feat: added bamtobed wrapper (#531)

* Added bamtobed wrapper

* Updated version in other wrappers

* improve envs

Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>

bio/bedtools/bamtobed/environment.yaml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - bedtools =2.30

bio/bedtools/bamtobed/meta.yaml

@@ -0,0 +1,12 @@
+name: bamToBed
+description: >
+  Conversion utility that converts sequence alignments in BAM format into BED, BED12, and/or BEDPE records.
+url: https://bedtools.readthedocs.io/en/latest/content/tools/bamtobed.html
+authors:
+  - Filipe G. Vieira
+input:
+  - BAM file
+output:
+  - BED file
+notes: |
+  * The `extra` param allows for additional program arguments.

bio/bedtools/bamtobed/test/Snakefile

@@ -0,0 +1,11 @@
+rule bamtobed:
+    input:
+        "{sample}.bam",
+    output:
+        "{sample}.bed",
+    log:
+        "logs/bamtobed/{sample}.log",
+    params:
+        extra="-bedpe",  # optional parameters
+    wrapper:
+        "master/bio/bedtools/bamtobed"

bio/bedtools/bamtobed/wrapper.py

@@ -0,0 +1,19 @@
+__author__ = "Filipe G. Vieira"
+__copyright__ = "Copyright 2022, Filipe G. Vieira"
+__license__ = "MIT"
+
+
+from snakemake.shell import shell
+
+
+log = snakemake.log_fmt_shell(stdout=False, stderr=True)
+extra = snakemake.params.get("extra", "")
+
+
+shell(
+    "(bamToBed"
+    " {extra}"
+    " -i {snakemake.input[0]}"
+    " > {snakemake.output[0]}"
+    ") {log}"
+)

bio/bedtools/complement/environment.yaml

@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - bedtools =2.29
+  - bedtools =2.30

bio/bedtools/complement/meta.yaml

@@ -1,10 +1,11 @@
-name: bedtools complement
+name: complementBed
 description: >
-  `Bedtools complement <https://bedtools.readthedocs.io/en/latest/content/tools/complement.html>`_ maps all regions of the genome which are not covered by the input.
+  Maps all regions of the genome which are not covered by the input.
+url: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html
 authors:
   - Antonie Vietor
 input:
   - BED/GFF/VCF files
-  - genome file (`genome file format <https://bedtools.readthedocs.io/en/latest/content/general-usage.html#genome-file-format>`_)
+  - genome file
 output:
   - complemented BED/GFF/VCF file

bio/bedtools/coveragebed/environment.yaml

@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - bedtools ==2.29.0
+  - bedtools =2.30

bio/bedtools/coveragebed/meta.yaml

@@ -1,6 +1,6 @@
-name: "coverageBed"
+name: coverageBed
 description:
-  Returns the depth and breadth of coverage of features from B
-  on the intervals in A.
+  Returns the depth and breadth of coverage of features from B on the intervals in A.
+url: https://bedtools.readthedocs.io/en/latest/content/tools/coverage.html
 authors:
   - Patrik Smeds

bio/bedtools/genomecov/environment.yaml

@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - bedtools ==2.29.2
+  - bedtools =2.30

bio/bedtools/genomecov/meta.yaml

@@ -1,8 +1,7 @@
-name: bedtools genomeCoverageBed
+name: genomeCoverageBed
 description: >
-  ``bedtools``'s genomeCoverageBed computes the coverage of a feature file as histograms, per-base reports or BEDGRAPH summaries among a given genome.
-  For usage information about genomeCoverageBed, please see ``bedtools``'s `documentation <https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html>`_.
-  For more information about ``bedtools``, also see the `source code <https://github.com/arq5x/bedtools2>`_.
+  Computes the coverage of a feature file as histograms, per-base reports or BEDGRAPH summaries among a given genome.
+url: https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html
 authors:
   - Antonie Vietor
 input:

bio/bedtools/intersect/environment.yaml

@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - bedtools =2.29.0
+  - bedtools =2.30

bio/bedtools/intersect/meta.yaml

@@ -1,4 +1,5 @@
-name: "bedtools intersect"
+name: intersectBed
 description: Intersect BED/BAM/VCF files with bedtools.
+url: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
 authors:
   - Jan Forster

bio/bedtools/merge/environment.yaml

@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - bedtools =2.29.0
+  - bedtools =2.30

bio/bedtools/merge/meta.yaml

@@ -1,4 +1,5 @@
-name: "bedtools merge"
+name: mergeBed
 description: Merge entries in one or multiple BED/BAM/VCF/GFF files with bedtools.
+url: https://bedtools.readthedocs.io/en/latest/content/tools/merge.html
 authors:
   - Jan Forster

bio/bedtools/slop/environment.yaml

@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - bedtools =2.29.0
+  - bedtools =2.30

bio/bedtools/slop/meta.yaml

@@ -1,4 +1,5 @@
-name: "bedtools slop"
+name: slopBed
 description: Increase the size of each feature in a BED/BAM/VCF by a specified factor.
+url: https://bedtools.readthedocs.io/en/latest/content/tools/slop.html
 authors:
   - Jan Forster

bio/bedtools/sort/environment.yaml

@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - bedtools =2.29
+  - bedtools =2.30

bio/bedtools/sort/meta.yaml

@@ -1,11 +1,12 @@
-name: bedtools sort
+name: sortBed
 description: >
-  Sorts bed, vcf or gff files by chromosome and other criteria, for more information please see `bedtools sort documentation <https://bedtools.readthedocs.io/en/latest/content/tools/sort.html>`_.
+  Sorts bed, vcf or gff files by chromosome and other criteria.
+url: https://bedtools.readthedocs.io/en/latest/content/tools/sort.html
 authors:
   - Antonie Vietor
 input:
   - BED/GFF/VCF files
   - optional a tab separating file that determines the sorting order and contains the chromosome names in the first column
   - optional a fasta index file
 output:
-  - complemented BED/GFF/VCF file
+  - sorted BED/GFF/VCF file

test.py

@@ -1028,6 +1028,14 @@ def test_bcftools_view_uncompressed_bcf():
     )
 
 
+@skip_if_not_modified
+def test_bedtools_bamtobed():
+    run(
+        "bio/bedtools/bamtobed",
+        ["snakemake", "--cores", "1", "a.bed", "--use-conda", "-F"],
+    )
+
+
 @skip_if_not_modified
 def test_bedtools_genomecoveragebed():
     run(