fix: remove NA string replacement, fixed upstream (snakemake#2940)

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Wrapper previously failed if the optional output `qc_metrics` was not
supplied due to NA replacement code that was not in a conditional. The
code is no longer required since NA strings are now output correctly in
deeptools/deepTools#1002

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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: Filipe G. Vieira <[email protected]>

bio/deeptools/plotfingerprint/test/Snakefile

@@ -2,21 +2,20 @@ rule plot_fingerprint:
     input:
         bam_files=expand("samples/{sample}.bam", sample=["a", "b"]),
         bam_idx=expand("samples/{sample}.bam.bai", sample=["a", "b"]),
-        jsd_sample="samples/b.bam" # optional, requires qc_metrics output
+        jsd_sample="samples/b.bam",  # optional, requires qc_metrics output
     output:
         # Please note that --plotFile and --outRawCounts are exclusively defined via output files.
         # Usable output variables, their extensions and which option they implicitly call are listed here:
         #         https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/deeptools/plotfingerprint.html.
         fingerprint="plot_fingerprint/plot_fingerprint.png",  # required
         # optional output
         counts="plot_fingerprint/raw_counts.tab",
-        qc_metrics="plot_fingerprint/qc_metrics.txt"
+        qc_metrics="plot_fingerprint/qc_metrics.txt",
     log:
-        "logs/deeptools/plot_fingerprint.log"
+        "logs/deeptools/plot_fingerprint.log",
     params:
         # optional parameters
-        "--numberOfSamples 200 "
-    threads:
-        8
+        extra="--numberOfSamples 200",
+    threads: 8
     wrapper:
         "master/bio/deeptools/plotfingerprint"

bio/deeptools/plotfingerprint/wrapper.py

@@ -1,12 +1,14 @@
 __author__ = "Antonie Vietor"
-__copyright__ = "Copyright 2020, Antonie Vietor"
+__copyright__ = "Copyright 2024, Antonie Vietor, Lance Parsons"
 __email__ = "[email protected]"
 __license__ = "MIT"
 
-from snakemake.shell import shell
 import re
 
+from snakemake.shell import shell
+
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+extra = snakemake.params.get("extra", "")
 
 jsd_sample = snakemake.input.get("jsd_sample")
 out_counts = snakemake.output.get("counts")
@@ -30,16 +32,5 @@
     "{optional_output} "
     "--numberOfProcessors {snakemake.threads} "
     "{jsd} "
-    "{snakemake.params}) {log}"
+    "{extra}) {log}"
 )
-# ToDo: remove the 'NA' string replacement when fixed in deepTools, see:
-# https://github.com/deeptools/deepTools/pull/999
-regex_passes = 2
-
-with open(out_metrics, "rt") as f:
-    metrics = f.read()
-    for i in range(regex_passes):
-        metrics = re.sub("\tNA(\t|\n)", "\tnan\\1", metrics)
-
-with open(out_metrics, "wt") as f:
-    f.write(metrics)

bio/deeptools/plotheatmap/test/Snakefile

@@ -14,6 +14,6 @@ rule plot_heatmap:
         "logs/deeptools/heatmap.log"
     params:
         # optional parameters
-        "--plotType=fill "
+        extra="--plotType=fill "
     wrapper:
         "master/bio/deeptools/plotheatmap"

bio/deeptools/plotheatmap/wrapper.py

@@ -6,6 +6,7 @@
 from snakemake.shell import shell
 
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+extra = snakemake.params.get("extra", "")
 
 out_region = snakemake.output.get("regions")
 out_matrix = snakemake.output.get("heatmap_matrix")
@@ -27,5 +28,5 @@
     "-m {snakemake.input[0]} "
     "-o {snakemake.output.heatmap_img} "
     "{optional_output} "
-    "{snakemake.params}) {log}"
+    "{extra}) {log}"
 )

bio/deeptools/plotprofile/test/Snakefile

@@ -15,9 +15,6 @@ rule plot_profile:
         "logs/deeptools/plot_profile.log"
     params:
         # optional parameters
-        "--plotType=fill "
-        "--perGroup "
-        "--colors red yellow blue "
-        "--dpi 150 "
+        extra="--plotType=fill --perGroup --colors red yellow blue --dpi 150"
     wrapper:
         "master/bio/deeptools/plotprofile"

bio/deeptools/plotprofile/wrapper.py

@@ -6,6 +6,7 @@
 from snakemake.shell import shell
 
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+extra = snakemake.params.get("extra", "")
 
 out_region = snakemake.output.get("regions")
 out_data = snakemake.output.get("data")
@@ -25,5 +26,5 @@
     "-m {snakemake.input[0]} "
     "-o {snakemake.output.plot_img} "
     "{optional_output} "
-    "{snakemake.params}) {log}"
+    "{extra}) {log}"
 )