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

* Revert assembly to short-read-mngs docker image * Test release * Update README
chanzuckerberg · Apr 8, 2024 · 373fbb2 · 373fbb2
1 parent 63c9aed
commit 373fbb2
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diff --git a/workflows/amr/Dockerfile b/workflows/amr/Dockerfile
@@ -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 && \

diff --git a/workflows/amr/README.md b/workflows/amr/README.md
@@ -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

diff --git a/workflows/amr/run.wdl b/workflows/amr/run.wdl
@@ -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,
         }
     }
 

diff --git a/workflows/amr/test/test_wdl.py b/workflows/amr/test/test_wdl.py
@@ -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")