perf: autobump bio/emu/abundance (#3256)

Automatic bump of bio/emu/abundance.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Co-authored-by: Filipe G. Vieira <1151762+fgvieira@users.noreply.github.com>

bio/emu/abundance/environment.linux-64.pin.txt

@@ -3,22 +3,23 @@
 # platform: linux-64
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
-https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda#23ab7665c5f63cfb9f1f6195256daac6
+https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.8.30-hbcca054_0.conda#c27d1c142233b5bc9ca570c6e2e0c244
 https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74
 https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.12-5_cp312.conda#0424ae29b104430108f5218a66db7260
 https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h8827d51_1.conda#8bfdead4e0fff0383ae4c9c50d0531bd
 https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_1.conda#23c255b008c4f2ae008f81edcabaca89
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
 https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.1.0-h77fa898_1.conda#002ef4463dd1e2b44a94a4ace468f5d2
+https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.3-h5888daf_0.conda#59f4c43bb1b5ef1c71946ff2cbf59524
 https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h69a702a_1.conda#1efc0ad219877a73ef977af7dbb51f17
 https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-14.1.0-hc5f4f2c_1.conda#10a0cef64b784d6ab6da50ebca4e984d
 https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-14.1.0-hc0a3c3a_1.conda#9dbb9699ea467983ba8a4ba89b08b066
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.2-hb9d3cd8_0.conda#4d638782050ab6faa27275bed57e9b4e
 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
 https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.33.1-heb4867d_0.conda#0d3c60291342c0c025db231353376dfb
 https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3
 https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.21-h4bc722e_0.conda#36ce76665bf67f5aac36be7a0d21b7f3
 https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172bf1cd1ff8629f2b1179945ed45055
-https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.2-h59595ed_0.conda#e7ba12deb7020dd080c6c70e7b6f6a3d
 https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3
 https://conda.anaconda.org/conda-forge/linux-64/libgfortran-14.1.0-h69a702a_1.conda#591e631bc1ae62c64f2ab4f66178c097
 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7
@@ -27,7 +28,6 @@ https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#
 https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
 https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h4ab18f5_6.conda#27329162c0dc732bcf67a4e0cd488125
 https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-he02047a_1.conda#70caf8bb6cf39a0b6b7efc885f51c0fe
-https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-hb9d3cd8_3.conda#6c566a46baae794daf34775d41eb180a
 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
 https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-14.1.0-h69a702a_1.conda#16cec94c5992d7f42ae3f9fa8b25df8d
@@ -43,24 +43,24 @@ https://conda.anaconda.org/bioconda/linux-64/k8-0.2.5-hdcf5f25_4.tar.bz2#d3c49a9
 https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.3-h659f571_0.conda#3f43953b7d3fb3aaa1d0d0723d91e368
 https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.27-pthreads_hac2b453_1.conda#ae05ece66d3924ac3d48b4aa3fa96cec
 https://conda.anaconda.org/conda-forge/linux-64/python-3.12.3-hab00c5b_0_cpython.conda#2540b74d304f71d3e89c81209db4db84
