bihealth · ericblanc20 · Apr 18, 2024 · Mar 22, 2024 · Mar 22, 2024 · Mar 22, 2024
diff --git a/snappy_wrappers/wrappers/alfred/qc/environment.yaml b/snappy_wrappers/wrappers/alfred/qc/environment.yaml
@@ -1,7 +1,7 @@
 channels:
-- conda-forge
-- bioconda
+  - conda-forge
+  - bioconda
 dependencies:
-- bedtools
-- alfred >=0.2.8,<0.3.0
-- jq
+  - bedtools==2.31.1
+  - alfred==0.2.8
+  - jq==1.7.1
diff --git a/snappy_wrappers/wrappers/arcashla/environment.yaml b/snappy_wrappers/wrappers/arcashla/environment.yaml
@@ -1,5 +1,5 @@
 channels:
-- conda-forge
-- bioconda
+  - conda-forge
+  - bioconda
 dependencies:
-- arcas-hla
+  - arcas-hla==0.6.0
diff --git a/snappy_wrappers/wrappers/arriba/environment.yaml b/snappy_wrappers/wrappers/arriba/environment.yaml
@@ -2,7 +2,6 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - star
-  - trimadap ==r11
-  - arriba
-
+  - star==2.7.11b
+  - trimadap==r11
+  - arriba==2.4.0
diff --git a/snappy_wrappers/wrappers/ascat/run_ascat/environment.yaml b/snappy_wrappers/wrappers/ascat/run_ascat/environment.yaml
@@ -2,8 +2,8 @@ channels:
 - conda-forge
 - bioconda
 dependencies:
-- r ==3.3.2
-- ascat ==2.5
-- bcftools ==1.5
-- samtools ==1.5
-- htslib ==1.5
+- r-base==3.3.2
+- ascat==2.5
+- bcftools==1.5
+- samtools==1.5
+- htslib==1.5
diff --git a/snappy_wrappers/wrappers/baf_file_generation/environment.yaml b/snappy_wrappers/wrappers/baf_file_generation/environment.yaml
@@ -1,7 +1,7 @@
 channels:
-- conda-forge
-- bioconda
+  - conda-forge
+  - bioconda
 dependencies:
-- bcftools ==1.15.1
-- htslib ==1.15.1
-- ucsc-wigtobigwig
+  - bcftools==1.15.1
+  - htslib==1.15.1
+  - ucsc-wigtobigwig==447
diff --git a/snappy_wrappers/wrappers/bbduk/environment.yaml b/snappy_wrappers/wrappers/bbduk/environment.yaml
@@ -2,5 +2,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bbmap =39
-  - openjdk >= 8 
+  - bbmap==39.06
+  - openjdk==20.0.2
diff --git a/snappy_wrappers/wrappers/bcftools_call/environment.yaml b/snappy_wrappers/wrappers/bcftools_call/environment.yaml
@@ -2,8 +2,8 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - gatk4
-  - parallel =20221122
-  - bcftools =1.16
-  - samtools =1.16
-  - htslib =1.16
+  - gatk4==4.5.0.0
+  - parallel==20221122
+  - bcftools==1.16
+  - samtools==1.16.1
+  - htslib==1.16
diff --git a/snappy_wrappers/wrappers/bcftools_roh/environment.yaml b/snappy_wrappers/wrappers/bcftools_roh/environment.yaml
@@ -1,6 +1,6 @@
 channels:
-- conda-forge
-- bioconda
+  - conda-forge
+  - bioconda
 dependencies:
-- bcftools ==1.15
-- htslib ==1.15
+  - bcftools==1.15
+  - htslib==1.15
diff --git a/snappy_wrappers/wrappers/bcftools_stats/run/environment.yaml b/snappy_wrappers/wrappers/bcftools_stats/run/environment.yaml
