feat: Add support for seqkit split2

bio/seqkit/environment.linux-64.pin.txt

@@ -1,30 +1,43 @@
 # This file may be used to create an environment using:
 # $ conda create --name <env> --file <this file>
 # platform: linux-64
-# created-by: conda 24.9.0
+# created-by: conda 24.9.2
 @EXPLICIT
 https://conda.anaconda.org/bioconda/linux-64/seqkit-2.9.0-h9ee0642_0.tar.bz2#14369282dc7a09cb3e117e4db9c9ddc2
 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-2024.8.30-hbcca054_0.conda#c27d1c142233b5bc9ca570c6e2e0c244
+https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.12.14-hbcca054_0.conda#720523eb0d6a9b0f6120c16b2aa4e7de
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.43-h712a8e2_2.conda#048b02e3962f066da18efe3a21b77672
+https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.13-5_cp313.conda#381bbd2a92c863f640a55b6ff3c35161
+https://conda.anaconda.org/conda-forge/noarch/tzdata-2024b-hc8b5060_0.conda#8ac3367aafb1cc0a068483c580af8015
 https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.2.0-h77fa898_1.conda#cc3573974587f12dda90d96e3e55a702
 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-14.2.0-h77fa898_1.conda#3cb76c3f10d3bc7f1105b2fc9db984df
-https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.2-heb4867d_0.conda#2b780c0338fc0ffa678ac82c54af51fd
+https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.4-hb9d3cd8_0.conda#e2775acf57efd5af15b8e3d1d74d72d3
+https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.23-h4ddbbb0_0.conda#8dfae1d2e74767e9ce36d5fa0d8605db
+https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.4-h5888daf_0.conda#db833e03127376d461e1e13e76f09b6c
 https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.2.0-h69a702a_1.conda#e39480b9ca41323497b05492a63bc35b
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.6.3-hb9d3cd8_1.conda#2ecf2f1c7e4e21fcfe6423a51a992d84
 https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-14.2.0-hc0a3c3a_1.conda#234a5554c53625688d51062645337328
 https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
-https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.2-hb9d3cd8_0.conda#4d638782050ab6faa27275bed57e9b4e
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.4.0-hb9d3cd8_0.conda#23cc74f77eb99315c0360ec3533147a9
 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
 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/libssh2-1.11.0-h0841786_0.conda#1f5a58e686b13bcfde88b93f547d23fe
+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/libmpdec-4.0.0-h4bc722e_0.conda#aeb98fdeb2e8f25d43ef71fbacbeec80
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.47.2-hee588c1_0.conda#b58da17db24b6e08bcbf8fed2fb8c915
+https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.1-hf672d98_0.conda#be2de152d8073ef1c01b7728475f2fe7
 https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.2.0-h4852527_1.conda#8371ac6457591af2cf6159439c1fd051
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
 https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-he02047a_1.conda#70caf8bb6cf39a0b6b7efc885f51c0fe
-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/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc
 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/libnghttp2-1.64.0-h161d5f1_0.conda#19e57602824042dfd0446292ef90488b
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4
 https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45
 https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.3-h659f571_0.conda#3f43953b7d3fb3aaa1d0d0723d91e368
-https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.10.1-hbbe4b11_0.conda#6e801c50a40301f6978c53976917b277
-https://conda.anaconda.org/bioconda/linux-64/htslib-1.21-h5efdd21_0.tar.bz2#06b995dc2244c024b45bbb3e53ae2f27
+https://conda.anaconda.org/conda-forge/linux-64/python-3.13.1-ha99a958_102_cp313.conda#6e7535f1d1faf524e9210d2689b3149b
+https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.11.1-h332b0f4_0.conda#2b3e0081006dc21e8bf53a91c83a055c
+https://conda.anaconda.org/conda-forge/noarch/pip-24.3.1-pyh145f28c_2.conda#76601b0ccfe1fe13a21a5f8813cb38de
+https://conda.anaconda.org/bioconda/noarch/snakemake-wrapper-utils-0.6.2-pyhdfd78af_0.tar.bz2#fd8759bbd04116eace828c4fab906096
+https://conda.anaconda.org/bioconda/linux-64/htslib-1.21-h566b1c6_1.tar.bz2#944598fba531a668e8fafea92ca39bb4

bio/seqkit/environment.yaml

@@ -5,3 +5,4 @@ channels:
 dependencies:
   - seqkit =2.9.0
   - htslib =1.21
+  - snakemake-wrapper-utils =0.6.2

