feat: implement ngs_mapping fingerprinting (#283)

.github/workflows/ci.yml

@@ -92,7 +92,7 @@ jobs:
           lfs: true
           fetch-depth: 2
       - name: Install mamba
-        run: conda install -y mamba==1.0.0
+        run: conda install -y mamba>=1.0.0
       - name: Prepare environment.yml file
         run: >
           cp environment.yml /tmp/environment.yml && sed -i -e

snappy_pipeline/workflows/ngs_mapping/Snakefile

@@ -258,3 +258,22 @@ rule ngs_mapping_bam_collect_doc_run:
         **wf.get_log_file("bam_collect_doc", "run"),
     wrapper:
         wf.wrapper_path("maelstrom/bam_collect_doc")
+
+
+# Compute fingerprint ---------------------------------------------------------
+
+
+rule ngs_mapping_ngs_chew_fingerprint:
+    input:
+        **wf.get_input_files("ngs_chew", "fingerprint")(),
+    output:
+        **wf.get_output_files("ngs_chew", "fingerprint"),
+    threads: wf.get_resource("ngs_chew", "fingerprint", "threads")
+    resources:
+        time=wf.get_resource("ngs_chew", "run", "time"),
+        memory=wf.get_resource("ngs_chew", "run", "memory"),
+        partition=wf.get_resource("ngs_chew", "run", "partition"),
+    log:
+        **wf.get_log_files("ngs_chew", "run"),
+    wrapper:
+        wf.wrapper_path("ngs_chew/fingerprint")

snappy_pipeline/workflows/ngs_mapping/__init__.py

@@ -348,6 +348,9 @@
     bam_collect_doc:
       enabled: false
       window_length: 1000
+    # Compute fingerprints with ngs-chew
+    ngs_chew_fingerprint:
+      enabled: true
     # Configuration for BWA
     bwa:
       path_index: REQUIRED # Required if listed in ngs_mapping.tools.dna; otherwise, can be removed.
@@ -1189,6 +1192,79 @@ def get_resource_usage(self, action):
         )
 
 
+class NgsChewStepPart(BaseStepPart):
+    """Analyze BAM File with ``ngs-chew``, e.g., ``fingerprint``"""
+
+    #: Step name
+    name = "ngs_chew"
+
+    #: Class available actions
+    actions = ("fingerprint",)
+
+    def __init__(self, parent):
+        super().__init__(parent)
+
+    def get_input_files(self, action):
+        """Return required input files"""
+        self._check_action(action)
+        return getattr(self, f"_get_input_files_{action}")
+
+    def _check_action(self, action):
+        if action not in self.actions:
+            actions_str = ", ".join(self.actions)
+            error_message = f"Action '{action}' is not supported. Valid options: {actions_str}"
+            raise UnsupportedActionException(error_message)
+
+    @dictify
+    def _get_input_files_run(self):
+        yield "bam", "work/{mapper_lib}/out/{mapper_lib}.bam"
+
+    def get_output_files(self, action):
+        """Return output files"""
+        self._check_action(action)
+        return getattr(self, "_get_output_files_{action}".format(action=action))()
+
+    @dictify
+    def _get_output_files_run(self):
+        yield "npz", "work/{mapper_lib}/report/fingerprint/{mapper_lib}.npz"
+        yield "npz_md5", "work/{mapper_lib}/report/fingerprint/{mapper_lib}.npz.md5"
+
+    def get_log_files(self, action):
+        self._check_action(action)
+        return getattr(self, "_get_log_files_{action}".format(action=action))()
+
+    @dictify
+    def _get_log_files_fingerprint(self):
+        prefix = "work/{mapper_lib}/log/{mapper_lib}.ngs_chew_fingerprint"
+        key_ext = (
+            ("log", ".log"),
+            ("conda_info", ".conda_info.txt"),
+            ("conda_list", ".conda_list.txt"),
+            ("wrapper", ".wrapper.py"),
+            ("env_yaml", ".environment.yaml"),
+        )
+        for key, ext in key_ext:
+            yield key, prefix + ext
+            yield key + "_md5", prefix + ext + ".md5"
+
+    def get_resource_usage(self, action):
+        """Get Resource Usage
+
+        :param action: Action (i.e., step) in the workflow, example: 'run'.
+        :type action: str
+
+        :return: Returns ResourceUsage for step.
+
+        :raises UnsupportedActionException: if action not in class defined list of valid actions.
+        """
+        self._check_action(action)
+        return ResourceUsage(
+            threads=1,
+            time="04:00:00",
+            memory="2G",
+        )
+
+
 class NgsMappingWorkflow(BaseStep):
     """Perform NGS Mapping"""
 
