feat: All ngsderive subcommands (#2732)

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This PR adds all [ngsderive](https://github.com/stjudecloud/ngsderive)
subcommands in a single wrapper, just like XSV and SeqKit.

### 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),
* the `environment.yaml` pinning has been updated by running
`snakedeploy pin-conda-envs environment.yaml` on a linux machine,
* 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: tdayris <[email protected]>
Co-authored-by: tdayris <[email protected]>
Co-authored-by: Johannes Köster <[email protected]>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Co-authored-by: Felix Mölder <[email protected]>
Co-authored-by: Christopher Schröder <[email protected]>
Co-authored-by: Filipe G. Vieira <[email protected]>

Author: 9 people

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

@@ -0,0 +1,113 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
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bio/ngsderive/environment.yaml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - ngsderive=3.3.2

bio/ngsderive/meta.yaml

@@ -0,0 +1,16 @@
+name: ngsderive
+description: Backwards computing information from next-generation sequencing data and annotating splice junctions
+url: "https://github.com/stjudecloud/ngsderive"
+authors:
+  - "Thibault Dayris"
+input:
+  - ngs: "Path to BAM/SAM/Fastq file. SAM/BAM files should be indexed."
+  - gene_model: "Path to sorted GTF/GFF file. Should be tabix indexed."
+output:
+  - tsv: Path to output file
+  - junctions: Optional path to junction directory, or list of paths to junction files with a common prefix
+params:
+  - subcommand: Name of the `ngsderive` subcommand
+  - extra: Optional parameters, besides `-o`, `-g`
+notes: |
+  GTF/GFF will be automatically sorted and tabix-indexed by `ngsderive` if needed.

bio/ngsderive/test/A.rg.bam

@@ -0,0 +1,101 @@
+rule test_ngsderive_endedness:
+    input:
+        ngs="A.rg.bam",
+    output:
+        tsv="A.endedness.tsv",
+    log:
+        "ngsderive/endedness.log",
+    params:
+        command="endedness",
+        extra="-n 2 --lenient",
+    wrapper:
+        "master/bio/ngsderive"
+
+
+rule test_ngsderive_junction_annotation:
+    input:
+        ngs="A.rg.bam",
+        gene_model="annotation.sorted.gtf.gz",
+    output:
+        tsv="A.junctions.tsv",
+        junction_dir=directory("junctions"),
+    log:
+        "ngsderive/junctions.log",
+    params:
+        command="junction-annotation",
+        extra="-i 2 -c",
+    wrapper:
+        "master/bio/ngsderive"
+
+
+rule test_ngsderive_junction_annotation_list:
+    input:
+        ngs="A.rg.bam",
+        gene_model="annotation.sorted.gtf.gz",
+    output:
+        tsv="A.junctions_list.tsv",
+        junction_dir=["junctions/A.rg.bam.junctions.tsv"],
+    log:
+        "ngsderive/junctions.log",
+    params:
+        command="junction-annotation",
+        extra="-i 2 -c",
+    wrapper:
+        "master/bio/ngsderive"        
+
+
+rule test_ngsderive_strandeness:
+    input:
+        ngs="A.rg.bam",
+        gene_model="annotation.sorted.gtf.gz",
+    output:
+        tsv="A.strandedness.tsv",
+    log:
+        "ngsderive/strand.log",
+    params:
+        command="strandedness",
+        extra="--verbose -m 2 -n 1",
+    wrapper:
+        "master/bio/ngsderive"
+
+
+rule test_ngsderive_encoding:
+    input:
+        ngs="A.rg.bam",
+    output:
+        tsv="A.encoding.tsv",
+    log:
+        "ngsderive/encoding.log",
+    params:
+        command="encoding",
+        extra="-n 2",
+    wrapper:
+        "master/bio/ngsderive"
+
+
+rule test_ngsderive_instrument:
+    input:
+        ngs="A.rg.bam",
+    output:
+        tsv="A.instrument.tsv",
+    log:
+        "ngsderive/instrument.log",
+    params:
+        command="instrument",
+        extra="-n 2 -v",
+    wrapper:
+        "master/bio/ngsderive"
+
+
+rule test_ngsderive_readlen:
+    input:
+        ngs="A.rg.bam",
+    output:
+        tsv="A.readlen.tsv",
+    log:
+        "ngsderive/readlen.log",
+    params:
+        command="readlen",
+        extra="-c 0.1 -n 2",
+    wrapper:
+        "master/bio/ngsderive"

bio/ngsderive/test/A.rg.bam.bai

@@ -0,0 +1,40 @@
+# coding: utf-8
+
+__author__ = "Thibault Dayris"
+__mail__ = "[email protected]"
+__copyright__ = "Copyright 2024, Thibault Dayris"
+__license__ = "MIT"
+
+from os.path import commonprefix, dirname
+from snakemake import shell
+from warnings import warn
+
+extra = snakemake.params.get("extra", "")
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+
+gene_model = snakemake.input.get("gene_model", "")
+if gene_model:
+    gene_model = f"--gene-model {gene_model}"
+
+
+junction_dir = snakemake.output.get("junction_dir", "")
+if isinstance(junction_dir, list):
+    junction_dir = commonprefix([dirname(fp) for fp in junction_dir])
+    if not junction_dir:
+        warn(
+            "No common prefix was found within the list of "
+            "files given as `junction_files_dir`. Falling "
+            "back to default ngsderive value"
+        )
+
+if junction_dir:
+    junction_dir = f"--junction-files-dir {junction_dir}"
+
+
+shell(
+    "ngsderive {snakemake.params.command} "
+    "{extra} {gene_model} {junction_dir} "
+    "{snakemake.input.ngs} "
+    "--outfile {snakemake.output.tsv} "
+    "{log} "
+)

bio/ngsderive/test/Snakefile

@@ -3658,6 +3658,45 @@ def test_nanosimh():
     )
 
 
+@skip_if_not_modified
+def test_ngsderive():
+    run(
+        "bio/ngsderive",
+        ["snakemake", "--cores", "1", "--use-conda", "-F", "A.readlen.tsv"],
+    )
+    run(
+        "bio/ngsderive",
+        ["snakemake", "--cores", "1", "--use-conda", "-F", "A.instrument.tsv"],
+    )
+    run(
+        "bio/ngsderive",
+        ["snakemake", "--cores", "1", "--use-conda", "-F", "A.strandedness.tsv"],
+    )
+    run(
+        "bio/ngsderive",
+        ["snakemake", "--cores", "1", "--use-conda", "-F", "A.encoding.tsv"],
+    )
+    run(
+        "bio/ngsderive",
+        ["snakemake", "--cores", "1", "--use-conda", "-F", "A.junctions.tsv"],
+    )
+    run(
+        "bio/ngsderive",
+        [
+            "snakemake",
+            "--cores",
+            "1",
+            "--use-conda",
+            "-F",
+            "junctions/A.rg.bam.junctions.tsv",
+        ],
+    )
+    run(
+        "bio/ngsderive",
+        ["snakemake", "--cores", "1", "--use-conda", "-F", "A.endedness.tsv"],
+    )
+
+
 @skip_if_not_modified
 def test_ngs_disambiguate():
     run(