-https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-23_linux64_openblas.conda#96c8450a40aa2b9733073a9460de972c
+https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-24_linux64_openblas.conda#80aea6603a6813b16ec119d00382b772
 https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.8.0-hca28451_1.conda#b8afb3e3cb3423cc445cf611ab95fdb0
 https://conda.anaconda.org/bioconda/linux-64/minimap2-2.28-he4a0461_3.tar.bz2#0e2b1e20347eddfa294608536ded59cf
 https://conda.anaconda.org/conda-forge/noarch/python-tzdata-2024.1-pyhd8ed1ab_0.conda#98206ea9954216ee7540f0c773f2104d
-https://conda.anaconda.org/conda-forge/noarch/pytz-2024.1-pyhd8ed1ab_0.conda#3eeeeb9e4827ace8c0c1419c85d590ad
-https://conda.anaconda.org/conda-forge/noarch/setuptools-72.2.0-pyhd8ed1ab_0.conda#1462aa8b243aad09ef5d0841c745eb89
+https://conda.anaconda.org/conda-forge/noarch/pytz-2024.2-pyhd8ed1ab_0.conda#260009d03c9d5c0f111904d851f053dc
+https://conda.anaconda.org/conda-forge/noarch/setuptools-74.1.2-pyhd8ed1ab_0.conda#56c9c11d004428e81d02eeb730fc6336
 https://conda.anaconda.org/conda-forge/noarch/six-1.16.0-pyh6c4a22f_0.tar.bz2#e5f25f8dbc060e9a8d912e432202afc2
 https://conda.anaconda.org/conda-forge/noarch/wheel-0.44.0-pyhd8ed1ab_0.conda#d44e3b085abcaef02983c6305b84b584
-https://conda.anaconda.org/conda-forge/noarch/zipp-3.20.1-pyhd8ed1ab_0.conda#74a4befb4b38897e19a107693e49da20
-https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-8.4.0-pyha770c72_0.conda#6e3dbc422d3749ad72659243d6ac8b2b
-https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-23_linux64_openblas.conda#eede29b40efa878cbe5bdcb767e97310
-https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-23_linux64_openblas.conda#2af0879961951987e464722fd00ec1e0
-https://conda.anaconda.org/conda-forge/linux-64/pathlib2-2.3.7.post1-py312h7900ff3_3.conda#3d6a6028b8378ac14fc145ce4c5f88fa
+https://conda.anaconda.org/conda-forge/noarch/zipp-3.20.2-pyhd8ed1ab_0.conda#4daaed111c05672ae669f7036ee5bba3
+https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-8.5.0-pyha770c72_0.conda#54198435fce4d64d8a89af22573012a8
+https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-24_linux64_openblas.conda#f5b8822297c9c790cec0795ca1fc9be6
+https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-24_linux64_openblas.conda#fd540578678aefe025705f4b58b36b2e
+https://conda.anaconda.org/conda-forge/linux-64/pathlib2-2.3.7.post1-py312h7900ff3_4.conda#3f0dd9053bff6c6f0bc0ad3dbcc63a2b
 https://conda.anaconda.org/conda-forge/noarch/pip-24.2-pyh8b19718_1.conda#6c78fbb8ddfd64bcb55b5cbafd2d2c43
 https://conda.anaconda.org/bioconda/linux-64/pysam-0.22.1-py312hcfdcdd7_2.tar.bz2#33baeca8a223d34355fd37bc9e14a128
 https://conda.anaconda.org/conda-forge/noarch/python-dateutil-2.9.0-pyhd8ed1ab_0.conda#2cf4264fffb9e6eff6031c5b6884d61c
 https://conda.anaconda.org/conda-forge/noarch/flatten-dict-0.4.2-pyhd8ed1ab_1.tar.bz2#ccfb30b92adfeb283d4dcae3d0b6441b
-https://conda.anaconda.org/conda-forge/linux-64/numpy-2.1.0-py312h1103770_0.conda#9709027e8a51a3476db65a3c0cf806c2
+https://conda.anaconda.org/conda-forge/linux-64/numpy-2.1.1-py312h58c1407_0.conda#839596d1c1c41f6fc01042e12cb7500c
 https://conda.anaconda.org/conda-forge/linux-64/biopython-1.84-py312h9a8786e_0.conda#6683d74a08fc106ef44d6ac403dc7aee
 https://conda.anaconda.org/conda-forge/linux-64/pandas-2.2.2-py312h1d6d2e6_1.conda#ae00b61f3000d2284d1f2584d4dfafa8
-https://conda.anaconda.org/bioconda/noarch/emu-3.4.6-hdfd78af_0.tar.bz2#6dd947250aaddea7918056f230ba8a4e
+https://conda.anaconda.org/bioconda/noarch/emu-3.5.0-hdfd78af_0.tar.bz2#a6c440f4420154f114e8a0904412ae4e

