feat: added wrapper for tadpole (#1152)

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### Description

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Add wrapper for tadpole (from bbtools).

### QC
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* [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).

bio/bbtools/bbduk/environment.yaml

@@ -4,4 +4,5 @@ channels:
   - nodefaults
 dependencies:
   - bbmap =39.01
+  - python =3.11.0
   - snakemake-wrapper-utils =0.5.0

bio/bbtools/bbduk/meta.yaml

@@ -5,15 +5,14 @@ description: |
 authors:
   - Filipe G. Vieira
 input:
-  - sample: list of paths. Raw fastq file with R1 reads, raw fastq file with R2 reads (PE only, optional)
+  - sample: list of raw R1 and (if PE) R2 fastq file(s)
 output:
-  - trimmed: trimmed fastq file with R1 reads, trimmed fastq file with R2 reads (PE only, optional)
+  - trimmed: list of trimmed R1 and (if PE) R2 fastq file(s)
   - singleton: fastq file with singleton reads (optional)
   - discarded: fastq file with discarded reads (optional)
-  - stats: stats file (optonal)
+  - stats: stats file (optional)
 params:
-  - extra: Optional parameters
+  - extra: additional program arguments
   - adapters: Literal adapters sequences
 notes: |
   * The `java_opts` param allows for additional arguments to be passed to the java compiler, e.g. "-XX:ParallelGCThreads=10" (not for `-XmX` or `-Djava.io.tmpdir`, since they are handled automatically).
-  * The `extra` param allows for additional program arguments.

bio/bbtools/bbduk/test/Snakefile

@@ -26,7 +26,7 @@ rule bbduk_pe:
         discarded="trimmed/pe/{sample}.discarded.fastq",
         stats="trimmed/pe/{sample}.stats.txt",
     log:
-        "logs/fastp/pe/{sample}.log"
+        "logs/bbduk/pe/{sample}.log"
     params:
         extra = lambda w, input: "ref={},adapters,artifacts ktrim=r k=23 mink=11 hdist=1 tpe tbo trimpolygright=10 minlen=25 maxns=30 entropy=0.5 entropywindow=50 entropyk=5".format(input.adapters),
     threads: 7

bio/bbtools/tadpole/environment.yaml

@@ -0,0 +1,8 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - bbmap =39.01
+  - python =3.11.0
+  - snakemake-wrapper-utils =0.5.2

bio/bbtools/tadpole/meta.yaml

@@ -0,0 +1,17 @@
+name: Tadpole
+url: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/tadpole-guide/
+description: |
+  Run Tadpole.
+authors:
+  - Filipe G. Vieira
+input:
+  - sample: list of R1 and (if PE) R2 fastq file(s)
+  - extra: kmer data, but not for error-correction or extension (optional)
+output:
+  - trimmed: trimmed fastq file with R1 reads, trimmed fastq file with R2 reads (PE only, optional)
+  - discarded: fastq file with discarded reads (optional)
+params:
+  - mode: Run mode (one of `contig`, `extend`, `correct`, `insert`, or `discard`; mandatory)
+  - extra: additional program arguments
+notes: |
+  * The `java_opts` param allows for additional arguments to be passed to the java compiler, e.g. `-XX:ParallelGCThreads=10` (not for `-XmX` or `-Djava.io.tmpdir`, since they are handled automatically).

