Fix #187 (#188)

* Fix #185 - update regenie to v3.2.8

* fix #187

* fix flake8 warnings

* fix flake8

* update REGENIE version

Author: ofrei

CHANGELOG.md

@@ -39,6 +39,16 @@ If MD5 sum is not listed for a certain release then it means that the container
 
 * Miscellaneous goes here
 
+## [1.3.4] - 2023-06-22
+
+### Updated
+
+* Update regenie to v3.2.8
+
+### Fixed
+
+* #187 - Regression in gwas.py in handling of info, maf, hwe and geno filters
+
 ## [1.3.3] - 2023-06-14
 
 ### Updated

docker/README.md

@@ -51,7 +51,7 @@ The detailed description of the available container [files](https://github.com/c
   | gwas.sif          | vcftools            | 0.1.17                                    | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
   | gwas.sif          | bcftools            | 1.12 (using htslib 1.12)                  | [MIT/Expat/GPLv3](https://github.com/samtools/bcftools/blob/develop/LICENSE)
   | gwas.sif          | flashpca_x86-64     | 2.0                                       | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
-  | gwas.sif          | regenie             | v2.0.2.gz                                 | [MIT/Boost](https://github.com/rgcgithub/regenie/blob/master/LICENSE)
+  | gwas.sif          | regenie             | v3.2.8                                    | [MIT/Boost](https://github.com/rgcgithub/regenie/blob/master/LICENSE)
   | gwas.sif          | GWAMA               | 2.2.2                                     | [BSD-3-Clause](https://opensource.org/licenses/BSD-3-Clause)
   | gwas.sif          | minimac4            | v4.1.0                                    | [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
   | gwas.sif          | bgenix              | 1.1.7                                     | [Boost](https://www.boost.org/LICENSE_1_0.txt)

docker/scripts/install_regenie.sh

@@ -1,6 +1,6 @@
 #!/bin/sh
-wget --no-check-certificate https://github.com/rgcgithub/regenie/releases/download/v2.0.2/regenie_v2.0.2.gz_x86_64_Linux_mkl.zip && \
-    unzip -j regenie_v2.0.2.gz_x86_64_Linux_mkl.zip && \
-    rm -rf regenie_v2.0.2.gz_x86_64_Linux_mkl.zip && \
-    mv regenie_v2.0.2.gz_x86_64_Linux_mkl regenie
+wget --no-check-certificate https://github.com/rgcgithub/regenie/releases/download/v3.2.8/regenie_v3.2.8.gz_x86_64_Linux_mkl.zip && \
+    unzip -j regenie_v3.2.8.gz_x86_64_Linux_mkl.zip && \
+    rm -rf regenie_v3.2.8.gz_x86_64_Linux_mkl.zip && \
+    mv regenie_v3.2.8.gz_x86_64_Linux_mkl regenie
 cp regenie /bin

scripts/gwas/config.yaml

@@ -11,10 +11,10 @@ slurm:
     - singularity/3.7.1
 
 # folder containing 'containers' subfolder with a full copy of https://github.com/comorment/containers
-comorment_folder: "/cluster/projects/p697/github/comorment"
+comorment_folder: "/ess/p697/data/durable/s3-api/github/comorment"
 
 # SINGULARITY_BIND variable to set in SLURM scripts
-singularity_bind: "$COMORMENT/containers/reference:/REF:ro"
+singularity_bind: "$COMORMENT/containers/reference:/REF:ro;/ess/p697:/ess/p697"
 
 saige:
   cpus_per_task_stage2: 1

scripts/gwas/gwas.py

@@ -488,7 +488,8 @@ def make_saige_commands(args, logistic, step):
 def pass_arguments_along(args, args_list):
     opts = vars(args)
     vals = [opts[arg.replace('-', '_')] for arg in args_list]
-    return ''.join([(' --{} {} '.format(arg, '' if val else val) if val else '') for arg, val in zip(args_list, vals)])
+    args = [(' --{} {} '.format(arg, '' if (val is True) else val) if val else '') for arg, val in zip(args_list, vals)]
+    return ''.join(args)
 
 def make_figures_commands(args):
     cmd = ''

singularity/gwas.sif

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:a398a2d346365381a7ab04b783aae48b0fbdb7d9c52f86fb4b65fbd03d9e77f0
-size 405090304
+oid sha256:db7a9e7dc6413a1b2cc5a58ee0abe8188675e63a4f2774d4b4580741edeed452
+size 405778432

version/version.py

@@ -2,7 +2,7 @@
 _MINOR = "3"
 # On main and in a nightly release the patch should be one ahead of the last
 # released build.
-_PATCH = "3"
+_PATCH = "4"
 # This is mainly for nightly builds which have the suffix ".dev$DATE". See
 # https://semver.org/#is-v123-a-semantic-version for the semantics.
 _SUFFIX = ""