diff --git a/snappy_wrappers/wrappers/alfred/qc/environment.yaml b/snappy_wrappers/wrappers/alfred/qc/environment.yaml index fec06132c..e92e5f777 100644 --- 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 index 98d126cbf..f4b7d6a9f 100644 --- 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 index c65b84579..7c36e1764 100644 --- 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 index 1b174851a..874c1c4e1 100644 --- 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 index ed57a5930..0ee88fbf3 100644 --- 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 index c7edb6027..30ddce518 100644 --- 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 index 9fed6ab48..4833f88ce 100644 --- 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 index 48bdec197..eb9ac5103 100644 --- 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 index 3ba9dbffc..d3dc15af8 100644 --- 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 index a62c85cc9..40c493534 100644 --- 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 index a62c85cc9..c289ec0dd 100644 --- 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 index 1c41f98fa..9467d4b56 100644 --- 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 index 2e413a37a..7fbe872a9 100644 --- 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 index 6af243354..cd6ce8d49 100644 --- 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 index 869a5e0d8..3a1b4df88 100644 --- 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 index 1f257fe3a..c782718b3 100644 --- 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 index 8ffc9cf47..f26c75a5c 100644 --- 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 index 77bc5a498..a054bd4ce 100644 --- 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 index 8ffc9cf47..f26c75a5c 100644 --- 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 index 5b6fd5393..346a15842 100644 --- 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 index 28ebc9a4e..a3fdd89a2 100644 --- 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 index 60d0d7253..5b6b98686 100644 --- 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 index 3e66bf242..3d60ff4ef 100644 --- 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 index fc516f992..6522d81be 100644 --- 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 index e559c6f74..959651cbf 100644 --- 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 diff --git a/snappy_wrappers/wrappers/delly2/germline/environment.yaml b/snappy_wrappers/wrappers/delly2/germline/environment.yaml index 7984a16c1..df54a107b 100644 --- a/snappy_wrappers/wrappers/delly2/germline/environment.yaml +++ b/snappy_wrappers/wrappers/delly2/germline/environment.yaml @@ -1,8 +1,7 @@ channels: -- conda-forge -- bioconda -- r + - conda-forge + - bioconda dependencies: -- bcftools >=1.9 -- htslib >=1.9 -- delly ==1.1.3 + - bcftools==1.19 + - htslib==1.19.1 + - delly==1.1.3 diff --git a/snappy_wrappers/wrappers/delly2/germline_cnv/environment.yaml b/snappy_wrappers/wrappers/delly2/germline_cnv/environment.yaml index 8b7c9b524..df54a107b 100644 --- a/snappy_wrappers/wrappers/delly2/germline_cnv/environment.yaml +++ b/snappy_wrappers/wrappers/delly2/germline_cnv/environment.yaml @@ -1,7 +1,7 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- bcftools >=1.9 -- htslib >=1.9 -- delly ==1.1.3 + - bcftools==1.19 + - htslib==1.19.1 + - delly==1.1.3 diff --git a/snappy_wrappers/wrappers/dupradar/environment.yaml b/snappy_wrappers/wrappers/dupradar/environment.yaml index 6a78d16cf..44b4312a2 100644 --- a/snappy_wrappers/wrappers/dupradar/environment.yaml +++ b/snappy_wrappers/wrappers/dupradar/environment.yaml @@ -1,7 +1,7 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- r -- bioconductor-dupradar -- samtools + - r-base==4.3 + - bioconductor-dupradar==1.32.0 + - samtools==1.19.2 diff --git a/snappy_wrappers/wrappers/eb_filter/environment.yaml b/snappy_wrappers/wrappers/eb_filter/environment.yaml index 3ea57ab34..e6306c146 100644 --- a/snappy_wrappers/wrappers/eb_filter/environment.yaml +++ b/snappy_wrappers/wrappers/eb_filter/environment.yaml @@ -1,12 +1,12 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- ebfilter >=0.2.2 -- vcfpy -- pysam -- scipy -- numpy -- samtools -- htslib -- bcftools + - ebfilter==0.2.2 + - vcfpy==0.13.8 + - pysam==0.22.0 + - scipy==1.12.0 + - numpy==1.26.4 + - samtools==1.19.2 + - htslib==1.19.1 + - bcftools==1.19 diff --git a/snappy_wrappers/wrappers/eb_filter_par/environment.yaml b/snappy_wrappers/wrappers/eb_filter_par/environment.yaml index a8bdc5167..968a8460c 100644 --- a/snappy_wrappers/wrappers/eb_filter_par/environment.yaml +++ b/snappy_wrappers/wrappers/eb_filter_par/environment.yaml @@ -1,16 +1,16 @@ channels: -- conda-forge -- bioconda -- http://conda.cubi.bihealth.org/cubiconda + - conda-forge + - bioconda + - http://conda.cubi.bihealth.org/cubiconda dependencies: -- ebfilter >=0.2.2 -- vcfpy -- pysam -- scipy -- numpy -- bcftools -- htslib -- samtools -- snakemake-minimal -- cffi -- pandas + - ebfilter==0.2.2 + - vcfpy==0.13.8 + - pysam==0.22.0 + - scipy==1.12.0 + - numpy==1.26.4 + - bcftools==1.19 + - htslib==1.19.1 + - samtools==1.19.2 + - snakemake-minimal==7.32.4 + - cffi==1.16.0 + - pandas==2.2.1 diff --git a/snappy_wrappers/wrappers/epitoper/environment.yaml b/snappy_wrappers/wrappers/epitoper/environment.yaml index 1093a3349..8fc7e0b74 100644 --- a/snappy_wrappers/wrappers/epitoper/environment.yaml +++ b/snappy_wrappers/wrappers/epitoper/environment.yaml @@ -1,9 +1,8 @@ channels: -- conda-forge -- bioconda -- r -- http://conda.cubi.bihealth.org/cubiconda/ + - conda-forge + - bioconda + - http://conda.cubi.bihealth.org/cubiconda/ dependencies: -- netmhccons ==1.1a -- epitoper ==0.3 -- blast ==2.6.0 + - netmhccons==1.1a + - epitoper==0.3 + - blast==2.6.0 diff --git a/snappy_wrappers/wrappers/epitoper_par/environment.yaml b/snappy_wrappers/wrappers/epitoper_par/environment.yaml index e634b6887..df05c0a0f 100644 --- a/snappy_wrappers/wrappers/epitoper_par/environment.yaml +++ b/snappy_wrappers/wrappers/epitoper_par/environment.yaml @@ -1,6 +1,5 @@ channels: -- conda-forge -- bioconda -- r + - conda-forge + - bioconda dependencies: -- zlib + - zlib==1.3.1 diff --git a/snappy_wrappers/wrappers/expansionhunter/environment.yaml b/snappy_wrappers/wrappers/expansionhunter/environment.yaml index f1d25cc30..b09355f58 100644 --- a/snappy_wrappers/wrappers/expansionhunter/environment.yaml +++ b/snappy_wrappers/wrappers/expansionhunter/environment.yaml @@ -1,5 +1,4 @@ channels: - bioconda dependencies: - - expansionhunter - + - expansionhunter==3.2.2 diff --git a/snappy_wrappers/wrappers/fastp/environment.yaml b/snappy_wrappers/wrappers/fastp/environment.yaml index fd549dec0..6aa71e0fb 100644 --- a/snappy_wrappers/wrappers/fastp/environment.yaml +++ b/snappy_wrappers/wrappers/fastp/environment.yaml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - fastp + - fastp==0.23.4 diff --git a/snappy_wrappers/wrappers/featurecounts/environment.yaml b/snappy_wrappers/wrappers/featurecounts/environment.yaml index 3458d97ce..d7b126ce3 100644 --- a/snappy_wrappers/wrappers/featurecounts/environment.yaml +++ b/snappy_wrappers/wrappers/featurecounts/environment.yaml @@ -1,6 +1,6 @@ channels: -- bioconda -- conda-forge + - conda-forge + - bioconda dependencies: -- subread ==1.6.0 -- samtools + - subread==1.6.0 + - samtools==1.9 diff --git a/snappy_wrappers/wrappers/flag_oxog_artifacts/environment.yaml b/snappy_wrappers/wrappers/flag_oxog_artifacts/environment.yaml index 8813fdab8..a113a79c0 100644 --- a/snappy_wrappers/wrappers/flag_oxog_artifacts/environment.yaml +++ b/snappy_wrappers/wrappers/flag_oxog_artifacts/environment.yaml @@ -1,7 +1,7 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- bedtools -- bcftools >=1.5 -- htslib >=1.5 + - bedtools==2.31.1 + - bcftools==1.19 + - htslib==1.19.1 diff --git a/snappy_wrappers/wrappers/fusioncatcher/run/environment.yaml b/snappy_wrappers/wrappers/fusioncatcher/run/environment.yaml index 45f64bf22..79c425747 100644 --- a/snappy_wrappers/wrappers/fusioncatcher/run/environment.yaml +++ b/snappy_wrappers/wrappers/fusioncatcher/run/environment.yaml @@ -1,7 +1,6 @@ channels: -- conda-forge -- bioconda -- r + - conda-forge + - bioconda dependencies: -- python =2 -- samtools ==0.1.19 + - python==2.7.15 + - samtools==0.1.19 diff --git a/snappy_wrappers/wrappers/gatk3_ug/environment.yaml b/snappy_wrappers/wrappers/gatk3_ug/environment.yaml index e9550b4d6..952ea9061 100644 --- a/snappy_wrappers/wrappers/gatk3_ug/environment.yaml +++ b/snappy_wrappers/wrappers/gatk3_ug/environment.yaml @@ -2,9 +2,9 @@ channels: - conda-forge - bioconda dependencies: - - gatk =3 - - gatk4 - - bcftools =1.16 - - samtools =1.16 - - htslib =1.16 - - parallel =20221122 + - gatk==3.8 + - gatk4==4.3.0.0 + - bcftools==1.16 + - samtools==1.16.1 + - htslib==1.16 + - parallel==20221122 diff --git a/snappy_wrappers/wrappers/gatk4_hc/environment.yaml b/snappy_wrappers/wrappers/gatk4_hc/environment.yaml index a94ed8f95..97b081f37 100644 --- a/snappy_wrappers/wrappers/gatk4_hc/environment.yaml +++ b/snappy_wrappers/wrappers/gatk4_hc/environment.yaml @@ -2,9 +2,9 @@ channels: - conda-forge - bioconda dependencies: - - gatk4 - - bcftools =1.16 - - samtools =1.16 - - htslib =1.16 - - parallel =20221122 - - picard-slim =2.27 + - gatk4==4.5.0.0 + - bcftools==1.16 + - samtools==1.16.1 + - htslib==1.16 + - parallel==20231122 + - picard-slim==2.27.4 diff --git a/snappy_wrappers/wrappers/gatk_hc_par/environment.yaml b/snappy_wrappers/wrappers/gatk_hc_par/environment.yaml index 6c22525d5..7afb05c3b 100644 --- a/snappy_wrappers/wrappers/gatk_hc_par/environment.yaml +++ b/snappy_wrappers/wrappers/gatk_hc_par/environment.yaml @@ -1,12 +1,11 @@ channels: -- conda-forge -- bioconda -- r -- http://conda.cubi.bihealth.org/cubiconda + - conda-forge + - bioconda + - http://conda.cubi.bihealth.org/cubiconda dependencies: -- gatk_nonfree ==3.7 -- bcftools ==1.12 -- samtools ==1.12 -- htslib ==1.12 -- coincbc -- snakemake-minimal + - gatk_nonfree==3.7 + - bcftools==1.12 + - samtools==1.12 + - htslib==1.12 + - coincbc==2.10.10 + - snakemake-minimal==7.32.4 diff --git a/snappy_wrappers/wrappers/gatk_phase_by_transmission/environment.yaml b/snappy_wrappers/wrappers/gatk_phase_by_transmission/environment.yaml index fd9dced58..ec5322eff 100644 --- a/snappy_wrappers/wrappers/gatk_phase_by_transmission/environment.yaml +++ b/snappy_wrappers/wrappers/gatk_phase_by_transmission/environment.yaml @@ -1,10 +1,9 @@ channels: -- conda-forge -- bioconda -- defaults -- http://conda.cubi.bihealth.org/cubiconda + - conda-forge + - bioconda + - http://conda.cubi.bihealth.org/cubiconda dependencies: -- gatk_nonfree ==3.7 -- bcftools ==1.9 -- samtools ==1.9 -- htslib ==1.9 + - gatk_nonfree==3.7 + - bcftools==1.9 + - samtools==1.9 + - htslib==1.9 diff --git a/snappy_wrappers/wrappers/gatk_read_backed_phasing/environment.yaml b/snappy_wrappers/wrappers/gatk_read_backed_phasing/environment.yaml index fccb453a3..eb83a7db2 100644 --- a/snappy_wrappers/wrappers/gatk_read_backed_phasing/environment.yaml +++ b/snappy_wrappers/wrappers/gatk_read_backed_phasing/environment.yaml @@ -1,11 +1,10 @@ channels: -- conda-forge -- bioconda -- r -- http://conda.cubi.bihealth.org/cubiconda + - conda-forge + - bioconda + - http://conda.cubi.bihealth.org/cubiconda dependencies: -- gatk_nonfree ==3.7 -- bcftools ==1.9 -- samtools ==1.9 -- htslib ==1.9 -- bedtools =2.27.1 + - gatk_nonfree==3.7 + - bcftools==1.9 + - samtools==1.9 + - htslib==1.9 + - bedtools==2.27.1 diff --git a/snappy_wrappers/wrappers/gatk_read_backed_phasing_par/environment.yaml b/snappy_wrappers/wrappers/gatk_read_backed_phasing_par/environment.yaml index fccb453a3..eb83a7db2 100644 --- a/snappy_wrappers/wrappers/gatk_read_backed_phasing_par/environment.yaml +++ b/snappy_wrappers/wrappers/gatk_read_backed_phasing_par/environment.yaml @@ -1,11 +1,10 @@ channels: -- conda-forge -- bioconda -- r -- http://conda.cubi.bihealth.org/cubiconda + - conda-forge + - bioconda + - http://conda.cubi.bihealth.org/cubiconda dependencies: -- gatk_nonfree ==3.7 -- bcftools ==1.9 -- samtools ==1.9 -- htslib ==1.9 -- bedtools =2.27.1 + - gatk_nonfree==3.7 + - bcftools==1.9 + - samtools==1.9 + - htslib==1.9 + - bedtools==2.27.1 diff --git a/snappy_wrappers/wrappers/gatk_ug_par/environment.yaml b/snappy_wrappers/wrappers/gatk_ug_par/environment.yaml index dfcc77db6..1d19b1091 100644 --- a/snappy_wrappers/wrappers/gatk_ug_par/environment.yaml +++ b/snappy_wrappers/wrappers/gatk_ug_par/environment.yaml @@ -1,11 +1,10 @@ channels: -- conda-forge -- bioconda -- r -- http://conda.cubi.bihealth.org/cubiconda + - conda-forge + - bioconda + - http://conda.cubi.bihealth.org/cubiconda dependencies: -- gatk_nonfree ==3.7 -- bcftools >=1.9 -- samtools >=1.9 -- htslib >=1.9 -- coincbc + - gatk_nonfree==3.7 + - bcftools==1.19 + - samtools==1.19.2 + - htslib==1.19.1 + - coincbc==2.10.10 diff --git a/snappy_wrappers/wrappers/gcnv/environment.yaml b/snappy_wrappers/wrappers/gcnv/environment.yaml index ad007789d..beadf2b75 100644 --- a/snappy_wrappers/wrappers/gcnv/environment.yaml +++ b/snappy_wrappers/wrappers/gcnv/environment.yaml @@ -2,41 +2,40 @@ channels: - conda-forge - bioconda dependencies: - - gatk4 ==4.3.0.0 - - bcftools - - htslib - - parallel + - gatk4==4.3.0.0 + - bcftools==1.10.2 + - htslib==1.10.2 + - parallel==20240122 # the hard to install gcnvkernel - - gcnvkernel ==0.8 + - gcnvkernel==0.8 # gcnvkernel dependencies - - conda-forge::python =3.6.10 - - pip =20.0.2 - - conda-forge::mkl =2019.5 - - conda-forge::mkl-service =2.3.0 - - conda-forge::numpy =1.17.5 - - conda-forge::theano =1.0.4 - - tensorflow =1.15.0 - - conda-forge::scipy =1.0.0 - - conda-forge::pymc3 =3.1 - - conda-forge::joblib =1.2.0 - - conda-forge::h5py =2.10.0 - - conda-forge::keras =2.2.4 - - intel-openmp =2019.4 - - conda-forge::scikit-learn =0.23.1 - - conda-forge::matplotlib =3.2.1 - - conda-forge::pandas =1.0.3 - - conda-forge::typing_extensions =4.1.1 - - conda-forge::dill =0.3.4 - - r-base =3.6.2 - - r-data.table =1.12.8 - - r-dplyr =0.8.5 - - r-getopt =1.20.3 - - r-ggplot2 =3.3.0 - - r-gplots =3.0.3 - - r-gsalib =2.1 - - r-optparse =1.6.4 - - r-backports =1.1.10 - - biopython =1.76 - - pyvcf =0.6.8 - - bioconda::pysam =0.15.3 - + - python==3.6.10 + - pip==21.3.1 + - mkl==2019.5 + - mkl-service==2.3.0 + - numpy==1.17.5 + - theano==1.0.4 + - tensorflow==1.10.0 + - scipy==1.0.0 + - pymc3==3.1 + - joblib==1.2.0 + - h5py==2.10.0 + - keras==2.2.4 + - intel-openmp==2022.1.0 + - scikit-learn==0.23.1 + - matplotlib==3.2.1 + - pandas==1.0.3 + - typing_extensions==4.1.1 + - dill==0.3.4 + - r-base==3.6.2 + - r-data.table==1.12.8 + - r-dplyr==0.8.5 + - r-getopt==1.20.3 + - r-ggplot2==3.3.0 + - r-gplots==3.0.3 + - r-gsalib==2.1 + - r-optparse==1.6.4 + - r-backports==1.1.10 + - biopython==1.76 + - pyvcf==0.6.8 + - pysam==0.15.3 diff --git a/snappy_wrappers/wrappers/gcnv/merge_multikit_families/environment.yaml b/snappy_wrappers/wrappers/gcnv/merge_multikit_families/environment.yaml index f4f8acb6e..6ff5c6d80 100644 --- a/snappy_wrappers/wrappers/gcnv/merge_multikit_families/environment.yaml +++ b/snappy_wrappers/wrappers/gcnv/merge_multikit_families/environment.yaml @@ -2,10 +2,10 @@ channels: - conda-forge - bioconda dependencies: - - attrs - - logzero - - ncls - - pandas - - vcfpy - - htslib - - python=3.10 + - attrs==23.2.0 + - logzero==1.7.0 + - ncls==0.0.68 + - pandas==2.2.1 + - vcfpy==0.13.8 + - htslib==1.19.1 + - python==3.10.14 diff --git a/snappy_wrappers/wrappers/hts_screen/environment.yaml b/snappy_wrappers/wrappers/hts_screen/environment.yaml index 8b2688fa4..f4a84f984 100644 --- a/snappy_wrappers/wrappers/hts_screen/environment.yaml +++ b/snappy_wrappers/wrappers/hts_screen/environment.yaml @@ -1,9 +1,8 @@ channels: -- conda-forge -- bioconda -- r + - conda-forge + - bioconda dependencies: -- bwa -- seqtk -- kraken -- gawk + - bwa==0.7.17 + - seqtk==1.4 + - kraken==1.1.1 + - gawk==5.3.0 diff --git a/snappy_wrappers/wrappers/jaffa/run/environment.yaml b/snappy_wrappers/wrappers/jaffa/run/environment.yaml index ada9290d5..7eeb456ad 100644 --- a/snappy_wrappers/wrappers/jaffa/run/environment.yaml +++ b/snappy_wrappers/wrappers/jaffa/run/environment.yaml @@ -2,6 +2,6 @@ channels: - conda-forge - bioconda dependencies: -- jaffa ==1.09 -- r-base ==3.3.2 -- htslib +- jaffa==1.09 +- r-base==4.2.2 +- htslib==1.17 diff --git a/snappy_wrappers/wrappers/jannovar/environment.yaml b/snappy_wrappers/wrappers/jannovar/environment.yaml index 4794f794e..6c1a26b2b 100644 --- a/snappy_wrappers/wrappers/jannovar/environment.yaml +++ b/snappy_wrappers/wrappers/jannovar/environment.yaml @@ -1,12 +1,10 @@ channels: -- conda-forge -- bioconda -- r + - conda-forge + - bioconda dependencies: -- bcftools ==1.12 -- htslib ==1.12 -- jannovar-cli ==0.34 -- snakemake-minimal -- ruamel -- ruamel.yaml - + - bcftools==1.12 + - htslib==1.12 + - jannovar-cli==0.34 + - snakemake-minimal==8.9.0 + - ruamel==1.0 + - ruamel.yaml==0.18.6 diff --git a/snappy_wrappers/wrappers/jannovar/statistics/environment.yaml b/snappy_wrappers/wrappers/jannovar/statistics/environment.yaml index 84b127697..6d0041060 100644 --- a/snappy_wrappers/wrappers/jannovar/statistics/environment.yaml +++ b/snappy_wrappers/wrappers/jannovar/statistics/environment.yaml @@ -1,7 +1,6 @@ channels: - conda-forge - bioconda -- r dependencies: - jannovar-cli ==0.33 - htslib ==1.8 diff --git a/snappy_wrappers/wrappers/link_in_bam/environment.yaml b/snappy_wrappers/wrappers/link_in_bam/environment.yaml index 1030d1b4d..e2cda9117 100644 --- a/snappy_wrappers/wrappers/link_in_bam/environment.yaml +++ b/snappy_wrappers/wrappers/link_in_bam/environment.yaml @@ -1,8 +1,7 @@ channels: - conda-forge - bioconda - - r dependencies: - - samtools =1.5 - - gnuplot ==5.0.5 - - libpng ==1.6.28 + - samtools ==1.19.2 + - gnuplot ==5.4.8 + - libpng ==1.6.43 diff --git a/snappy_wrappers/wrappers/lohhla/environment.yaml b/snappy_wrappers/wrappers/lohhla/environment.yaml index 2c367b162..2c1109d11 100644 --- a/snappy_wrappers/wrappers/lohhla/environment.yaml +++ b/snappy_wrappers/wrappers/lohhla/environment.yaml @@ -1,7 +1,6 @@ channels: -- conda-forge -- anaconda -- bioconda + - conda-forge + - bioconda dependencies: -- lohhla -- jellyfish ==2.2.6 + - lohhla==20171108 + - kmer-jellyfish==2.3.1 diff --git a/snappy_wrappers/wrappers/maelstrom/environment.yaml b/snappy_wrappers/wrappers/maelstrom/environment.yaml index d468acd8f..74328c8d4 100644 --- a/snappy_wrappers/wrappers/maelstrom/environment.yaml +++ b/snappy_wrappers/wrappers/maelstrom/environment.yaml @@ -1,7 +1,6 @@ channels: - conda-forge - bioconda -- r dependencies: - bcftools ==1.12 - samtools ==1.12 diff --git a/snappy_wrappers/wrappers/manta/germline_wgs/environment.yaml b/snappy_wrappers/wrappers/manta/germline_wgs/environment.yaml index 28de1836d..014b555a5 100644 --- a/snappy_wrappers/wrappers/manta/germline_wgs/environment.yaml +++ b/snappy_wrappers/wrappers/manta/germline_wgs/environment.yaml @@ -1,7 +1,6 @@ channels: -- conda-forge -- bioconda -- r + - conda-forge + - bioconda dependencies: -- manta ==1.6.0 -- samtools ==1.9.0 + - manta==1.6.0 + - samtools==1.9 diff --git a/snappy_wrappers/wrappers/manta/somatic_wgs/environment.yaml b/snappy_wrappers/wrappers/manta/somatic_wgs/environment.yaml index 0deb7c7a5..7ea2d4319 100644 --- a/snappy_wrappers/wrappers/manta/somatic_wgs/environment.yaml +++ b/snappy_wrappers/wrappers/manta/somatic_wgs/environment.yaml @@ -1,6 +1,5 @@ channels: -- conda-forge -- bioconda -- r + - conda-forge + - bioconda dependencies: -- manta ==1.5.0 + - manta==1.5.0 diff --git a/snappy_wrappers/wrappers/mbcs/environment.yaml b/snappy_wrappers/wrappers/mbcs/environment.yaml index b8e195dec..e08f88778 100644 --- a/snappy_wrappers/wrappers/mbcs/environment.yaml +++ b/snappy_wrappers/wrappers/mbcs/environment.yaml @@ -1,16 +1,15 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- cffi -- pandas -- numpy -- snakemake-minimal ==7.32.4 -- openjdk =17 -- seqtk -- samtools -- bwa-mem2 ==2.2.1 -- gatk4 -- trimadap -- samblaster - + - cffi==1.16.0 + - pandas==2.2.1 + - numpy==1.26.4 + - snakemake-minimal==7.32.4 + - openjdk==17.0.10 + - seqtk==1.4 + - samtools==1.19 + - bwa-mem2==2.2.1 + - gatk4==4.5.0.0 + - trimadap==r11 + - samblaster==0.1.26 diff --git a/snappy_wrappers/wrappers/mehari/environment.yaml b/snappy_wrappers/wrappers/mehari/environment.yaml index f77f715c7..1682b165a 100644 --- a/snappy_wrappers/wrappers/mehari/environment.yaml +++ b/snappy_wrappers/wrappers/mehari/environment.yaml @@ -2,10 +2,10 @@ channels: - conda-forge - bioconda dependencies: - - bcftools >=1.9 - - htslib >=1.9 - - samtools >=1.9 - - mehari ==0.21.1 - - jq - - vcfpy - - pysam + - bcftools==1.19 + - htslib==1.19.1 + - samtools==1.19.2 + - mehari==0.21.1 + - jq==1.7.1 + - vcfpy==0.13.8 + - pysam==0.22.0 diff --git