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feat: enable gzip output for bedtools wrappers #3642

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9c5f406
updated for use of gzip
gtuckerkellogg Feb 7, 2025
2e0bfdc
gzip support for bedtools bamtobed and complement (with tests)
gtuckerkellogg Feb 8, 2025
4f493c0
updated test_wrappers and tests for all current bedtools wrappers for…
gtuckerkellogg Feb 8, 2025
e313300
Merge branch 'snakemake:master' into bedtools-gzip-output
gtuckerkellogg Feb 8, 2025
cd57a18
addressed CodeRabbit review
gtuckerkellogg Feb 8, 2025
4c1265b
from gzip to bgzip
gtuckerkellogg Feb 8, 2025
40fe0c9
merged to bgzip
gtuckerkellogg Feb 8, 2025
0665f1a
all bgzip, no gzip
gtuckerkellogg Feb 8, 2025
8056dc6
all bgzip, no gzip
gtuckerkellogg Feb 8, 2025
760a76f
Merge remote-tracking branch 'refs/remotes/origin/bedtools-gzip-outpu…
gtuckerkellogg Feb 8, 2025
d2028aa
Update bio/bedtools/complement/wrapper.py
gtuckerkellogg Feb 8, 2025
bf9a66b
added hstlib dependency for bgzip in environment.yaml across bedtools…
gtuckerkellogg Feb 9, 2025
10eebb0
black check
gtuckerkellogg Feb 18, 2025
7be0d52
removed vscode cruft
gtuckerkellogg Feb 18, 2025
b926c85
Merge branch 'master' into bedtools-gzip-output
gtuckerkellogg Feb 18, 2025
76245e7
nitpicking resolved
gtuckerkellogg Feb 18, 2025
dda0a28
When coderabbit says nitpick, it means nitpick!
gtuckerkellogg Feb 18, 2025
d891935
Update bio/bedtools/bamtobed/wrapper.py
gtuckerkellogg Feb 18, 2025
db85a32
Remove unused import
fgvieira Feb 18, 2025
2c98855
Merge branch 'snakemake:master' into bedtools-gzip-output
gtuckerkellogg Feb 19, 2025
33aaf57
pinned environments
gtuckerkellogg Feb 19, 2025
4e00419
fixed mistakenly compressed bed file
gtuckerkellogg Feb 19, 2025
1599f1c
also for complement
gtuckerkellogg Feb 19, 2025
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31 changes: 24 additions & 7 deletions bio/bedtools/bamtobed/environment.linux-64.pin.txt
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@@ -1,13 +1,30 @@
# This file may be used to create an environment using:
# $ conda create --name <env> --file <this file>
# platform: linux-64
# created-by: conda 24.11.3
@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/libstdcxx-ng-13.2.0-h7e041cc_3.conda#937eaed008f6bf2191c5fe76f87755e9
https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_3.conda#7124cbb46b13d395bdde68f2d215c989
https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2025.1.31-hbcca054_0.conda#19f3a56f68d2fd06c516076bff482c52
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-ng-13.2.0-h807b86a_3.conda#23fdf1fef05baeb7eadc2aed5fb0011f
https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
https://conda.anaconda.org/bioconda/linux-64/bedtools-2.31.1-hf5e1c6e_0.tar.bz2#c7afd961b4189429e8491cd059660c45
https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.2.0-h77fa898_1.conda#3cb76c3f10d3bc7f1105b2fc9db984df
https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.4-hb9d3cd8_0.conda#e2775acf57efd5af15b8e3d1d74d72d3
https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.23-h4ddbbb0_0.conda#8dfae1d2e74767e9ce36d5fa0d8605db
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/liblzma-5.6.4-hb9d3cd8_0.conda#42d5b6a0f30d3c10cd88cb8584fda1cb
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/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
https://conda.anaconda.org/conda-forge/linux-64/openssl-3.4.1-h7b32b05_0.conda#41adf927e746dc75ecf0ef841c454e48
https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3
https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20250104-pl5321h7949ede_0.conda#c277e0a4d549b03ac1e9d6cbbe3d017b
https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172bf1cd1ff8629f2b1179945ed45055
https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.1-hf672d98_0.conda#be2de152d8073ef1c01b7728475f2fe7
https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.2.0-h4852527_1.conda#8371ac6457591af2cf6159439c1fd051
https://conda.anaconda.org/bioconda/linux-64/bedtools-2.31.1-h13024bc_3.tar.bz2#99c4e90e82db906439e00beafb343d16
https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.3-h659f571_0.conda#3f43953b7d3fb3aaa1d0d0723d91e368
https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.64.0-h161d5f1_0.conda#19e57602824042dfd0446292ef90488b
https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45
https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.12.1-h332b0f4_0.conda#45e9dc4e7b25e2841deb392be085500e
https://conda.anaconda.org/bioconda/linux-64/htslib-1.21-h566b1c6_1.tar.bz2#944598fba531a668e8fafea92ca39bb4
1 change: 1 addition & 0 deletions bio/bedtools/bamtobed/environment.yaml
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Expand Up @@ -4,3 +4,4 @@ channels:
- nodefaults
dependencies:
- bedtools =2.31.1
- htslib =1.21
13 changes: 13 additions & 0 deletions bio/bedtools/bamtobed/test/Snakefile
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@@ -1,3 +1,4 @@