bio/seqkit/test/Snakefile

@@ -190,3 +190,22 @@ rule seqkit_concat:
     threads: 2
     wrapper:
         "master/bio/seqkit"
+
+
+rule seqkit_split2_part:
+    input:
+        fasta="data/{sample}.fa",
+    output:
+        fasta=[
+            "out/split2/part/{sample}.1-of-2.fas",
+            "out/split2/part/{sample}.2-of-2.fas",
+        ],
+    log:
+        "logs/split/part/{sample}.log",
+    params:
+        command="split2",
+        extra="--by-part 2",
+        out_bgzip=True,
+    threads: 2
+    wrapper:
+        "master/bio/seqkit"

bio/seqkit/wrapper.py

@@ -2,19 +2,35 @@
 __copyright__ = "Copyright 2023, Filipe G. Vieira"
 __license__ = "MIT"
 
-from snakemake.shell import shell
+import tempfile
 from pathlib import Path
+from snakemake.shell import shell
+from snakemake_wrapper_utils.snakemake import is_arg
 
 
 extra = snakemake.params.get("extra", "")
 log = snakemake.log_fmt_shell(stdout=False, stderr=True)
 
-# subcommands concat and common use multiple input files
+
+# Subcommands with multiple input files
 if snakemake.params.command in ["concat", "common", "stats"]:
     input = " ".join(snakemake.input)
+# Subcommands with a single input file (if more than one provided, concat'em all)
+elif snakemake.params.command in [
+    "stats",
+    "sum",
+    "rmdup",
+    "split",
+    "split2",
+    "sample",
+    "sort",
+]:
+    input = "<(cat " + " ".join(snakemake.input) + ")"
 else:
     input = snakemake.input[0]
 
+
+# Extra input
 extra_input = " ".join(
     [
         (
@@ -26,6 +42,8 @@
     ][1:]
 )
 
+
+# Extra output
 extra_output = " ".join(
     [
         (
@@ -38,15 +56,32 @@
 )
 
 
-if snakemake.params.get("out_bgzip"):
-    assert Path(snakemake.output[0]).suffix in [
-        ".gz",
-        ".bgz",
-        ".bgzip",
-    ], "invalid output file extension"
-    input = input + f" | bgzip --threads {snakemake.threads} > {snakemake.output[0]}"
+if snakemake.params.command in ["split", "split2"]:
+    # Check type of splitting
+    if is_arg("-i", extra) or is_arg("--by-id", extra):
+        split_by = "id"
+    elif is_arg("-p", extra) or is_arg("--by-part", extra):
+        split_by = "part"
+    elif is_arg("-r", extra) or is_arg("--by-region", extra):
+        split_by = "region"
+    elif is_arg("-s", extra) or is_arg("--by-size", extra):
+        split_by = "size"
+    elif is_arg("-l", extra) or is_arg("--by-length", extra):
+        split_by = "length"
+
+    out_dir = Path(snakemake.output[0]).parent
+    output = f"--out-dir {out_dir} --by-{split_by}-prefix output_part. --extension .fas"
 else:
-    input = f"--out-file {snakemake.output[0]} " + input
+    if snakemake.params.get("out_bgzip"):
+        assert Path(snakemake.output[0]).suffix in [
+            ".gz",
+            ".bgz",
+            ".bgzip",
+        ], "invalid output file extension"
+        output = f"| bgzip --threads {snakemake.threads} > {snakemake.output[0]}"
+    else:
+        output = f"--out-file {snakemake.output[0]}"
+
 
 shell(
     "(seqkit {snakemake.params.command}"
@@ -55,5 +90,12 @@
     " {extra_output}"
     " {extra}"
     " {input}"
+    " {output}"
     ") {log}"
 )
+
+
+# Rename output files
+if snakemake.params.command in ["split", "split2"]:
+    for idx, output_file in enumerate(snakemake.output, start=1):
+        shell("mv {out_dir}/output_part.{idx:03d}.fas {output_file}")

test_wrappers.py

@@ -461,6 +461,20 @@ def test_seqkit_concat(run):
         ],
     )
 
+def test_seqkit_split2_part(run):
+    run(
+        "bio/seqkit",
+        [
+            "snakemake",
+            "--cores",
+            "2",
+            "--use-conda",
+            "-F",
+            "out/split2/part/a.1-of-2.fas",
+            "out/split2/part/a.2-of-2.fas",
+        ],
+    )
+
 
 def test_sickle_pe(run):
     run(