2024-04-09

Author: pjhesbest

envs/conda/phylogeny_env.yml

@@ -1,10 +1,10 @@
 name: phylogeny_env
 channels:
-  - bioconda
-  - conda-forge
+- bioconda
+- conda-forge
 dependencies:
-  - bioconda::iqtree=2.3.6
-  - bioconda::mafft=7.525
-  - bioconda::seqkit=2.9.0
-  - bioconda::snp-sites=2.5.1
-  - bioconda::treetime=0.11.4
+- bioconda::iqtree=2.4.0
+- bioconda::mafft=7.525
+- bioconda::seqkit=2.10.0
+- bioconda::snp-sites=2.5.1
+- bioconda::treetime=0.11.4

envs/conda/snp_profiling_env.yml

@@ -4,9 +4,9 @@ channels:
 - bioconda
 dependencies:
 - bioconda::bcftools=1.21
-- bioconda::snpeff=5.2
-- bioconda::varscan=2.4.3
-- bioconda::vcftools=0.1.16
-- bioconda::seqkit=2.9.0
+- bioconda::emboss=6.6.0
+- bioconda::seqkit=2.10.0
 - bioconda::snp-sites=2.5.1
-- bioconda::emboss=6.6.0
+- bioconda::snpeff=5.2
+- bioconda::varscan=2.4.6
+- bioconda::vcftools=0.1.16

envs/conda/tbprofiler_env.yml

@@ -1,7 +1,6 @@
 name: tb-profiler_env
 channels:
-  - bioconda
-  - conda-forge
-  - defaults
+- conda-forge
+- bioconda
 dependencies:
-  - bioconda::tb-profiler=6.6.3
+- bioconda::tb-profiler=6.6.3

envs/containers/docker.yml

@@ -1,16 +1,16 @@
-mtbseq_rnv:
-- 
+mtbseq_env:
+- community.wave.seqera.io/library/mtbseq:1.1.0--3ef3983aae64199d
 phylogeny_env:
-- 
+- community.wave.seqera.io/library/iqtree_mafft_seqkit_snp-sites_treetime:030632716d453b3f
 r-phylogeny_env:
 - community.wave.seqera.io/library/bioconductor-ggtree_bioconductor-treeio_r-ape_r-argparse_pruned:eea7baf72f9560d9
 r-stats_env:
 - community.wave.seqera.io/library/r-argparse_r-base_r-dplyr_r-ggrepel_pruned:9fa710c1508e1cb6
 snp_profiling_env:
-- 
+- community.wave.seqera.io/library/bcftools_emboss_seqkit_snp-sites_pruned:1a1022abcb91db63
 taxonkit_env:
 - 
 taxonomy_env:
 - 
 tbprofiler_env:
-- 
+- community.wave.seqera.io/library/tb-profiler:6.6.3--fb34c34b4a27d1b8

envs/containers/singulairty.yml

@@ -1,9 +1,9 @@
-mtbseq_rnv:
-- 
-- 
+mtbseq_env:
+- oras://community.wave.seqera.io/library/mtbseq:1.1.0--d0a0774ca038b4d3
+- https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ce/ce098dd570838fdcb0eb401b3afe4ebf4bc88d1038768ec18b3f970deb28c313/data
 phylogeny_env:
-- 
-- 
+- oras://community.wave.seqera.io/library/iqtree_mafft_seqkit_snp-sites_treetime:1ec44de5738a92e4
+- https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/19/1969316c878dcf7c6e1cc6a5ccf9da86409a6effa02b8c84b7214f0aff6d8922/data
 r-phylogeny_env:
 - oras://community.wave.seqera.io/library/bioconductor-ggtree_bioconductor-treeio_r-ape_r-argparse_pruned:3933fdc29e2b7516
 - https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/3a/3a292e33635c69a2545fd6842116f83f1ae86066444339706cc6b1cdd02558ca/data
@@ -20,6 +20,6 @@ taxonomy_env:
 - 
 - 
 tbprofiler_env:
-- 
-- 
+- oras://community.wave.seqera.io/library/tb-profiler:6.6.3--400be6f998a9ed1b
+- https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1c/1c8630f93dc3f64b11a2ff508d950a3e06c4e33e949476ed2b475beb8cafd1c9/data