@@ -1218,6 +1294,7 @@ def __init__(self, workflow, config, config_lookup_paths, config_paths, workdir)
                 StarStepPart,
                 TargetCoverageReportStepPart,
                 BamCollectDocStepPart,
+                NgsChewStepPart,
             )
         )
         self.sub_steps["link_out"].disable_patterns = expand("**/*{ext}", ext=EXT_VALUES)
@@ -1281,9 +1358,14 @@ def get_result_files(self):
         yield from self._yield_result_files(
             os.path.join("output", name_pattern, "out", name_pattern + "{ext}"), ext=EXT_VALUES
         )
-        infixes = ["mapping", "target_cov_report"]
+        infixes = [
+            "mapping",
+            "target_cov_report",
+        ]
         if self.config["bam_collect_doc"]["enabled"]:
             infixes.append("bam_collect_doc")
+        if self.config["ngs_chew_fingerprint"]["enabled"]:
+            infixes.append("ngs_chew_fingerprint")
         for infix in infixes:
             yield from self._yield_result_files(
                 os.path.join("output", name_pattern, "log", "{mapper}.{ngs_library.name}.{ext}"),
@@ -1305,6 +1387,13 @@ def get_result_files(self):
                 os.path.join("output", name_pattern, "report", "cov", name_pattern + ".cov.{ext}"),
                 ext=("vcf.gz", "vcf.gz.md5", "vcf.gz.tbi", "vcf.gz.tbi.md5", "bw", "bw.md5"),
             )
+        if self.config["ngs_chew_fingerprint"]["enabled"]:
+            yield from self._yield_result_files(
+                os.path.join(
+                    "output", name_pattern, "report", "fingerprint", name_pattern + ".{ext}"
+                ),
+                ext=("npz", "npz.md5"),
+            )
         yield from self._yield_result_files(
             os.path.join(
                 "output", name_pattern, "report", "bam_qc", name_pattern + ".bam.{report}.txt"

snappy_wrappers/wrappers/ngs_chew/fingerprint/environment.yaml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - file:///data/gpfs-1/users/holtgrem_c/scratch/art/LinuxArtifacts/packages
+dependencies:
+  - ngs-chew >=0.5.0,<0.6.0