rule bamtobed:
input:
"{sample}.bam",
Expand All @@ -9,3 +10,15 @@ rule bamtobed:
extra="-bedpe", # optional parameters
wrapper:
"master/bio/bedtools/bamtobed"

rule bamtobed_gz:
input:
"{sample}.bam",
output:
"{sample}.bed.gz",
log:
"logs/bamtobed/{sample}.gz.log",
params:
extra="-bedpe", # optional parameters
wrapper:
"master/bio/bedtools/bamtobed"
4 changes: 2 additions & 2 deletions bio/bedtools/bamtobed/wrapper.py
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Expand Up @@ -2,18 +2,18 @@
__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", "")

compress = "| bgzip" if snakemake.output[0].endswith(".gz") else ""

shell(
"(bamToBed"
" {extra}"
" -i {snakemake.input[0]}"
" {compress}"
" > {snakemake.output[0]}"
") {log}"
)
31 changes: 24 additions & 7 deletions bio/bedtools/complement/environment.linux-64.pin.txt
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@@ -1,13 +1,30 @@
# This file may be used to create an environment using:
# $ conda create --name <env> --file <this file>
# platform: linux-64
# created-by: conda 24.11.3
@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/libstdcxx-ng-13.2.0-h7e041cc_3.conda#937eaed008f6bf2191c5fe76f87755e9
https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_3.conda#7124cbb46b13d395bdde68f2d215c989
https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2025.1.31-hbcca054_0.conda#19f3a56f68d2fd06c516076bff482c52
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-ng-13.2.0-h807b86a_3.conda#23fdf1fef05baeb7eadc2aed5fb0011f
https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
https://conda.anaconda.org/bioconda/linux-64/bedtools-2.31.1-hf5e1c6e_0.tar.bz2#c7afd961b4189429e8491cd059660c45
https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.2.0-h77fa898_1.conda#3cb76c3f10d3bc7f1105b2fc9db984df
https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.4-hb9d3cd8_0.conda#e2775acf57efd5af15b8e3d1d74d72d3
https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.23-h4ddbbb0_0.conda#8dfae1d2e74767e9ce36d5fa0d8605db
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/liblzma-5.6.4-hb9d3cd8_0.conda#42d5b6a0f30d3c10cd88cb8584fda1cb
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/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
https://conda.anaconda.org/conda-forge/linux-64/openssl-3.4.1-h7b32b05_0.conda#41adf927e746dc75ecf0ef841c454e48
https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3
https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20250104-pl5321h7949ede_0.conda#c277e0a4d549b03ac1e9d6cbbe3d017b
https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172bf1cd1ff8629f2b1179945ed45055
https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.1-hf672d98_0.conda#be2de152d8073ef1c01b7728475f2fe7
https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.2.0-h4852527_1.conda#8371ac6457591af2cf6159439c1fd051
https://conda.anaconda.org/bioconda/linux-64/bedtools-2.31.1-h13024bc_3.tar.bz2#99c4e90e82db906439e00beafb343d16
https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.3-h659f571_0.conda#3f43953b7d3fb3aaa1d0d0723d91e368
https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.64.0-h161d5f1_0.conda#19e57602824042dfd0446292ef90488b
https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45
https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.12.1-h332b0f4_0.conda#45e9dc4e7b25e2841deb392be085500e
https://conda.anaconda.org/bioconda/linux-64/htslib-1.21-h566b1c6_1.tar.bz2#944598fba531a668e8fafea92ca39bb4
1 change: 1 addition & 0 deletions bio/bedtools/complement/environment.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,3 +4,4 @@ channels:
- nodefaults
dependencies:
- bedtools =2.31.1
- htslib =1.21
14 changes: 14 additions & 0 deletions bio/bedtools/complement/test/Snakefile
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Expand Up @@ -12,6 +12,20 @@ rule bedtools_complement_bed:
wrapper:
"master/bio/bedtools/complement"

