perf: autobump bio/gatk/applybqsrspark/environment.yaml

bio/gatk/applybqsr/test/Snakefile

@@ -7,7 +7,46 @@ rule gatk_applybqsr:
     output:
         bam="recal/{sample}.bam",
     log:
-        "logs/gatk/gatk_applybqsr/{sample}.log",
+        "logs/gatk/applybqsr/{sample}.log",
+    params:
+        extra="",  # optional
+        java_opts="",  # optional
+    resources:
+        mem_mb=1024,
+    wrapper:
+        "master/bio/gatk/applybqsr"
+
+
+rule gatk_applybqsr_cram:
+    input:
+        bam="mapped/{sample}.bam",
+        ref="genome.fasta",
+        dict="genome.dict",
+        recal_table="recal/{sample}.grp",
+    output:
+        bam="recal/{sample}.cram",
+    log:
+        "logs/gatk/applybqsr/{sample}.cram.log",
+    params:
+        extra="",  # optional
+        java_opts="",  # optional
+        embed_ref=False,  # embed the reference in cram output
+    resources:
+        mem_mb=1024,
+    wrapper:
+        "master/bio/gatk/applybqsr"
+
+
+rule gatk_applybqsr_cram_embed:
+    input:
+        bam="mapped/{sample}.bam",
+        ref="genome.fasta",
+        dict="genome.dict",
+        recal_table="recal/{sample}.grp",
+    output:
+        bam="recal/{sample}.embed.cram",
+    log:
+        "logs/gatk/applybqsr/{sample}.embed.cram.log",
     params:
         extra="",  # optional
         java_opts="",  # optional

bio/gatk/applybqsr/wrapper.py

@@ -10,7 +10,6 @@
 
 # Extract arguments
 extra = snakemake.params.get("extra", "")
-reference = snakemake.input.get("ref")
 embed_ref = snakemake.params.get("embed_ref", False)
 java_opts = get_java_opts(snakemake)
 
@@ -19,9 +18,7 @@
 if snakemake.output.bam.endswith(".cram"):
     embed = " --output-fmt-option embed_ref" if embed_ref else ""
     output = "/dev/stdout"
-    pipe_cmd = (
-        " | samtools view -h -O cram {embed} -T {reference} -o {snakemake.output.bam} -"
-    )
+    pipe_cmd = "| samtools view --with-header --reference {snakemake.input.ref} --output-fmt cram {embed} --output {snakemake.output.bam}"
 else:
     output = snakemake.output.bam
     pipe_cmd = ""
@@ -31,7 +28,7 @@
         "(gatk --java-options '{java_opts}' ApplyBQSR"
         " --input {snakemake.input.bam}"
         " --bqsr-recal-file {snakemake.input.recal_table}"
-        " --reference {reference}"
+        " --reference {snakemake.input.ref}"
         " {extra}"
         " --tmp-dir {tmpdir}"
         " --output {output}" + pipe_cmd + ") {log}"

