image #344

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704eed1
Revert assembly to short-read-mngs docker image
lvreynoso Apr 8, 2024
f751f54
Test release
lvreynoso Apr 8, 2024
919ee69
Update README
lvreynoso Apr 8, 2024
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5 changes: 0 additions & 5 deletions workflows/amr/Dockerfile
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Expand Up @@ -27,11 +27,6 @@ RUN curl -L https://github.com/arpcard/rgi/archive/refs/tags/6.0.3.tar.gz | tar
git apply ../rgi_bam_parsing.patch && \
pip3 install .

# Install SPAdes
RUN curl -LO https://github.com/ablab/spades/releases/download/v3.11.1/SPAdes-3.11.1-Linux.tar.gz && \
tar -xzf SPAdes-3.11.1-Linux.tar.gz && \
ln -s /SPAdes-3.11.1-Linux/bin/spades.py /usr/local/bin/spades.py

# Install seqfu (used for interleaving input files)
ARG SEQFU_VER="1.16.0"
RUN curl -LO https://github.com/telatin/seqfu2/releases/download/v${SEQFU_VER}/SeqFu-v${SEQFU_VER}-Linux-x86_64.zip && \
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6 changes: 6 additions & 0 deletions workflows/amr/README.md
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Expand Up @@ -4,6 +4,12 @@ CZ ID's AMR workflow implements the [Resistance Gene Identifier (RGI)](https://g

# Changelog

## 1.4.2 - 2024-04-08

### Fixed

- Fixed an issue that caused assembly to fail for RawSample inputs.

## 1.4.1 - 2024-04-07

### Changed
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2 changes: 1 addition & 1 deletion workflows/amr/run.wdl
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Expand Up @@ -61,7 +61,7 @@ workflow amr {
input:
reduplicated_reads = RunRedupRaw.redups_fa,
min_contig_length = min_contig_length,
docker_image_id = docker_image_id,
docker_image_id = host_filtering_docker_image_id,
}
}

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40 changes: 0 additions & 40 deletions workflows/amr/test/test_wdl.py
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Expand Up @@ -177,43 +177,3 @@ def testRunRedup(self):
for read_id, read_sequence in output_2.items():
assert read_id in host_filter_2
assert read_sequence == host_filter_2[read_id]

# NOTE: These two tests rely on the short-read-mngs docker image. An issue with this is that
# any PR that makes a change to AMR's RunSpades task that depends on a change also made to
# the short-read-mngs docker image will cause these tests to fail, because they can't use the
# updated image with our current setup.
def testRunSpadesAssemblyFailedNonUniformCoverage(self):
inputs = {
"reduplicated_reads": [
relpath("RunSpades", "subsampled_1.fa"),
relpath("RunSpades", "subsampled_2.fa")
],
"min_contig_length": 100,
}

res = self.run_miniwdl(
task="RunSpades",
task_input=inputs,
)

with open(res["outputs"]["RunSpades.contigs"]) as contigs_fa:
lines = contigs_fa.readlines()
assert lines[0].startswith(";ASSEMBLY FAILED")

def testRunSpadesAssemblyFailedExitCodeZero(self):
inputs = {
"reduplicated_reads": [
relpath("RunSpades", "redups_1.fa"),
relpath("RunSpades", "redups_2.fa")
],
"min_contig_length": 100,
}

res = self.run_miniwdl(
task="RunSpades",
task_input=inputs,
)

with open(res["outputs"]["RunSpades.contigs"]) as contigs_fa:
lines = contigs_fa.readlines()
assert lines[0].startswith(";ASSEMBLY FAILED")
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