rule bedtools_complement_bed_gz:
input:
in_file="a.bed",
genome="dummy.genome"
output:
"results/bed-complement/a.complement.bed.gz"
params:
## Add optional parameters
extra="-L"
log:
"logs/a.complement.bed.gz.log"
wrapper:
"master/bio/bedtools/complement"

rule bedtools_complement_vcf:
input:
in_file="a.vcf",
Expand Down
0 ...t/results/bed-complement/a.complement.bed → .../expected/bed-complement/a.complement.bed
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Binary file added bio/bedtools/complement/test/expected/bed-complement/a.complement.bed.gz
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0 ...t/results/vcf-complement/a.complement.vcf → .../expected/vcf-complement/a.complement.vcf
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3 changes: 3 additions & 0 deletions bio/bedtools/complement/wrapper.py
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Expand Up @@ -7,13 +7,16 @@

extra = snakemake.params.get("extra", "")

compress = "| bgzip" if snakemake.output[0].endswith(".gz") else ""

log = snakemake.log_fmt_shell(stdout=True, stderr=True)

shell(
"(bedtools complement"
" {extra}"
" -i {snakemake.input.in_file}"
" -g {snakemake.input.genome}"
" {compress}"
" > {snakemake.output[0]})"
" {log}"
)
31 changes: 24 additions & 7 deletions bio/bedtools/coveragebed/environment.linux-64.pin.txt
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Original file line number Diff line number Diff line change
@@ -1,13 +1,30 @@
# This file may be used to create an environment using:
# $ conda create --name <env> --file <this file>
# platform: linux-64
# created-by: conda 24.11.3
@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/libstdcxx-ng-13.2.0-h7e041cc_3.conda#937eaed008f6bf2191c5fe76f87755e9
https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_3.conda#7124cbb46b13d395bdde68f2d215c989
https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2025.1.31-hbcca054_0.conda#19f3a56f68d2fd06c516076bff482c52
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-ng-13.2.0-h807b86a_3.conda#23fdf1fef05baeb7eadc2aed5fb0011f
https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
https://conda.anaconda.org/bioconda/linux-64/bedtools-2.31.1-hf5e1c6e_0.tar.bz2#c7afd961b4189429e8491cd059660c45
https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.2.0-h77fa898_1.conda#3cb76c3f10d3bc7f1105b2fc9db984df
https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.4-hb9d3cd8_0.conda#e2775acf57efd5af15b8e3d1d74d72d3
https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.23-h4ddbbb0_0.conda#8dfae1d2e74767e9ce36d5fa0d8605db
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/liblzma-5.6.4-hb9d3cd8_0.conda#42d5b6a0f30d3c10cd88cb8584fda1cb
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/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
https://conda.anaconda.org/conda-forge/linux-64/openssl-3.4.1-h7b32b05_0.conda#41adf927e746dc75ecf0ef841c454e48
https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3
https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20250104-pl5321h7949ede_0.conda#c277e0a4d549b03ac1e9d6cbbe3d017b
https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172bf1cd1ff8629f2b1179945ed45055
https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.1-hf672d98_0.conda#be2de152d8073ef1c01b7728475f2fe7
https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.2.0-h4852527_1.conda#8371ac6457591af2cf6159439c1fd051
https://conda.anaconda.org/bioconda/linux-64/bedtools-2.31.1-h13024bc_3.tar.bz2#99c4e90e82db906439e00beafb343d16
https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.3-h659f571_0.conda#3f43953b7d3fb3aaa1d0d0723d91e368
https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.64.0-h161d5f1_0.conda#19e57602824042dfd0446292ef90488b
https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45
https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.12.1-h332b0f4_0.conda#45e9dc4e7b25e2841deb392be085500e
https://conda.anaconda.org/bioconda/linux-64/htslib-1.21-h566b1c6_1.tar.bz2#944598fba531a668e8fafea92ca39bb4
1 change: 1 addition & 0 deletions bio/bedtools/coveragebed/environment.yaml
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Expand Up @@ -4,3 +4,4 @@ channels:
- nodefaults
dependencies:
- bedtools =2.31.1
- htslib =1.21
4 changes: 3 additions & 1 deletion bio/bedtools/coveragebed/wrapper.py
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Expand Up @@ -3,7 +3,6 @@
__email__ = "[email protected]"
__license__ = "MIT"