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

@@ -1,86 +1,87 @@
 # This file may be used to create an environment using:
 # $ conda create --name <env> --file <this file>
 # platform: linux-64
-# created-by: conda 24.9.2
+# created-by: conda 26.1.0
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 https://conda.anaconda.org/conda-forge/linux-64/freetype-2.14.1-ha770c72_0.conda#4afc585cd97ba8a23809406cd8a9eda8
-https://conda.anaconda.org/bioconda/linux-64/htslib-1.22.1-h566b1c6_0.tar.bz2#646b491ab86e0ab7173d35eb3a5f3241
+https://conda.anaconda.org/bioconda/linux-64/htslib-1.23-h566b1c6_0.conda#307124911d36a3d976cd76f350085ead
+https://conda.anaconda.org/conda-forge/noarch/packaging-26.0-pyhcf101f3_0.conda#b76541e68fea4d511b1ac46a28dcd2c6
+https://conda.anaconda.org/conda-forge/noarch/setuptools-82.0.0-pyh332efcf_0.conda#1d00d46c634177fc8ede8b99d6089239
+https://conda.anaconda.org/bioconda/noarch/snakemake-wrapper-utils-0.8.0-pyhdfd78af_0.conda#1650e521333852f45468d97b1b2fdcce
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxi-1.8.2-hb9d3cd8_0.conda#17dcc85db3c7886650b8908b183d6876
-https://conda.anaconda.org/conda-forge/linux-64/xorg-libxrandr-1.5.4-hb9d3cd8_0.conda#2de7f99d6581a4a7adbff607b5c278ca
 https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.15.0-h7e30c49_1.conda#8f5b0b297b59e1ac160ad4beec99dbee
-https://conda.anaconda.org/bioconda/linux-64/samtools-1.22.1-h96c455f_0.tar.bz2#7088984cee084e606b2826b1fc3b5906
+https://conda.anaconda.org/bioconda/linux-64/samtools-1.23-h96c455f_0.conda#f5426f4f0024640896a5582a5e75f285
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.46.3-pyhd8ed1ab_0.conda#bdbd7385b4a67025ac2dba4ef8cb6a8f
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxtst-1.2.5-hb9d3cd8_3.conda#7bbe9a0cc0df0ac5f5a8ad6d6a11af2f
-https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.4-h3394656_0.conda#09262e66b19567aff4f592fb53b28760
-https://conda.anaconda.org/conda-forge/linux-64/harfbuzz-11.5.0-h15599e2_0.conda#47599428437d622bfee24fbd06a2d0b4
-https://conda.anaconda.org/conda-forge/linux-64/openjdk-17.0.15-h5ddf6bc_0.conda#f333eeb76d4f1847213838c96e98d6ba
-https://conda.anaconda.org/bioconda/noarch/gatk4-4.6.2.0-py310hdfd78af_0.tar.bz2#be5aed540522531ee4b30d5bc0b3b30c
+https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.4-he90730b_1.conda#bb6c4808bfa69d6f7f6b07e5846ced37
+https://conda.anaconda.org/conda-forge/noarch/pip-26.0.1-pyh8b19718_0.conda#67bdec43082fd8a9cffb9484420b39a2
+https://conda.anaconda.org/conda-forge/linux-64/harfbuzz-12.3.2-h6083320_0.conda#d170a70fc1d5c605fcebdf16851bd54a
+https://conda.anaconda.org/conda-forge/linux-64/openjdk-22.0.1-h8651b0f_1.conda#672153e7c3d4f70bc65993f3ee513768
+https://conda.anaconda.org/bioconda/noarch/gatk4-4.6.2.0-py310hdfd78af_1.conda#547a9895d237eb7daf8bb08763994ea5

bio/gatk/applybqsrspark/environment.yaml

@@ -3,6 +3,7 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
+  - openjdk <23
   - gatk4 =4.6.2.0
   - snakemake-wrapper-utils =0.8.0
-  - samtools =1.22.1
+  - samtools =1.23

bio/gatk/applybqsrspark/test/Snakefile

@@ -7,7 +7,7 @@ rule gatk_applybqsr_spark:
     output:
         bam="recal/{sample}.bam",
     log:
-        "logs/gatk/gatk_applybqsr_spark/{sample}.log",
+        "logs/gatk/applybqsr_spark/{sample}.log",
     params:
         extra="",  # optional
         java_opts="",  # optional
@@ -20,3 +20,27 @@ rule gatk_applybqsr_spark:
         mem_mb=1024,
     wrapper:
         "master/bio/gatk/applybqsrspark"
+
+
+rule gatk_applybqsr_spark_cram:
+    input:
+        bam="mapped/{sample}.bam",
+        ref="genome.fasta",
+        dict="genome.dict",
+        recal_table="recal/{sample}.grp",
+    output:
+        bam="recal/{sample}.cram",
+    log:
+        "logs/gatk/applybqsr_spark/{sample}.cram.log",
+    params:
+        extra="",  # optional
+        java_opts="",  # optional
+        #spark_runner="",  # optional, local by default
+        #spark_master="",  # optional
+        #spark_extra="", # optional
+        embed_ref=True,  # embed reference in cram output
+        exceed_thread_limit=True,  # samtools is also parallized
+    resources:
+        mem_mb=1024,
+    wrapper:
+        "master/bio/gatk/applybqsrspark"