bio/bbtools/tadpole/test/Snakefile

@@ -0,0 +1,70 @@
+rule tadpole_correct_se:
+    input:
+        sample=["reads/se/{sample}.fastq"],
+    output:
+        out="out/correct_se/{sample}.fastq.gz",
+        discarded="out/correct_se/{sample}.discarded.fastq.gz",
+    log:
+        "logs/correct_se/{sample}.log",
+    params:
+        mode="correct",
+        extra="",
+    threads: 2
+    resources:
+        mem_mb=1024,
+    wrapper:
+        "master/bio/bbtools/tadpole"
+
+
+rule tadpole_correct_pe:
+    input:
+        sample=["reads/pe/{sample}.1.fastq", "reads/pe/{sample}.2.fastq"],
+    output:
+        out=["out/correct_pe/{sample}.1.fastq", "out/correct/pe/{sample}.2.fastq"],
+        discarded="out/correct_pe/{sample}.discarded.fastq",
+    log:
+        "logs/correct_pe/{sample}.log",
+    params:
+        mode="correct",
+        extra="",
+    threads: 2
+    resources:
+        mem_mb=1024,
+    wrapper:
+        "master/bio/bbtools/tadpole"
+
+
+rule tadpole_extend_se:
+    input:
+        sample=["reads/se/{sample}.fastq"],
+    output:
+        out="out/extend_se/{sample}.fastq.gz",
+        discarded="out/extend_se/{sample}.discarded.fastq.gz",
+    log:
+        "logs/extend_se/{sample}.log",
+    params:
+        mode="extend",
+        extra="",
+    threads: 2
+    resources:
+        mem_mb=1024,
+    wrapper:
+        "master/bio/bbtools/tadpole"
+
+
+rule tadpole_extend_pe:
+    input:
+        sample=["reads/pe/{sample}.1.fastq", "reads/pe/{sample}.2.fastq"],
+    output:
+        out=["out/extend_pe/{sample}.1.fastq", "out/extend/pe/{sample}.2.fastq"],
+        discarded="out/extend_pe/{sample}.discarded.fastq",
+    log:
+        "logs/extend_pe/{sample}.log",
+    params:
+        mode="extend",
+        extra="",
+    threads: 2
+    resources:
+        mem_mb=1024,
+    wrapper:
+        "master/bio/bbtools/tadpole"

bio/bbtools/tadpole/test/reads/pe/a.1.fastq

@@ -0,0 +1,4 @@
+@1
+ACGGCAT
++
+!!!!!!!

bio/bbtools/tadpole/test/reads/pe/a.2.fastq

@@ -0,0 +1,4 @@
+@1
+ACGGCAT
++
+!!!!!!!

bio/bbtools/tadpole/test/reads/se/a.fastq

@@ -0,0 +1,4 @@
+@1
+ACGGCAT
++
+!!!!!!!

bio/bbtools/tadpole/wrapper.py

@@ -0,0 +1,49 @@
+__author__ = "Filipe G. Vieira"
+__copyright__ = "Copyright 2023, Filipe G. Vieira"
+__license__ = "MIT"
+
+
+from snakemake.shell import shell
+from snakemake_wrapper_utils.java import get_java_opts
+
+
+java_opts = get_java_opts(snakemake)
+extra = snakemake.params.get("extra", "")
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+
+
+assert snakemake.params.mode in ["contig", "extend", "correct", "insert", "discard"]
+
+
+n = len(snakemake.input.sample)
+assert (
+    n == 1 or n == 2
+), "input->sample must have 1 (single-end) or 2 (paired-end) elements."
+
+if n == 1:
+    reads = "in={}".format(snakemake.input.sample)
+    out = "out={}".format(snakemake.output.out)
+else:
+    reads = "in={} in2={}".format(*snakemake.input.sample)
+    out = "out={} out2={}".format(*snakemake.output.out)
+
+
+extra = snakemake.output.get("extra", "")
+if extra:
+    reads += f" extra={extra}"
+
+
+discarded = snakemake.output.get("discarded", "")
+if discarded:
+    out += f" outd={discarded}"
+
+
+shell(
+    "tadpole.sh {java_opts}"
+    " threads={snakemake.threads}"
+    " mode={snakemake.params.mode}"
+    " {reads}"
+    " {extra}"
+    " {out}"
+    " {log}"
+)

test.py

@@ -140,6 +140,23 @@ def run(wrapper, cmd, check_log=None):
 
 
 
+@skip_if_not_modified
+def test_tadpole():
+    run(
+        "bio/bbtools/tadpole",
+        [
+            "snakemake",
+            "--cores",
+            "2",
+            "--use-conda",
+            "-F",
+            "out/correct_se/a.fastq.gz",
+            "out/correct_pe/a.1.fastq",
+            "out/extend_se/a.fastq.gz",
+            "out/extend_pe/a.1.fastq",
+        ],
+    )
+
 @skip_if_not_modified
 def test_seqkit_stats():
     run(