@@ -1,7 +1,6 @@
 channels:
-- conda-forge
-- bioconda
-- r
+  - conda-forge
+  - bioconda
 dependencies:
-- bcftools ==1.3.1
-- htslib ==1.3.2
+  - bcftools==1.3.1
+  - htslib==1.3.2
diff --git a/snappy_wrappers/wrappers/bed_jaccard_operations/environment.yaml b/snappy_wrappers/wrappers/bed_jaccard_operations/environment.yaml
@@ -1,6 +1,5 @@
 channels:
-- conda-forge
-- bioconda
-- r
+  - conda-forge
+  - bioconda
 dependencies:
-- bedtools ==2.26.0
+  - bedtools==2.26.0
diff --git a/snappy_wrappers/wrappers/bed_venn/environment.yaml b/snappy_wrappers/wrappers/bed_venn/environment.yaml
@@ -1,6 +1,5 @@
 channels:
 - conda-forge
 - bioconda
-- r
 dependencies:
 - bedtools ==2.26.0
diff --git a/snappy_wrappers/wrappers/bwa/environment.yaml b/snappy_wrappers/wrappers/bwa/environment.yaml
@@ -2,8 +2,8 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bwa ==0.7.17
-  - samtools =1.16
-  - samblaster ==0.1.26
-  - seqtk ==1.3
-  - trimadap ==r11
+  - bwa==0.7.17
+  - samtools==1.16.1
+  - samblaster==0.1.26
+  - seqtk==1.3
+  - trimadap==r11
diff --git a/snappy_wrappers/wrappers/bwa_mem2/environment.yaml b/snappy_wrappers/wrappers/bwa_mem2/environment.yaml
@@ -2,9 +2,9 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bwa-mem2 =2
-  - samtools =1.16
-  - htslib =1.16
-  - samblaster =0.1.26
-  - seqtk =1.3
-  - trimadap =r11
+  - bwa-mem2==2.2.1
+  - samtools==1.16.1
+  - htslib==1.16
+  - samblaster==0.1.26
+  - seqtk==1.3
+  - trimadap==r11
diff --git a/snappy_wrappers/wrappers/canvas/somatic_wgs/environment.yaml b/snappy_wrappers/wrappers/canvas/somatic_wgs/environment.yaml
@@ -1,6 +1,5 @@
 channels:
-- conda-forge
-- bioconda
-- r
+  - conda-forge
+  - bioconda
 dependencies:
-- htslib ==1.4.1
+  - htslib==1.4.1
diff --git a/snappy_wrappers/wrappers/cbioportal/generate_cna/environment.yaml b/snappy_wrappers/wrappers/cbioportal/generate_cna/environment.yaml
@@ -1,14 +1,13 @@
 name: generate_cna
 
 channels:
-- conda-forge
-- bioconda
-- r
+  - conda-forge
+  - bioconda
 
 dependencies:
-- r-base
-- r-tidyverse
-- r-igraph
-- bioconductor-genomicranges
-- bioconductor-genomicfeatures
-- bioconductor-deseq2
+  - r-base==4.3.3
+  - r-tidyverse==2.0.0
+  - r-igraph==2.0.2
+  - bioconductor-genomicranges==1.54.1
+  - bioconductor-genomicfeatures==1.54.1
+  - bioconductor-deseq2==1.42.0
diff --git a/snappy_wrappers/wrappers/cbioportal/merge_tables/environment.yaml b/snappy_wrappers/wrappers/cbioportal/merge_tables/environment.yaml
@@ -1,14 +1,13 @@
 name: merge_tables
 
 channels:
-- conda-forge
-- bioconda
-- r
+  - conda-forge
+  - bioconda
 
 dependencies:
-- r-base
-- r-tidyverse
-- r-igraph
-- bioconductor-genomicranges
-- bioconductor-genomicfeatures
-- bioconductor-deseq2