snappy_wrappers/wrappers/ngs_chew/fingerprint/wrapper.py

@@ -0,0 +1,128 @@
+# -*- coding: utf-8 -*-
+"""Wrapper for running ``ngs-chew fingerprint``."""
+
+from snakemake.shell import shell
+
+__author__ = "Manuel Holtgrewe"
+__email__ = "[email protected]"
+
+path_ref = snakemake.config["static_data_config"]["reference"]["path"]
+if "hg19" in path_ref or "37" in path_ref:
+    genome_release = "GRCh37"
+else:
+    genome_release = "GRCh38"
+
+shell(
+    r"""
+set -x
+
+# Write out information about conda and save a copy of the wrapper with picked variables
+# as well as the environment.yaml file.
+conda list >{snakemake.log.conda_list}
+conda info >{snakemake.log.conda_info}
+md5sum {snakemake.log.conda_list} >{snakemake.log.conda_list_md5}
+md5sum {snakemake.log.conda_info} >{snakemake.log.conda_info_md5}
+cp {__real_file__} {snakemake.log.wrapper}
+md5sum {snakemake.log.wrapper} >{snakemake.log.wrapper_md5}
+cp $(dirname {__file__})/environment.yaml {snakemake.log.env_yaml}
+md5sum {snakemake.log.env_yaml} >{snakemake.log.env_yaml_md5}
+
+# Also pipe stderr to log file
+if [[ -n "{snakemake.log.log}" ]]; then
+    if [[ "$(set +e; tty; set -e)" != "" ]]; then
+        rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log})
+        exec 2> >(tee -a "{snakemake.log.log}" >&2)
+    else
+        rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log})
+        echo "No tty, logging disabled" >"{snakemake.log.log}"
+    fi
+fi
+
+export TMPDIR=$(mktemp -d)
+trap "rm -rf $TMPDIR" EXIT
+mkdir -p $TMPDIR/{{out,sorted,sort.tmp}}
+
+if [[ "{library_kit}" == "PacBio HiFi" ]]; then
+    preset=map-hifi
+elif [[ "{library_kit}" == "PacBio CLR" ]]; then
+    preset=map-pb
+elif [[ "{library_kit}" == ONT* ]]; then
+    preset=map-ont
+else
+    >&2 echo "Unknown library kit {library_kit}"
+    exit 1
+fi
+
+ngs-chew fingerprint \
+    --min-coverage 5 \
+    --reference {snakemake.config[static_data_config][reference][path]} \
+    --output-fingerprint {snakemake.ouput.npz} \
+    --input-bam {snakemake.input.bam}
+    --genome-release {genome_release}
+
+
+# Compute MD5 sums
+pushd $(dirname $out_bam)
+md5sum $(basename $out_bam) >$(basename $out_bam).md5
+md5sum $(basename $out_bam).bai >$(basename $out_bam).bai.md5
+popd
+
+# QC Report ---------------------------------------------------------------------------------------
+
+# gather statistics from BAM file
+# TODO: use pipes for only reading once from disk?
+samtools stats    {snakemake.output.bam} > {snakemake.output.report_bamstats_txt}
+samtools flagstat {snakemake.output.bam} > {snakemake.output.report_flagstats_txt}
+samtools idxstats {snakemake.output.bam} > {snakemake.output.report_idxstats_txt}
+
+# call plot-bamstats
+mkdir $TMPDIR/bamstats.d
+plot-bamstats \
+    -p $TMPDIR/bamstats.d/ \
+    {snakemake.output.report_bamstats_txt} \
+|| true  # ignore failure
+
+# Patch inline-html if necessary.
+cat >$TMPDIR/inline-html.diff <<EOF
+diff --git a/inline_html/inline_html.py b/inline_html/inline_html.py
+index 893086c..cbef6dd 100644
+--- a/inline_html/inline_html.py
++++ b/inline_html/inline_html.py
+@@ -20,7 +20,10 @@ def resource_to_data(path, in_file):
+     mime, _ = mimetypes.guess_type(path)
+     with open(path, 'rb') as fp:
+         data = fp.read()
+-        data64 = b''.join(base64.encodestring(data).splitlines())
++        try:
++            data64 = b''.join(base64.encodestring(data).splitlines())
++        except AttributeError:
++            data64 = b''.join(base64.encodebytes(data).splitlines())
+         return 'data:%s;base64,%s' % (mime, data64.decode('ascii'))
+EOF
+pushd $(python3 -c 'import inline_html; print(inline_html.__path__[0])')
+if ! grep encodebytes inline_html.py; then
+    patch -p2 <$TMPDIR/inline-html.diff
+fi
+popd
+
+# Convert HTML report into one file.
+inline-html \
+    --in-file $TMPDIR/bamstats.d/index.html \
+    --out-file {snakemake.output.report_bamstats_html} \
+|| touch {snakemake.output.report_bamstats_html}
+
+# Build MD5 files for the reports
+md5sum {snakemake.output.report_bamstats_html} > {snakemake.output.report_bamstats_html_md5}
+md5sum {snakemake.output.report_bamstats_txt} > {snakemake.output.report_bamstats_txt_md5}
+md5sum {snakemake.output.report_flagstats_txt} >{snakemake.output.report_flagstats_txt_md5}
+md5sum {snakemake.output.report_idxstats_txt} > {snakemake.output.report_idxstats_txt_md5}
+"""
+)
+
+# Compute MD5 sums of logs.
+shell(
+    r"""
+sleep 1s  # try to wait for log file flush
+md5sum {snakemake.log.log} >{snakemake.log.log_md5}
+"""
+)

