feat: sortmerna wrapper (#2320)

### Description

Add  [sortmerna wrapper](https://sortmerna.readthedocs.io/en/latest/). 


### QC

* [x] I confirm that:

For all wrappers added by this PR, 

* there is a test case which covers any introduced changes,
* `input:` and `output:` file paths in the resulting rule can be changed
arbitrarily,
* either the wrapper can only use a single core, or the example rule
contains a `threads: x` statement with `x` being a reasonable default,
* rule names in the test case are in
[snake_case](https://en.wikipedia.org/wiki/Snake_case) and somehow tell
what the rule is about or match the tools purpose or name (e.g.,
`map_reads` for a step that maps reads),
* all `environment.yaml` specifications follow [the respective best
practices](https://stackoverflow.com/a/64594513/2352071),
* wherever possible, command line arguments are inferred and set
automatically (e.g. based on file extensions in `input:` or `output:`),
* all fields of the example rules in the `Snakefile`s and their entries
are explained via comments (`input:`/`output:`/`params:` etc.),
* `stderr` and/or `stdout` are logged correctly (`log:`), depending on
the wrapped tool,
* temporary files are either written to a unique hidden folder in the
working directory, or (better) stored where the Python function
`tempfile.gettempdir()` points to (see
[here](https://docs.python.org/3/library/tempfile.html#tempfile.gettempdir);
this also means that using any Python `tempfile` default behavior
works),
* the `meta.yaml` contains a link to the documentation of the respective
tool or command,
* `Snakefile`s pass the linting (`snakemake --lint`),
* `Snakefile`s are formatted with
[snakefmt](https://github.com/snakemake/snakefmt),
* Python wrapper scripts are formatted with
[black](https://black.readthedocs.io).
* Conda environments use a minimal amount of channels, in recommended
ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as
conda-forge should have highest priority and defaults channels are
usually not needed because most packages are in conda-forge nowadays).

---------

Co-authored-by: Filipe G. Vieira <1151762+fgvieira@users.noreply.github.com>

bio/sortmerna/environment.yaml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - sortmerna =4.3.6

bio/sortmerna/meta.yaml

@@ -0,0 +1,15 @@
+name: SortMeRNA
+description: SortMeRNA is a local sequence alignment tool for filtering, mapping and OTU clustering.
+url: https://sortmerna.readthedocs.io/
+authors:
+  - Curro Campuzano Jiménez
+input:
+  - Reference FASTA files (one or more)
+  - Query FASTA file (single or paired-end)
+output:
+  - Aligned reads
+  - Unaligned reads (other)
+params:
+  - extra: aditional program arguments
+notes: |
+  * The kvdb (key value database) will be created in a temporary directory. Then, you don't have to prune it before each run. If you want to re-use the index, you can specify the idx-dir parameter.

bio/sortmerna/test/Snakefile

@@ -0,0 +1,36 @@
+rule sortmerna_pe:
+    input:
+        ref=["database1.fa", "database2.fa"],
+        reads=["reads_1.fq.gz", "reads_2.fq.gz"],
+    output:
+        aligned=["aligned_1.fastq.gz", "aligned_2.fastq.gz"],
+        other=["unpaired_1.fastq.gz", "unpaired_2.fastq.gz"],
+        stats="sortmerna_pe_stats.log",
+    params:
+        extra="--idx-dir idx --paired_in --out2",
+    threads: 16
+    resources:
+        mem_mb=3072,  # amount of memory for building the index
+    log:
+        "logs/sortmerna/reads_pe.log",
+    wrapper:
+        "master/bio/sortmerna"
+
+
+rule sortmerna_se:
+    input:
+        ref=["database1.fa", "database2.fa"],
+        reads="reads.fq",
+    output:
+        aligned="aligned.fastq",
+        other="unpaired.fastq",
+        stats="sortmerna_se_stats.log",
+    params:
+        extra="--idx-dir idx",
+    threads: 16
+    resources:
+        mem_mb=3072,  # amount of memory for building the index
+    log:
+        "logs/sortmerna/reads_se.log",
+    wrapper:
+        "master/bio/sortmerna"