+  - r-base==4.3.3
+  - r-tidyverse==2.0.0
+  - r-igraph==2.0.2
+  - bioconductor-genomicranges==1.54.1
+  - bioconductor-genomicfeatures==1.54.1
+  - bioconductor-deseq2==1.42.0
diff --git a/snappy_wrappers/wrappers/cnvetti/on_target/coverage/environment.yaml b/snappy_wrappers/wrappers/cnvetti/on_target/coverage/environment.yaml
@@ -1,8 +1,7 @@
 channels:
-- conda-forge
-- bioconda
-- r
+  - conda-forge
+  - bioconda
 dependencies:
-- cnvetti ==0.2.0
-- bcftools ==1.9
-- htslib ==1.9
+  - cnvetti==0.2.0
+  - bcftools==1.9
+  - htslib==1.9
diff --git a/snappy_wrappers/wrappers/cnvetti/on_target/postprocess/environment.yaml b/snappy_wrappers/wrappers/cnvetti/on_target/postprocess/environment.yaml
@@ -1,20 +1,19 @@
 channels:
-- conda-forge
-- bioconda
-- anaconda
+  - conda-forge
+  - bioconda
 dependencies:
-- r
-- r-rcpp
-- r-dplyr
-- r-assertthat
-- r-matrixstats
-- bioconductor-copywriter
-- bioconductor-dnacopy
-- bioconductor-cghcall
-- bioconductor-rsamtools
-- bioconductor-org.hs.eg.db
-- bioconductor-txdb.hsapiens.ucsc.hg19.knowngene
-- bcftools ==1.5
-- samtools ==1.5
-- htslib ==1.5
-- openblas
+  - r-base==4.2
+  - r-rcpp==1.0.12
+  - r-dplyr==1.1.4
+  - r-assertthat==0.2.1
+  - r-matrixstats==1.2.0
+  - bioconductor-copywriter==2.29.0
+  - bioconductor-dnacopy==1.72.0
+  - bioconductor-cghcall==2.60.0
+  - bioconductor-rsamtools==2.14.0
+  - bioconductor-org.hs.eg.db==3.16.0
+  - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene==3.2.2
+  - bcftools==1.5
+  - samtools==1.5
+  - htslib==1.5
+  - openblas==0.3.26
diff --git a/snappy_wrappers/wrappers/cnvetti/wgs/environment.yaml b/snappy_wrappers/wrappers/cnvetti/wgs/environment.yaml
@@ -1,8 +1,7 @@
 channels:
-- conda-forge
-- bioconda
-- r
+  - conda-forge
+  - bioconda
 dependencies:
-- cnvetti ==0.2.0
-- bcftools ==1.9
-- htslib ==1.9
+  - cnvetti==0.2.0
+  - bcftools==1.9
+  - htslib==1.9
diff --git a/snappy_wrappers/wrappers/cnvkit/environment.yaml b/snappy_wrappers/wrappers/cnvkit/environment.yaml
@@ -1,8 +1,7 @@
 channels:
-- conda-forge
-- bioconda
-- r
+  - conda-forge
+  - bioconda
 dependencies:
-- python >3.7
-- cnvkit
-- htslib
+  - python==3.10.14
+  - cnvkit==0.9.10
+  - htslib==1.19.1
diff --git a/snappy_wrappers/wrappers/cnvkit/postprocess/environment.yaml b/snappy_wrappers/wrappers/cnvkit/postprocess/environment.yaml
@@ -1,8 +1,7 @@
 channels:
-- conda-forge
-- bioconda
-- r
+  - conda-forge
+  - bioconda
 dependencies:
-- r-base
-- bioconductor-genomicranges
-- htslib
+  - r-base==4.3.3
+  - bioconductor-genomicranges==1.54.1
+  - htslib==1.19
diff --git a/snappy_wrappers/wrappers/control_freec/environment.yaml b/snappy_wrappers/wrappers/control_freec/environment.yaml
@@ -1,8 +1,7 @@