tests/snappy_pipeline/workflows/test_workflows_ngs_mapping.py

@@ -793,6 +793,7 @@ def test_ngs_mapping_workflow_steps(ngs_mapping_workflow):
         "link_out",
         "link_out_bam",
         "minimap2",
+        "ngs_chew",
         "star",
         "target_coverage_report",
     ]
@@ -811,7 +812,7 @@ def test_ngs_mapping_workflow_files(ngs_mapping_workflow):
         for i in range(1, 7)
         for ext in ("bam", "bam.bai", "bam.md5", "bam.bai.md5")
     ]
-    for infix in ("bam_collect_doc", "mapping", "target_cov_report"):
+    for infix in ("bam_collect_doc", "mapping", "target_cov_report", "ngs_chew_fingerprint"):
         expected += [
             "output/bwa.P00{i}-N1-DNA1-WGS1/log/bwa.P00{i}-N1-DNA1-WGS1.{ext}".format(i=i, ext=ext)
             for i in range(1, 7)
@@ -850,6 +851,13 @@ def test_ngs_mapping_workflow_files(ngs_mapping_workflow):
         for ext in ("bw", "bw.md5", "vcf.gz", "vcf.gz.md5", "vcf.gz.tbi", "vcf.gz.tbi.md5")
         for i in range(1, 7)
     ]
+    expected += [
+        "output/bwa.P00{i}-N1-DNA1-WGS1/report/fingerprint/bwa.P00{i}-N1-DNA1-WGS1.{ext}".format(
+            i=i, ext=ext
+        )
+        for ext in ("npz", "npz.md5")
+        for i in range(1, 7)
+    ]
     expected += [
         "output/bwa.P00{i}-N1-DNA1-WGS1/report/cov_qc/bwa.P00{i}-N1-DNA1-WGS1.{ext}".format(
             i=i, ext=ext

tests/snappy_pipeline/workflows/test_workflows_ngs_mapping_processed_fastq.py

@@ -724,6 +724,7 @@ def test_ngs_mapping_workflow_steps(ngs_mapping_workflow):
         "link_out",
         "link_out_bam",
         "minimap2",
+        "ngs_chew",
         "star",
         "target_coverage_report",
     ]
@@ -742,7 +743,7 @@ def test_ngs_mapping_workflow_files(ngs_mapping_workflow):
         for i in range(1, 7)
         for ext in ("bam", "bam.bai", "bam.md5", "bam.bai.md5")
     ]
-    for infix in ("bam_collect_doc", "mapping", "target_cov_report"):
+    for infix in ("bam_collect_doc", "mapping", "target_cov_report", "ngs_chew_fingerprint"):
         expected += [
             "output/bwa.P00{i}-N1-DNA1-WGS1/log/bwa.P00{i}-N1-DNA1-WGS1.{ext}".format(i=i, ext=ext)
             for i in range(1, 7)
@@ -781,6 +782,13 @@ def test_ngs_mapping_workflow_files(ngs_mapping_workflow):
         for ext in ("bw", "bw.md5", "vcf.gz", "vcf.gz.md5", "vcf.gz.tbi", "vcf.gz.tbi.md5")
         for i in range(1, 7)
     ]
+    expected += [
+        "output/bwa.P00{i}-N1-DNA1-WGS1/report/fingerprint/bwa.P00{i}-N1-DNA1-WGS1.{ext}".format(
+            i=i, ext=ext
+        )
+        for ext in ("npz", "npz.md5")
+        for i in range(1, 7)
+    ]
     expected += [
         "output/bwa.P00{i}-N1-DNA1-WGS1/report/cov_qc/bwa.P00{i}-N1-DNA1-WGS1.{ext}".format(
             i=i, ext=ext