bio/sortmerna/test/database1.fa

@@ -0,0 +1,24 @@
+>AY846379.1.1791 Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Chlorophyceae;Sphaeropleales;Monoraphidium;Monoraphidium sp. Itas 9/21 14-6w
+CCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACUGCUUAUACUGU
+GAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUAUUUGAUGGUACCUCUACACGGAUAACCGUAGUAAUUCUAGAGC
+UAAUACGUGCGUAAAUCCCGACUUCUGGAAGGGACGUAUUUAUUAGAUAAAAGGCCGACCGAGCUUUGCUCGACCCGCGG
+UGAAUCAUGAUAACUUCACGAAUCGCAUAGCCUUGUGCUGGCGAUGUUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAU
+GGUAGGAUAGAGGCCUACCAUGGUGGUAACGGGUGACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGG
+CUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGAUACGGGGAGGUAGUGACAAUAAAUAACAAUGC
+CGGGCAUUUCAUGUCUGGCAAUUGGAAUGAGUACAAUCUAAAUCCCUUAACGAGGAUCAAUUGGAGGGCAAGUCUGGUGC
+CAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCGGGUG
+GGUUCCAGCGGUCCGCCUAUGGUGAGUACUGCUGUGGCCCUCCUUUUUGUCGGGGACGGGCUCCUGGGCUUCAUUGUCCG
+GGACUCGGAGUCGACGAUGAUACUUUGAGUAAAUUAGAGUGUUCAAAGCAAGCCUACGCUCUGAAUACUUUAGCAUGGAA
+UAUCGCGAUAGGACUCUGGCCUAUCUCGUUGGUCUGUAGGACCGGAGUAAUGAUUAAGAGGGACAGUCGGGGGCAUUCGU
+AUUUCAUUGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUA
+AUCAAGAACGAAAGUUGGGGGCUCGAAGACGAUUAGAUACCGUCGUAGUCUCAACCAUAAACGAUGCCGACUAGGGAUUG
+GAGGAUGUUCUUUUGAUGACUUCUCCAGCACCUUAUGAGAAAUCAAAGUUUUUGGGUUCCGGGGGGAGUAUGGUCGCAAG
+GCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACU
+UACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUU
+AGUUGGUGGGUUGCCUUGUCAGGUUGAUUCCGGUAACGAACGAGACCUCAGCCUGCUAAAUAUGUCACAUUCGCUUUUUG
+CGGAUGGCCGACUUCUUAGAGGGACUAUUGGCGUUUAGUCAAUGGAAGUAUGAGGCAAUAACAGGUCUGUGAUGCCCUUA
+GAUGUUCUGGGCCGCACGCGCGCUACACUGACGCAUUCAGCAAGCCUAUCCUUGACCGAGAGGUCUGGGUAAUCUUUGAA
+ACUGCGUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAGUCUUCAACGAGGAAUGCCUAGUAAGCGCAAGUCAUCAGCUUG
+CGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGGGUGUGCUGGUGAAGUGUUCGGAUUGG
+CAGAGCGGGUGGCAACACUUGCUUUUGCCGAGAAGUUCAUUAAACCCUCCCACCUAGAGGAAGGAGAAGUCGUAACAAGG
+UUUCCGUAGGUGAACCUGCAGAAG

bio/sortmerna/test/database2.fa

@@ -0,0 +1,16 @@
+>AB001445.1.1538 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Pseudomonas amygdali pv. morsprunorum
+AGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAGUCGAGCGGCAGCACGGGUACUUGUAC
+CUGGUGGCGAGCGGCGGACGGGUGAGUAAUGCCUAGGAAUCUGCCUGGUAGUGGGGGAUAACGCUCGGAAACGGACGCUA
+AUACCGCAUACGUCCUACGGGAGAAAGCAGGGGACCUUCGGGCCUUGCGCUAUCAGAUGAGCCUAGGUCGGAUUAGCUAG
+UUGGUGAGGUAAUGGCUCACCAAGGCGACGAUCCGUAACUGGUCUGAGAGGAUGAUCAGUCACACUGGAACUGAGACACG
+GUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGCGAAAGCCUGAUCCAGCCAUGCCGCGUGUGUGA
+AGAAGGUCUUCGGAUUGUAAAGCACUUUAAGUUGGGAGGAAGGGCAGUUACCUAAUACGUAUCUGUUUUGACGUUACCGA
+CAGAAUAAGCACCGGCUAACUCUGUGCCAGCAGCCGCGGUAAUACAGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGU
+AAAGCGCGCGUAGGUGGUUUGUUAAGUUGAAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCCAAAACUGGCAAGC
+UAGAGUAUGGUAGAGGGUGGUGGAAUUUCCUGUGUAGCGGUGAAAUGCGUAGAUAUAGGAAGGAACACCAGUGGCGAAGG
+CGACCACCUGGACUGAUACUGACACUGAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCC
+GUAAACGAUGUCAACUAGCCGUUGGGAGCCUUGAGCUCUUAGUGGCGCAGCUAACGCAUUAAGUUGACCGCCUGGGGAGU
+ACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACG
+CGAAGAACCUUACCAGGCCUUGACAUCCAAUGAAUCCUUUAGAGAUAGAGGAGUGCCUUCGGGAGCAUUGAGACAGGUGC
+UGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGUAACGAGCGCAACCCUUGUCCUUAGUUACCAG
+CACGUCAUGGUGGGCACUCUAAGGAGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCC

bio/sortmerna/test/reads.fq

@@ -0,0 +1,4 @@
+@AY846379.1.1791 Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Chlorophyceae;Sphaeropleales;Monoraphidium;Monoraphidium sp. Itas 9/21 14-6w
+CCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACUGCUUAUACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUAUUUGAUGGUACCUCUACACGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCGUAAAUCCCGACUUCUGGAAGGGACGUAUUUAUUAGAUAAAAGGCCGACCGAGCUUUGCUCGACCCGCGGUGAAUCAUGAUAACUUCACGAAUCGCAUAGCCUUGUGCUGGCGAUGUUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGAGGCCUACCAUGGUGGUAACGGGUGACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGAUACGGGGAGGUAGUGACAAUAAAUAACAAUGCCGGGCAUUUCAUGUCUGGCAAUUGGAAUGAGUACAAUCUAAAUCCCUUAACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCGGGUGGGUUCCAGCGGUCCGCCUAUGGUGAGUACUGCUGUGGCCCUCCUUUUUGUCGGGGACGGGCUCCUGGGCUUCAUUGUCCGGGACUCGGAGUCGACGAUGAUACUUUGAGUAAAUUAGAGUGUUCAAAGCAAGCCUACGCUCUGAAUACUUUAGCAUGGAAUAUCGCGAUAGGACUCUGGCCUAUCUCGUUGGUCUGUAGGACCGGAGUAAUGAUUAAGAGGGACAGUCGGGGGCAUUCGUAUUUCAUUGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUGGGGGCUCGAAGACGAUUAGAUACCGUCGUAGUCUCAACCAUAAACGAUGCCGACUAGGGAUUGGAGGAUGUUCUUUUGAUGACUUCUCCAGCACCUUAUGAGAAAUCAAAGUUUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGGUUGCCUUGUCAGGUUGAUUCCGGUAACGAACGAGACCUCAGCCUGCUAAAUAUGUCACAUUCGCUUUUUGCGGAUGGCCGACUUCUUAGAGGGACUAUUGGCGUUUAGUCAAUGGAAGUAUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGACGCAUUCAGCAAGCCUAUCCUUGACCGAGAGGUCUGGGUAAUCUUUGAAACUGCGUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAGUCUUCAACGAGGAAUGCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGGGUGUGCUGGUGAAGUGUUCGGAUUGGCAGAGCGGGUGGCAACACUUGCUUUUGCCGAGAAGUUCAUUAAACCCUCCCACCUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAG
++
+########################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################

bio/sortmerna/wrapper.py

@@ -0,0 +1,79 @@
+__author__ = "Curro Campuzano Jiménez"
+__copyright__ = "Copyright 2023, Curro Campuzano Jiménez"
+__email__ = "campuzanocurro@gmail.com"
+__license__ = "MIT"
+
+
+import tempfile
+from snakemake.shell import shell
+
+extra = snakemake.params.get("extra", "")
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+
+ref = snakemake.input.ref
+reads = snakemake.input.reads
+aligned = snakemake.output.get("aligned", None)
+other = snakemake.output.get("other", None)
+stats = snakemake.output.get("stats", None)
+mem_mb = snakemake.resources.get("mem_mb", 3072)  # Default value
+
+if isinstance(ref, list):
+    ref = " --ref ".join(ref)
+
+if aligned:
+    if isinstance(aligned, list):
+        assert (
+            len(aligned) == 2
+        ), "if paired input, aligned must be a list of two files, if any"
+        assert isinstance(
+            reads, list
+        ), "if paired input, reads must be a list of two files"
+
+if other:
+    if isinstance(other, list):
+        assert (
+            len(other) == 2
+        ), "if paired input, other must be a list of two files, if any"
+        assert isinstance(
+            reads, list
+        ), "if paired input, reads must be a list of two files"
+    extra = f"--fastx {extra}"
+
+is_paired = False
+if isinstance(reads, list):
+    assert len(reads) == 2, "if paired input, reads must be a list of two files"
+    reads = " --reads ".join(reads)
+    is_paired = True
+
+if stats:
+    assert isinstance(stats, str), "stats must be a single file"
+
+
+with tempfile.TemporaryDirectory() as temp_workdir:
+    shell(
+        " sortmerna --ref {ref}"
+        " --reads {reads}"
+        " --workdir {temp_workdir}"
+        " --threads {snakemake.threads}"
+        " -m {mem_mb}"
+        " --aligned {temp_workdir}/aligned_reads"
+        " --other {temp_workdir}/other_reads"
+        " {extra}"
+        " {log}"
+    )
+
+    if is_paired:
+        if aligned:
+            # Handle the case were no alignment
+            shell("mv {temp_workdir}/aligned_reads_fwd.* {aligned[0]}")
+            shell("mv {temp_workdir}/aligned_reads_rev.* {aligned[1]}")
+        if other:
+            shell("mv {temp_workdir}/other_reads_fwd.* {other[0]}")
+            shell("mv {temp_workdir}/other_reads_rev.* {other[1]}")
+    else:
+        if aligned:
+            shell("mv {temp_workdir}/aligned_reads.f* {aligned}")
+        if other:
+            shell("mv {temp_workdir}/other_reads.f* {other}")
+    if stats:
+        shell("mv {temp_workdir}/aligned_reads.log {stats}")