Merge branch 'master' into samtools_faidx

bio/bgzip/meta.yaml

@@ -3,7 +3,12 @@ description: Block compression/decompression utility
 url: https://github.com/samtools/htslib
 authors:
   - William Rowell
+  - Filipe G. Vieira
 input:
   - file to be compressed or decompressed
 output:
-  - compressed or decompressed output
+  - compressed or decompressed output
+params:
+  - extra: additional bgzip parameters
+notes: |
+  * Run mode (compression/decompression) is automatically inferred from the extension of the input file.

bio/bgzip/wrapper.py

@@ -9,9 +9,11 @@
 extra = snakemake.params.get("extra", "")
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)
 
+
+if snakemake.input[0].endswith(".gz"):
+    extra += " --decompress"
+
+
 shell(
-    """
-    (bgzip -c {extra} --threads {snakemake.threads} \
-        {snakemake.input} > {snakemake.output}) {log}
-    """
+    "bgzip --threads {snakemake.threads} {extra} --output {snakemake.output[0]} {snakemake.input[0]} {log}"
 )

bio/gatk/applybqsr/environment.linux-64.pin.txt

@@ -7,37 +7,36 @@ https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca05
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+https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_2.conda#cbbe59391138ea5ad3658c76912e147f
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h55db66e_0.conda#10569984e7db886e4f1abc2b47ad79a1
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406
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-https://conda.anaconda.org/conda-forge/linux-64/openssl-3.2.1-hd590300_0.conda#51a753e64a3027bd7e23a189b1f6e91e
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.0-hd590300_0.conda#c0f3abb4a16477208bbd43a39bd56f18
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@@ -50,43 +49,43 @@ https://conda.anaconda.org/conda-forge/linux-64/xorg-renderproto-0.11.1-h7f98852
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bio/gatk/applybqsr/environment.yaml

@@ -5,4 +5,4 @@ channels:
 dependencies:
   - gatk4 =4.5.0.0
   - snakemake-wrapper-utils =0.6.2
-  - samtools =1.19.2
+  - samtools =1.20