from snakemake.shell import shell

shell.executable("bash")
Expand All @@ -17,6 +16,8 @@

output_file = snakemake.output[0]

compress = "| bgzip" if snakemake.output[0].endswith(".gz") else ""

if not isinstance(output_file, str) and len(snakemake.output) != 1:
raise ValueError("Output should be one file: " + str(output_file) + "!")

Expand All @@ -25,6 +26,7 @@
" -a {input_a}"
" -b {input_b}"
" {extra_params}"
" {compress}"
" > {output_file}"
" {log}"
)
31 changes: 24 additions & 7 deletions bio/bedtools/genomecov/environment.linux-64.pin.txt
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@@ -1,13 +1,30 @@
# This file may be used to create an environment using:
# $ conda create --name <env> --file <this file>
# platform: linux-64
# created-by: conda 24.11.3
@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/libstdcxx-ng-13.2.0-h7e041cc_3.conda#937eaed008f6bf2191c5fe76f87755e9
https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_3.conda#7124cbb46b13d395bdde68f2d215c989
https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2025.1.31-hbcca054_0.conda#19f3a56f68d2fd06c516076bff482c52
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-ng-13.2.0-h807b86a_3.conda#23fdf1fef05baeb7eadc2aed5fb0011f
https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
https://conda.anaconda.org/bioconda/linux-64/bedtools-2.31.1-hf5e1c6e_0.tar.bz2#c7afd961b4189429e8491cd059660c45
https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.2.0-h77fa898_1.conda#3cb76c3f10d3bc7f1105b2fc9db984df
https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.4-hb9d3cd8_0.conda#e2775acf57efd5af15b8e3d1d74d72d3
https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.23-h4ddbbb0_0.conda#8dfae1d2e74767e9ce36d5fa0d8605db
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/liblzma-5.6.4-hb9d3cd8_0.conda#42d5b6a0f30d3c10cd88cb8584fda1cb
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/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
https://conda.anaconda.org/conda-forge/linux-64/openssl-3.4.1-h7b32b05_0.conda#41adf927e746dc75ecf0ef841c454e48
https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3
https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20250104-pl5321h7949ede_0.conda#c277e0a4d549b03ac1e9d6cbbe3d017b
https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172bf1cd1ff8629f2b1179945ed45055
https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.1-hf672d98_0.conda#be2de152d8073ef1c01b7728475f2fe7
https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.2.0-h4852527_1.conda#8371ac6457591af2cf6159439c1fd051
https://conda.anaconda.org/bioconda/linux-64/bedtools-2.31.1-h13024bc_3.tar.bz2#99c4e90e82db906439e00beafb343d16
https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.3-h659f571_0.conda#3f43953b7d3fb3aaa1d0d0723d91e368
https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.64.0-h161d5f1_0.conda#19e57602824042dfd0446292ef90488b
https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45
https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.12.1-h332b0f4_0.conda#45e9dc4e7b25e2841deb392be085500e
https://conda.anaconda.org/bioconda/linux-64/htslib-1.21-h566b1c6_1.tar.bz2#944598fba531a668e8fafea92ca39bb4
1 change: 1 addition & 0 deletions bio/bedtools/genomecov/environment.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,3 +4,4 @@ channels:
- nodefaults
dependencies:
- bedtools =2.31.1
- htslib =1.21
3 changes: 3 additions & 0 deletions bio/bedtools/genomecov/wrapper.py
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Expand Up @@ -19,10 +19,13 @@
input_file = "-i " + snakemake.input.get("bed")
genome = "-g " + snakemake.input.get("ref")

compress = "| bgzip" if snakemake.output[0].endswith(".gz") else ""

shell(
"(genomeCoverageBed"
" {snakemake.params}"
" {input_file}"
" {genome}"
" {compress}"
" > {snakemake.output[0]}) {log}"
)
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