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feat: Add support for regions file and arbitrary FAI/GZI paths (snake…
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…make#2936)

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### 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: Christian Meesters <[email protected]>
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2 people authored and Vito Zanotelli committed Jun 22, 2024
1 parent 2b45d76 commit 5243881
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Showing 8 changed files with 113 additions and 8 deletions.
12 changes: 9 additions & 3 deletions bio/samtools/faidx/meta.yaml
Original file line number Diff line number Diff line change
@@ -1,12 +1,18 @@
name: samtools faidx
description: index reference sequence in FASTA format from reference sequence.
url: http://www.htslib.org/doc/samtools-faidx.html
authors:
- Michael Chambers
- Filipe G. Vieira
input:
- reference sequence file (.fa)
- regions: file with regions
- fai: index for reference file (optional)
- gzi: index for BGZip'ed reference file (optional)
output:
- indexed reference sequence file (.fai)
notes: |
* The `extra` param allows for additional program arguments (not `-o`).
* For more information see, http://www.htslib.org/doc/samtools-faidx.html
- fai: index for reference file (optional)
- gzi: index for BGZip'ed reference file (optional)
params:
- region: region to extract from input file (optional)
- extra: additional program arguments (not `-o`).
64 changes: 61 additions & 3 deletions bio/samtools/faidx/test/Snakefile
Original file line number Diff line number Diff line change
@@ -1,11 +1,69 @@
rule samtools_index:
rule samtools_faidx:
input:
"{sample}.fa",
output:
"{sample}.fa.fai",
"out/{sample}.fa.fai",
log:
"{sample}.log",
params:
extra="", # optional params string
extra="",
wrapper:
"master/bio/samtools/faidx"


rule samtools_faidx_named:
input:
"{sample}.fa",
output:
fai="out/{sample}.named.fa.fai",
log:
"{sample}.named.log",
params:
extra="",
wrapper:
"master/bio/samtools/faidx"


rule samtools_faidx_bgzip:
input:
"{sample}.fa.bgz",
output:
fai="out/{sample}.fas.bgz.fai",
gzi="out/{sample}.fas.bgz.gzi",
log:
"{sample}.bzgip.log",
params:
extra="",
wrapper:
"master/bio/samtools/faidx"


rule samtools_faidx_region:
input:
"{sample}.fa",
fai="idx/{sample}.fa.fai",
output:
"out/{sample}.fas",
log:
"{sample}.region.log",
params:
region="ref",
extra="--length 5",
wrapper:
"master/bio/samtools/faidx"


rule samtools_faidx_bgzip_region:
input:
"{sample}.fa.bgz",
fai="idx/{sample}.fa.bgz.fai",
gzi="idx/{sample}.fa.bgz.gzi",
output:
"out/{sample}.bgz.fas",
log:
"{sample}.bgzip_region.log",
params:
region="ref",
extra="--length 5",
wrapper:
"master/bio/samtools/faidx"
Binary file added bio/samtools/faidx/test/genome.fa.bgz
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2 changes: 2 additions & 0 deletions bio/samtools/faidx/test/idx/genome.fa.bgz.fai
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
ref 45 5 45 46
ref2 40 57 40 41
Binary file added bio/samtools/faidx/test/idx/genome.fa.bgz.gzi
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2 changes: 2 additions & 0 deletions bio/samtools/faidx/test/idx/genome.fa.fai
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
ref 45 5 45 46
ref2 40 57 40 41
26 changes: 25 additions & 1 deletion bio/samtools/faidx/wrapper.py
Original file line number Diff line number Diff line change
Expand Up @@ -13,4 +13,28 @@
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)

shell("samtools faidx {samtools_opts} {extra} {snakemake.input[0]} {log}")

# Get regions (if present)
regions = snakemake.input.get("regions", "")
if regions:
regions = f"--regions-file {regions}"

region = snakemake.params.get("region", "")

# Get FAI and GZI files
if region or regions:
fai = snakemake.input.get("fai", "")
gzi = snakemake.input.get("gzi", "")
else:
fai = snakemake.output.get("fai", "")
gzi = snakemake.output.get("gzi", "")

if fai:
fai = f"--fai-idx {fai}"
if gzi:
gzi = f"--gzi-idx {gzi}"


shell(
"samtools faidx {fai} {gzi} {regions} {samtools_opts} {extra} {snakemake.input[0]} {region:q} {log}"
)
15 changes: 14 additions & 1 deletion test.py
Original file line number Diff line number Diff line change
Expand Up @@ -1453,6 +1453,7 @@ def test_goleft_indexcov():
["snakemake", "--cores", "1", "--use-conda", "-Fp"],
)


@skip_if_not_modified
def test_gridss_call():
run(
Expand Down Expand Up @@ -4171,7 +4172,19 @@ def test_samtools_fastq_separate():
def test_samtools_faidx():
run(
"bio/samtools/faidx",
["snakemake", "--cores", "1", "genome.fa.fai", "--use-conda", "-F"],
[
"snakemake",
"--cores",
"1",
"out/genome.fa.fai",
"out/genome.named.fa.fai",
"out/genome.fas.bgz.fai",
"out/genome.fas.bgz.gzi",
"out/genome.fas",
"out/genome.bgz.fas",
"--use-conda",
"-F",
],
)


Expand Down

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