 channels:
-- conda-forge
-- bioconda
-- base
+  - conda-forge
+  - bioconda
 dependencies:
-- control-freec
-- sambamba
-- bcftools
+  - control-freec==11.6
+  - sambamba==1.0
+  - bcftools==1.19
diff --git a/snappy_wrappers/wrappers/control_freec/transform/environment.yaml b/snappy_wrappers/wrappers/control_freec/transform/environment.yaml
@@ -1,16 +1,14 @@
 channels:
-- bioconda
-- conda-forge
-- anaconda
+  - conda-forge
+  - bioconda
 dependencies:
-- r-base
-- r-tidyverse
-- bioconductor-annotationdbi
-- bioconductor-bsgenome
-- bioconductor-genomicranges
-- bioconductor-org.hs.eg.db
-- bioconductor-txdb.hsapiens.ucsc.hg19.knowngene
-- bioconductor-txdb.hsapiens.ucsc.hg38.knowngene
-- bioconductor-bsgenome.hsapiens.1000genomes.hs37d5
-- bioconductor-bsgenome.hsapiens.ucsc.hg38
-
+  - r-base==4.3.3
+  - r-tidyverse==2.0.0
+  - bioconductor-annotationdbi==1.64.1
+  - bioconductor-bsgenome==1.70.1
+  - bioconductor-genomicranges==1.54.1
+  - bioconductor-org.hs.eg.db==3.18.0
+  - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene==3.2.2
+  - bioconductor-txdb.hsapiens.ucsc.hg38.knowngene==3.18.0
+  - bioconductor-bsgenome.hsapiens.1000genomes.hs37d5==0.99.1
+  - bioconductor-bsgenome.hsapiens.ucsc.hg38==1.4.5
diff --git a/snappy_wrappers/wrappers/copywriter/environment.yaml b/snappy_wrappers/wrappers/copywriter/environment.yaml
@@ -1,23 +1,22 @@
 channels:
-- conda-forge
-- bioconda
-- anaconda
+  - conda-forge
+  - bioconda
 dependencies:
-- r=3.6
-- r-rcpp
-- r-dplyr
-- r-assertthat
-- r-matrixstats
-- bioconductor-copywriter
-- bioconductor-dnacopy
-- bioconductor-cghcall
-- bioconductor-rsamtools
-- bioconductor-org.hs.eg.db
-- bioconductor-ensdb.hsapiens.v75
-- bioconductor-ensdb.hsapiens.v86
-- bioconductor-txdb.hsapiens.ucsc.hg19.knownGene
-- bioconductor-txdb.hsapiens.ucsc.hg38.knownGene
-- bcftools
-- samtools
-- htslib
-- openblas
+  - r-base==3.6
+  - r-rcpp==1.0.6
+  - r-dplyr==1.0.6
+  - r-assertthat==0.2.1
+  - r-matrixstats==0.58.0
+  - bioconductor-copywriter==2.18.0
+  - bioconductor-dnacopy==1.60.0
+  - bioconductor-cghcall==2.48.0
+  - bioconductor-rsamtools==2.2.0
+  - bioconductor-org.hs.eg.db==3.10.0
+  - bioconductor-ensdb.hsapiens.v75==2.99.0
+  - bioconductor-ensdb.hsapiens.v86==2.99.0
+  - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene==3.2.2
+  - bioconductor-txdb.hsapiens.ucsc.hg38.knowngene==3.10.0
+  - bcftools==1.12
+  - samtools==1.12
+  - htslib==1.12
+  - openblas==0.3.12
diff --git a/snappy_wrappers/wrappers/defuse/environment.yaml b/snappy_wrappers/wrappers/defuse/environment.yaml
@@ -1,7 +1,6 @@
 channels:
-- r
+- conda-forge
 - bioconda
 - https://conda.anaconda.org/dranew
-- conda-forge
 dependencies:
 - defuse ==0.8.1