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perf: autobump bio/varlociraptor/estimate-alignment-properties #3546

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merged 13 commits into from
Jan 23, 2025
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perf: autobump bio/varlociraptor/estimate-alignment-properties #3546

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23ae123
perf: update bio/varlociraptor/estimate-alignment-properties/environm…
snakedeploy-bot[bot] Dec 13, 2024
d8fbc96
perf: update env pinning.
snakedeploy-bot[bot] Dec 13, 2024
37726a6
perf: update bio/varlociraptor/estimate-alignment-properties/environm…
snakedeploy-bot[bot] Dec 20, 2024
2350e5e
perf: update env pinning.
snakedeploy-bot[bot] Dec 20, 2024
9cdd12e
perf: update bio/varlociraptor/estimate-alignment-properties/environm…
snakedeploy-bot[bot] Dec 27, 2024
e67b022
perf: update env pinning.
snakedeploy-bot[bot] Dec 27, 2024
fbc3b04
perf: update bio/varlociraptor/estimate-alignment-properties/environm…
snakedeploy-bot[bot] Jan 3, 2025
9f01cd4
perf: update env pinning.
snakedeploy-bot[bot] Jan 3, 2025
b7a81b7
perf: update bio/varlociraptor/estimate-alignment-properties/environm…
snakedeploy-bot[bot] Jan 10, 2025
98a4702
perf: update env pinning.
snakedeploy-bot[bot] Jan 10, 2025
16d4523
perf: update bio/varlociraptor/estimate-alignment-properties/environm…
snakedeploy-bot[bot] Jan 17, 2025
d9b11e2
perf: update env pinning.
snakedeploy-bot[bot] Jan 17, 2025
6c0b591
adapt to changes
johanneskoester Jan 23, 2025
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11 changes: 6 additions & 5 deletions bio/varlociraptor/estimate-alignment-properties/environment.linux-64.pin.txt
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Expand Up @@ -4,20 +4,21 @@
# created-by: conda 24.9.2
@EXPLICIT
https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.8.30-hbcca054_0.conda#c27d1c142233b5bc9ca570c6e2e0c244
https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.12.14-hbcca054_0.conda#720523eb0d6a9b0f6120c16b2aa4e7de
https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.2.0-h77fa898_1.conda#cc3573974587f12dda90d96e3e55a702
https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.2.0-h77fa898_1.conda#3cb76c3f10d3bc7f1105b2fc9db984df
https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.2.0-h69a702a_1.conda#e39480b9ca41323497b05492a63bc35b
https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-14.2.0-hd5240d6_1.conda#9822b874ea29af082e5d36098d25427d
https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.6.3-hb9d3cd8_1.conda#2ecf2f1c7e4e21fcfe6423a51a992d84
https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-14.2.0-hc0a3c3a_1.conda#234a5554c53625688d51062645337328
https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
https://conda.anaconda.org/conda-forge/linux-64/openssl-3.4.0-hb9d3cd8_0.conda#23cc74f77eb99315c0360ec3533147a9
https://conda.anaconda.org/conda-forge/linux-64/openssl-3.4.0-h7b32b05_1.conda#4ce6875f75469b2757a65e10a5d05e31
https://conda.anaconda.org/conda-forge/linux-64/blis-0.9.0-h4ab18f5_2.conda#6f77ba1352b69c4a6f8a6d20def30e4e
https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
https://conda.anaconda.org/conda-forge/linux-64/libgfortran-14.2.0-h69a702a_1.conda#f1fd30127802683586f768875127a987
https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.28-pthreads_h94d23a6_1.conda#62857b389e42b36b686331bec0922050
https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-25_linux64_openblas.conda#8ea26d42ca88ec5258802715fe1ee10b
https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-25_linux64_openblas.conda#5dbd1b0fc0d01ec5e0e1fbe667281a11
https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-26_linux64_openblas.conda#ac52800af2e0c0e7dac770b435ce768a
https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-26_linux64_openblas.conda#ebcc5f37a435aa3c19640533c82f8d76
https://conda.anaconda.org/conda-forge/linux-64/gsl-2.7-he838d99_0.tar.bz2#fec079ba39c9cca093bf4c00001825de
https://conda.anaconda.org/bioconda/linux-64/varlociraptor-8.4.14-ha8ac579_0.tar.bz2#f7dd473a6baf8bac20a872b241002499
https://conda.anaconda.org/bioconda/linux-64/varlociraptor-8.6.0-ha8ac579_0.tar.bz2#571f777f35713761959a0720cc6cb192
2 changes: 1 addition & 1 deletion bio/varlociraptor/estimate-alignment-properties/environment.yaml
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Expand Up @@ -3,4 +3,4 @@ channels:
- bioconda
- nodefaults
dependencies:
- varlociraptor =8.4.14
- varlociraptor =8.6.0
2 changes: 1 addition & 1 deletion bio/varlociraptor/estimate-alignment-properties/meta.yaml
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Expand Up @@ -6,6 +6,6 @@ authors:
- Johannes Köster
input:
- reference genome
- read alignments
- read alignments (may be multiple bams)
output:
- varlociraptor alignment properties
4 changes: 2 additions & 2 deletions bio/varlociraptor/estimate-alignment-properties/test/Snakefile
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@@ -1,9 +1,9 @@
rule varlociraptor_alignment_properties:
input:
ref="resources/genome.fasta",
alignments="results/alignments/{sample}.bam",
alignments=["results/alignments/{sample}.bam"],
ref_idx="resources/genome.fasta.fai",
aln_idx="results/alignments/{sample}.bam.bai",
aln_idx=["results/alignments/{sample}.bam.bai"],
output:
"results/alignment-properties/{sample}.json",
log:
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2 changes: 1 addition & 1 deletion bio/varlociraptor/estimate-alignment-properties/wrapper.py
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Expand Up @@ -5,7 +5,7 @@
sp.run(
"varlociraptor estimate alignment-properties "
f"{snakemake.params.get('extra', '')} {snakemake.input.ref} "
f"--bam {snakemake.input.alignments} "
f"--bams {snakemake.input.alignments} "
f"> {snakemake.output[0]} {log}",
check=True,
shell=True,
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