bio/emu/abundance/environment.yaml

@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - emu =3.4.6
+  - emu =3.5.0

bio/emu/abundance/meta.yaml

@@ -4,11 +4,12 @@ url: https://github.com/treangenlab/emu
 authors:
   - Curro Campuzano
 input:
-  - reads: single fastq file or paired fastq files
+  - reads: single FASTA file or paired FASTQ files
   - db: emu database (optional; check documentation for pre-built databases and how to build them).
 output:
   - abundances: TSV with relative (and optionally, absolute abundances).
   - alignments: SAM file with the alignments (optional).
-  - unclassified: FASTA file with unclassified sequences (optional).
+  - unclassified: FASTA/Q file with unclassified sequences (optional).
+  - unmapped: FASTA/Q file with unmapped sequences (optional).
 params:
   extra: Any optimal parameter such as --type (sequencer) or --min-abundance. Optional flags involving output are handled automatically (e.g. --output-dir, --output-basename ...)

bio/emu/abundance/test/Snakefile

@@ -5,7 +5,8 @@ rule abundance:
     output:
         abundances="{sample}_rel-abundance.tsv",
         alignments="{sample}_emu_alignments.sam",
-        unclassified="{sample}_unclassified.fa",
+        unclassified="{sample}_unclassified.fas",
+        unmapped="{sample}_unmapped.fas",
     log:
         "logs/emu/{sample}_abundance.log",
     params:
@@ -21,6 +22,9 @@ rule abundance_paired:
         db="database",
     output:
         abundances="{sample}_rel-abundance_paired.tsv",
+        alignments="{sample}_emu_alignments_paired.sam",
+        unclassified="{sample}_unclassified_paired.fq",
+        unmapped="{sample}_unmapped_paired.fq",
     log:
         "logs/emu/{sample}_abundance_paired.log",
     params:

bio/emu/abundance/wrapper.py

@@ -10,8 +10,13 @@
 
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)
 extra = snakemake.params.get("extra", "")
-db = snakemake.input.get("db", "")
-if db:
+
+# Infer format of input file
+in_fmt = "fasta"
+if isinstance(snakemake.input.reads, list) and len(snakemake.input.reads) == 2:
+    in_fmt = "fastq"
+
+if db := snakemake.input.get("db", ""):
     db = f"--db {db}"
 
 with tempfile.TemporaryDirectory() as tmpdir:
@@ -27,5 +32,7 @@
         shell("mv {tmpdir}/output_rel-abundance.tsv {out_tsv}")
     if out_sam := snakemake.output.get("alignments"):
         shell("mv {tmpdir}/output_emu_alignments.sam {out_sam}")
-    if out_fa := snakemake.output.get("unclassified"):
-        shell("mv {tmpdir}/output_unclassified.fa {out_fa}")
+    if out_unclassified_fq := snakemake.output.get("unclassified"):
+        shell("mv {tmpdir}/output_unclassified_mapped.{in_fmt} {out_unclassified_fq}")
+    if out_unmapped_fq := snakemake.output.get("unmapped"):
+        shell("mv {tmpdir}/output_unmapped.{in_fmt} {out_unmapped_fq}")

test.py

@@ -6870,7 +6870,8 @@ def test_emu_abundance():
             "1",
             "sample_rel-abundance.tsv",
             "sample_emu_alignments.sam",
-            "sample_unclassified.fa",
+            "sample_unclassified.fas",
+            "sample_unmapped.fas",
             "--use-conda",
             "-F",
         ],
@@ -6886,6 +6887,9 @@ def test_emu_abundance_paired():
             "--cores",
             "1",
             "short_read_rel-abundance_paired.tsv",
+            "short_read_emu_alignments_paired.sam",
+            "short_read_unclassified_paired.fq",
+            "short_read_unmapped_paired.fq",
             "--use-conda",
             "-F",
         ],