a/snappy_wrappers/wrappers/melt/environment.yaml b/snappy_wrappers/wrappers/melt/environment.yaml index 4e2a951e0..be92d8f89 100644 --- a/snappy_wrappers/wrappers/melt/environment.yaml +++ b/snappy_wrappers/wrappers/melt/environment.yaml @@ -2,9 +2,9 @@ channels: - conda-forge - bioconda dependencies: - - htslib =1.16 - - bcftools =1.16 - - samtools =1.16 - - perl - - bowtie2 - - openjdk + - htslib==1.16 + - bcftools==1.16 + - samtools==1.16.1 + - perl==5.32.1 + - bowtie2==2.5.3 + - openjdk==21.0.2 diff --git a/snappy_wrappers/wrappers/minialign/run/environment.yaml b/snappy_wrappers/wrappers/minialign/run/environment.yaml index 8bcdd0ddb..fcf757ba1 100644 --- a/snappy_wrappers/wrappers/minialign/run/environment.yaml +++ b/snappy_wrappers/wrappers/minialign/run/environment.yaml @@ -1,10 +1,9 @@ channels: -- conda-forge -- bioconda -- r -- http://conda.cubi.bihealth.org/cubiconda + - conda-forge + - bioconda + - http://conda.cubi.bihealth.org/cubiconda dependencies: -- minialign ==0.5.3 -- samtools ==1.9 -- htslib ==1.9 -- inline-html ==0.1.2 + - minialign==0.5.3 + - samtools==1.9 + - htslib==1.9 + - inline-html==0.1.2 diff --git a/snappy_wrappers/wrappers/minimap2/environment.yaml b/snappy_wrappers/wrappers/minimap2/environment.yaml index 6d0e6d757..aec7afcc3 100644 --- a/snappy_wrappers/wrappers/minimap2/environment.yaml +++ b/snappy_wrappers/wrappers/minimap2/environment.yaml @@ -1,8 +1,7 @@ channels: - conda-forge - bioconda - - defaults dependencies: - - minimap2 ==2.24 - - samtools ==1.9 - - htslib ==1.9 + - minimap2==2.24 + - samtools==1.9 + - htslib==1.9 diff --git a/snappy_wrappers/wrappers/mutect/environment.yaml b/snappy_wrappers/wrappers/mutect/environment.yaml index 1b7a906ab..d9bee5aff 100644 --- a/snappy_wrappers/wrappers/mutect/environment.yaml +++ b/snappy_wrappers/wrappers/mutect/environment.yaml @@ -1,9 +1,8 @@ channels: -- conda-forge -- bioconda -- r -- http://conda.cubi.bihealth.org/cubiconda + - conda-forge + - bioconda + - http://conda.cubi.bihealth.org/cubiconda dependencies: -- mutect_nonfree ==1.1.7 -- htslib >=1.9 -- bcftools >=1.9 + - mutect_nonfree==1.1.7 + - htslib==1.19.1 + - bcftools==1.19 diff --git a/snappy_wrappers/wrappers/mutect2/environment.yaml b/snappy_wrappers/wrappers/mutect2/environment.yaml index 8b4834863..a74188fee 100644 --- a/snappy_wrappers/wrappers/mutect2/environment.yaml +++ b/snappy_wrappers/wrappers/mutect2/environment.yaml @@ -1,17 +1,18 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- python =3.9 -- gatk4 =4.3 -- htslib >=1.9 -- bcftools >=1.9 -- datrie -- gawk =5.1 -# snakemake needed by the parallel wrapper -- snakemake-minimal =7 -# needed by snakemake -- cffi -- numpy -- pandas + - python==3.9.19 + - gatk4==4.3.0.0 + - htslib==1.19.1 + - bcftools==1.19 + - datrie==0.8.2 + - gawk==5.1.0 + # snakemake needed by the parallel wrapper + - snakemake-minimal==7.32.4 + # needed by snakemake + - cffi==1.16.0 + - numpy==1.26.4 + - pandas==2.2.1 + diff --git a/snappy_wrappers/wrappers/ngs_chew/fingerprint/environment.yaml b/snappy_wrappers/wrappers/ngs_chew/fingerprint/environment.yaml index a0ee9d084..e1f68c6d5 100644 --- a/snappy_wrappers/wrappers/ngs_chew/fingerprint/environment.yaml +++ b/snappy_wrappers/wrappers/ngs_chew/fingerprint/environment.yaml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - ngs-chew >=0.9.0,<0.10.0 + - ngs-chew==0.9.4 diff --git a/snappy_wrappers/wrappers/optitype/environment.yaml b/snappy_wrappers/wrappers/optitype/environment.yaml index 3a33a1c97..cf2902755 100644 --- a/snappy_wrappers/wrappers/optitype/environment.yaml +++ b/snappy_wrappers/wrappers/optitype/environment.yaml @@ -2,8 +2,8 @@ channels: - conda-forge - bioconda dependencies: - - samtools - - seqtk ==1.3 - - samtools - - yara - - optitype + - samtools==1.19.2 + - seqtk==1.3 + - samtools==1.19.2 + - yara==1.0.2 + - optitype==1.3.5 diff --git a/snappy_wrappers/wrappers/peddy/run/environment.yaml b/snappy_wrappers/wrappers/peddy/run/environment.yaml index e0f1bc787..9c19eb13b 100644 --- a/snappy_wrappers/wrappers/peddy/run/environment.yaml +++ b/snappy_wrappers/wrappers/peddy/run/environment.yaml @@ -1,5 +1,5 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- peddy ==0.4.8 + - peddy==0.4.8 diff --git a/snappy_wrappers/wrappers/picard/environment.yaml b/snappy_wrappers/wrappers/picard/environment.yaml index 758c031e7..8b2eeb888 100644 --- a/snappy_wrappers/wrappers/picard/environment.yaml +++ b/snappy_wrappers/wrappers/picard/environment.yaml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - picard - - bedtools + - picard==3.1.1 + - bedtools==2.31.1 diff --git a/snappy_wrappers/wrappers/platypus/call_joint/environment.yaml b/snappy_wrappers/wrappers/platypus/call_joint/environment.yaml index 06f44457c..feec36d48 100644 --- a/snappy_wrappers/wrappers/platypus/call_joint/environment.yaml +++ b/snappy_wrappers/wrappers/platypus/call_joint/environment.yaml @@ -1,7 +1,7 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- python =2 -- platypus-variant ==0.8.1.1 -- htslib ==1.5 + - python==2.7.15 + - platypus-variant==0.8.1.1 + - htslib==1.5 diff --git a/snappy_wrappers/wrappers/popdel/environment.yaml b/snappy_wrappers/wrappers/popdel/environment.yaml index 46e58dc1b..e60378bd4 100644 --- a/snappy_wrappers/wrappers/popdel/environment.yaml +++ b/snappy_wrappers/wrappers/popdel/environment.yaml @@ -1,9 +1,8 @@ channels: -- conda-forge -- bioconda -- r + - conda-forge + - bioconda dependencies: -- popdel ==1.1.2 -- htslib >=1.9 -- bcftools >=1.9 -- samtools >=1.9 + - popdel==1.1.2 + - htslib==1.19.1 + - bcftools==1.19 + - samtools==1.19.2 diff --git a/snappy_wrappers/wrappers/purecn/environment.yaml b/snappy_wrappers/wrappers/purecn/environment.yaml index 514a8220e..ce385084a 100644 --- a/snappy_wrappers/wrappers/purecn/environment.yaml +++ b/snappy_wrappers/wrappers/purecn/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - - bioconda + - conda-forge + - bioconda dependencies: - - htslib + - htslib==1.19.1 diff --git a/snappy_wrappers/wrappers/r/environment.yaml b/snappy_wrappers/wrappers/r/environment.yaml index 20218ccdf..75aa14a02 100644 --- a/snappy_wrappers/wrappers/r/environment.yaml +++ b/snappy_wrappers/wrappers/r/environment.yaml @@ -1,7 +1,7 @@ channels: - - conda-forge - - bioconda + - conda-forge + - bioconda dependencies: - - r-base - - r-remotes - - r-biocmanager \ No newline at end of file + - r-base==4.3.3 + - r-remotes==2.5.0 + - r-biocmanager==1.30.22 diff --git a/snappy_wrappers/wrappers/rnaqc/duplication/environment.yaml b/snappy_wrappers/wrappers/rnaqc/duplication/environment.yaml index 2bdb4ca75..025ff75c0 100644 --- a/snappy_wrappers/wrappers/rnaqc/duplication/environment.yaml +++ b/snappy_wrappers/wrappers/rnaqc/duplication/environment.yaml @@ -1,6 +1,6 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- samtools -- rseqc + - samtools==1.19.2 + - rseqc==5.0.3 diff --git a/snappy_wrappers/wrappers/rnaqc/dupradar/environment.yaml b/snappy_wrappers/wrappers/rnaqc/dupradar/environment.yaml index 7f6aa9fc7..fdbeb3288 100644 --- a/snappy_wrappers/wrappers/rnaqc/dupradar/environment.yaml +++ b/snappy_wrappers/wrappers/rnaqc/dupradar/environment.yaml @@ -1,8 +1,8 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- samtools -- r -- bioconductor-dupradar -- freetype=2.9.1 + - samtools==1.12 + - r-base==4.0 + - bioconductor-dupradar==1.20.0 + - freetype==2.9.1 diff --git a/snappy_wrappers/wrappers/rnaqc/environment.yaml b/snappy_wrappers/wrappers/rnaqc/environment.yaml index 6d7c5e1ad..f4e627ad0 100644 --- a/snappy_wrappers/wrappers/rnaqc/environment.yaml +++ b/snappy_wrappers/wrappers/rnaqc/environment.yaml @@ -1,11 +1,11 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- r -- bioconductor-dupradar -- samtools -- rna-seqc ==1.1.8 -- openjdk=7 -- rseqc -- freetype=2.9.1 + - r-base==4.0 + - bioconductor-dupradar==1.20.0 + - samtools==1.12 + - rna-seqc==1.1.8 + - openjdk==7.0.161 + - rseqc==5.0.3 + - freetype==2.9.1 diff --git a/snappy_wrappers/wrappers/rnaqc/rnaseqc/environment.yaml b/snappy_wrappers/wrappers/rnaqc/rnaseqc/environment.yaml index c8a4bdd82..fa1bb6d2e 100644 --- a/snappy_wrappers/wrappers/rnaqc/rnaseqc/environment.yaml +++ b/snappy_wrappers/wrappers/rnaqc/rnaseqc/environment.yaml @@ -1,7 +1,7 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- samtools -- rna-seqc ==1.1.8 -- openjdk=7 + - samtools==1.19.2 + - rna-seqc==1.1.8 + - openjdk==7.0.161 diff --git a/snappy_wrappers/wrappers/rnaqc/stats/environment.yaml b/snappy_wrappers/wrappers/rnaqc/stats/environment.yaml index 2a5049a4c..9f3a8ebde 100644 --- a/snappy_wrappers/wrappers/rnaqc/stats/environment.yaml +++ b/snappy_wrappers/wrappers/rnaqc/stats/environment.yaml @@ -1,5 +1,5 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- samtools + - samtools==1.19.2 diff --git a/snappy_wrappers/wrappers/rseqc/environment.yaml b/snappy_wrappers/wrappers/rseqc/environment.yaml index fdcfcf759..c0331ee34 100644 --- a/snappy_wrappers/wrappers/rseqc/environment.yaml +++ b/snappy_wrappers/wrappers/rseqc/environment.yaml @@ -1,4 +1,4 @@ channels: -- bioconda + - bioconda dependencies: -- rseqc + - rseqc==5.0.3 diff --git a/snappy_wrappers/wrappers/salmon/environment.yaml b/snappy_wrappers/wrappers/salmon/environment.yaml index ad6c4264f..d9402f561 100644 --- a/snappy_wrappers/wrappers/salmon/environment.yaml +++ b/snappy_wrappers/wrappers/salmon/environment.yaml @@ -1,5 +1,5 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- salmon + - salmon==1.10.3 diff --git a/snappy_wrappers/wrappers/samtools/bam_qc_report/environment.yaml b/snappy_wrappers/wrappers/samtools/bam_qc_report/environment.yaml index 56c76e8ac..f0b39d21f 100644 --- a/snappy_wrappers/wrappers/samtools/bam_qc_report/environment.yaml +++ b/snappy_wrappers/wrappers/samtools/bam_qc_report/environment.yaml @@ -2,8 +2,7 @@ channels: - conda-forge - bioconda dependencies: - - samtools ==1.9 + - samtools==1.9 # NB: gnuplot 5.2.7 is incompatible with samtools ==1.9 # see https://github.com/samtools/samtools/issues/1065 - - gnuplot ==5.2.6 - + - gnuplot==5.2.6 diff --git a/snappy_wrappers/wrappers/scalpel/somatic/environment.yaml b/snappy_wrappers/wrappers/scalpel/somatic/environment.yaml index 6b33c2f2d..04af996c4 100644 --- a/snappy_wrappers/wrappers/scalpel/somatic/environment.yaml +++ b/snappy_wrappers/wrappers/scalpel/somatic/environment.yaml @@ -1,8 +1,7 @@ channels: -- conda-forge -- bioconda -- r + - conda-forge + - bioconda dependencies: -- scalpel ==0.5.3 -- htslib >=1.3 -- bcftools >=1.3 + - scalpel==0.5.3 + - htslib==1.15.1 + - bcftools==1.15.1 diff --git a/snappy_wrappers/wrappers/scarHRD/environment.yaml b/snappy_wrappers/wrappers/scarHRD/environment.yaml index cc9110d4d..cf6ab1250 100644 --- a/snappy_wrappers/wrappers/scarHRD/environment.yaml +++ b/snappy_wrappers/wrappers/scarHRD/environment.yaml @@ -2,18 +2,18 @@ channels: - conda-forge - bioconda dependencies: - - python =3.9 - - r-base - - r-remotes + - python==3.9.19 + - r-base==4.3.3 + - r-remotes==2.5.0 # scarHRD requirements (+sequenza) - - r-data.table + - r-data.table==1.15.2 # sequenza requirements (+copynumber) - - r-pbapply - - r-squash - - r-iotools ==0.3-2 # See https://groups.google.com/g/sequenza-user-group/c/UA5bBNBeN18?pli=1 - - r-readr - - r-seqminer + - r-pbapply==1.7_2 + - r-squash==1.0.9 + - r-iotools==0.3_2 # See https://groups.google.com/g/sequenza-user-group/c/UA5bBNBeN18?pli=1 + - r-readr==2.1.5 + - r-seqminer==9.4 # copynumber requirements - - bioconductor-S4Vectors - - bioconductor-IRanges - - bioconductor-GenomicRanges + - bioconductor-s4vectors==0.40.2 + - bioconductor-iranges==2.36.0 + - bioconductor-genomicranges==1.54.1 diff --git a/snappy_wrappers/wrappers/scramble/environment.yaml b/snappy_wrappers/wrappers/scramble/environment.yaml index 92063a2c6..b869b32dc 100644 --- a/snappy_wrappers/wrappers/scramble/environment.yaml +++ b/snappy_wrappers/wrappers/scramble/environment.yaml @@ -1,6 +1,7 @@ channels: + - conda-forge - bioconda dependencies: - - scramble >=1.0.2 - - bcftools ==1.15.1 - - htslib ==1.15.1 + - scramble==1.0.2 + - bcftools==1.15.1 + - htslib==1.15.1 diff --git a/snappy_wrappers/wrappers/sequenza/gcreference/environment.yaml b/snappy_wrappers/wrappers/sequenza/gcreference/environment.yaml index 72d44247a..fca8893f0 100644 --- a/snappy_wrappers/wrappers/sequenza/gcreference/environment.yaml +++ b/snappy_wrappers/wrappers/sequenza/gcreference/environment.yaml @@ -2,6 +2,6 @@ channels: - conda-forge - bioconda dependencies: - - python =3.9 - - sequenza-utils - - samtools + - python==3.9.19 + - sequenza-utils==3.0.0 + - samtools==1.19.2 diff --git a/snappy_wrappers/wrappers/sequenza/install/environment.yaml b/snappy_wrappers/wrappers/sequenza/install/environment.yaml index ccadc06d7..f323cc3b6 100644 --- a/snappy_wrappers/wrappers/sequenza/install/environment.yaml +++ b/snappy_wrappers/wrappers/sequenza/install/environment.yaml @@ -2,17 +2,17 @@ channels: - conda-forge - bioconda dependencies: - - python =3.9 - - r-base - - r-remotes + - python==3.9.19 + - r-base==4.3.3 + - r-remotes==2.5.0 # sequenza requirements (+copynumber) - - r-pbapply - - r-squash - - r-iotools ==0.3-2 # See https://groups.google.com/g/sequenza-user-group/c/UA5bBNBeN18?pli=1 - - r-readr - - r-seqminer - - r-data.table + - r-pbapply==1.7_2 + - r-squash==1.0.9 + - r-iotools==0.3_2 # See https://groups.google.com/g/sequenza-user-group/c/UA5bBNBeN18?pli=1 + - r-readr==2.1.5 + - r-seqminer==9.4 + - r-data.table==1.15.2 # copynumber requirements - - bioconductor-S4Vectors - - bioconductor-IRanges - - bioconductor-GenomicRanges + - bioconductor-s4vectors==0.40.2 + - bioconductor-iranges==2.36.0 + - bioconductor-genomicranges==1.54.1 diff --git a/snappy_wrappers/wrappers/signatures/deconstruct_sigs/environment.yaml b/snappy_wrappers/wrappers/signatures/deconstruct_sigs/environment.yaml index 9a7d26784..62640ee60 100644 --- a/snappy_wrappers/wrappers/signatures/deconstruct_sigs/environment.yaml +++ b/snappy_wrappers/wrappers/signatures/deconstruct_sigs/environment.yaml @@ -1,10 +1,9 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- r #==3.2.2 -- r-tidyverse -- r-deconstructsigs -- bioconductor-bsgenome.hsapiens.ucsc.hg19 -- openblas - + - r-base==4.3 + - r-tidyverse==2.0.0 + - r-deconstructsigs==1.9.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg19==1.4.3 + - openblas==0.3.26 diff --git a/snappy_wrappers/wrappers/singularity/environment.yaml b/snappy_wrappers/wrappers/singularity/environment.yaml index 894ebc8c5..e2a10049a 100644 --- a/snappy_wrappers/wrappers/singularity/environment.yaml +++ b/snappy_wrappers/wrappers/singularity/environment.yaml @@ -1,2 +1,2 @@ dependencies: - - python + - python==3.12.2 diff --git a/snappy_wrappers/wrappers/sniffles2/germline/environment.yaml b/snappy_wrappers/wrappers/sniffles2/germline/environment.yaml index e114bdd8c..e2950bd70 100644 --- a/snappy_wrappers/wrappers/sniffles2/germline/environment.yaml +++ b/snappy_wrappers/wrappers/sniffles2/germline/environment.yaml @@ -2,6 +2,6 @@ channels: - conda-forge - bioconda dependencies: - - sniffles >=2.0,<3 - - htslib ==1.16 - - bcftools ==1.16 + - sniffles==2.2 + - htslib==1.16 + - bcftools==1.16 diff --git a/snappy_wrappers/wrappers/somatic_cnv_checking/environment.yaml b/snappy_wrappers/wrappers/somatic_cnv_checking/environment.yaml index 6421a7e1b..ec13031f3 100644 --- a/snappy_wrappers/wrappers/somatic_cnv_checking/environment.yaml +++ b/snappy_wrappers/wrappers/somatic_cnv_checking/environment.yaml @@ -1,9 +1,9 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- r-base -- r-dplyr -- r-ggplot2 -- bioconductor-variantannotation -- bioconductor-biostrings + - r-base==4.3.3 + - r-dplyr==1.1.4 + - r-ggplot2==3.5.0 + - bioconductor-variantannotation==1.48.1 + - bioconductor-biostrings==2.70.1 diff --git a/snappy_wrappers/wrappers/somatic_variant_filtration/apply_all_filters/environment.yaml b/snappy_wrappers/wrappers/somatic_variant_filtration/apply_all_filters/environment.yaml index ce90936e0..038715618 100644 --- a/snappy_wrappers/wrappers/somatic_variant_filtration/apply_all_filters/environment.yaml +++ b/snappy_wrappers/wrappers/somatic_variant_filtration/apply_all_filters/environment.yaml @@ -1,6 +1,6 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- htslib -- bcftools + - htslib==1.19.1 + - bcftools==1.19 diff --git a/snappy_wrappers/wrappers/somatic_variant_filtration/apply_filters/environment.yaml b/snappy_wrappers/wrappers/somatic_variant_filtration/apply_filters/environment.yaml index ce90936e0..038715618 100644 --- a/snappy_wrappers/wrappers/somatic_variant_filtration/apply_filters/environment.yaml +++ b/snappy_wrappers/wrappers/somatic_variant_filtration/apply_filters/environment.yaml @@ -1,6 +1,6 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- htslib -- bcftools + - htslib==1.19.1 + - bcftools==1.19 diff --git a/snappy_wrappers/wrappers/somatic_variant_filtration/filter_to_exons/environment.yaml b/snappy_wrappers/wrappers/somatic_variant_filtration/filter_to_exons/environment.yaml index 6a43a7465..233f2cc55 100644 --- a/snappy_wrappers/wrappers/somatic_variant_filtration/filter_to_exons/environment.yaml +++ b/snappy_wrappers/wrappers/somatic_variant_filtration/filter_to_exons/environment.yaml @@ -1,6 +1,6 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- htslib ==1.5 -- bedtools ==2.26.0 + - htslib==1.5 + - bedtools==2.26.0 diff --git a/snappy_wrappers/wrappers/star_fusion/environment.yaml b/snappy_wrappers/wrappers/star_fusion/environment.yaml index 1d78ac401..28886e1fc 100644 --- a/snappy_wrappers/wrappers/star_fusion/environment.yaml +++ b/snappy_wrappers/wrappers/star_fusion/environment.yaml @@ -1,6 +1,6 @@ channels: -- bioconda -- conda-forge + - conda-forge + - bioconda dependencies: -- star-fusion ==1.0 -- samtools >=1.0 + - star-fusion==1.0.0 + - samtools==1.9 diff --git a/snappy_wrappers/wrappers/strelka2/environment.yaml b/snappy_wrappers/wrappers/strelka2/environment.yaml index 016a93c28..2dca7cbb0 100644 --- a/snappy_wrappers/wrappers/strelka2/environment.yaml +++ b/snappy_wrappers/wrappers/strelka2/environment.yaml @@ -1,8 +1,8 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- manta -- strelka -- htslib -- bcftools + - manta==1.6.0 + - strelka==2.9.10 + - htslib==1.17 + - bcftools==1.17 diff --git a/snappy_wrappers/wrappers/svtk/environment.yaml b/snappy_wrappers/wrappers/svtk/environment.yaml index 3063a8cbb..01c155a34 100644 --- a/snappy_wrappers/wrappers/svtk/environment.yaml +++ b/snappy_wrappers/wrappers/svtk/environment.yaml @@ -1,7 +1,7 @@ channels: - - bioconda - conda-forge + - bioconda dependencies: - - svtk - - bcftools - - htslib + - svtk==0.0.20190615 + - bcftools==1.19 + - htslib==1.19.1 diff --git a/snappy_wrappers/wrappers/varfish_annotator/environment.yaml b/snappy_wrappers/wrappers/varfish_annotator/environment.yaml index f01133f66..a2804d69e 100644 --- a/snappy_wrappers/wrappers/varfish_annotator/environment.yaml +++ b/snappy_wrappers/wrappers/varfish_annotator/environment.yaml @@ -2,11 +2,11 @@ channels: - conda-forge - bioconda dependencies: - - bcftools >=1.9 - - htslib >=1.9 - - samtools >=1.9 - - varfish-annotator-cli ==0.32 - - openjdk >=8,<9 - - jq - - vcfpy - - pysam + - bcftools==1.19 + - htslib==1.19.1 + - samtools==1.19.2 + - varfish-annotator-cli==0.32 + - openjdk==8.0.382 + - jq==1.7.1 + - vcfpy==0.13.8 + - pysam==0.22.0 diff --git a/snappy_wrappers/wrappers/variant_filtration/collect_msdn/environment.yaml b/snappy_wrappers/wrappers/variant_filtration/collect_msdn/environment.yaml index b07bda0f4..46bf5a9fa 100644 --- a/snappy_wrappers/wrappers/variant_filtration/collect_msdn/environment.yaml +++ b/snappy_wrappers/wrappers/variant_filtration/collect_msdn/environment.yaml @@ -1,5 +1,5 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- htslib ==1.5 + - htslib==1.5 diff --git a/snappy_wrappers/wrappers/variant_filtration/environment.yaml b/snappy_wrappers/wrappers/variant_filtration/environment.yaml index 58ca2870c..d4e506a99 100644 --- a/snappy_wrappers/wrappers/variant_filtration/environment.yaml +++ b/snappy_wrappers/wrappers/variant_filtration/environment.yaml @@ -1,7 +1,7 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- bcftools =1.9 -- htslib =1.9 -- bedtools ==2.27.0 + - bcftools==1.9 + - htslib==1.9 + - bedtools==2.27.0 diff --git a/snappy_wrappers/wrappers/variant_filtration/filter_denovo/environment.yaml b/snappy_wrappers/wrappers/variant_filtration/filter_denovo/environment.yaml index c42560410..ce385084a 100644 --- a/snappy_wrappers/wrappers/variant_filtration/filter_denovo/environment.yaml +++ b/snappy_wrappers/wrappers/variant_filtration/filter_denovo/environment.yaml @@ -1,5 +1,5 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- htslib + - htslib==1.19.1 diff --git a/snappy_wrappers/wrappers/variant_filtration/filter_denovo_hard/environment.yaml b/snappy_wrappers/wrappers/variant_filtration/filter_denovo_hard/environment.yaml index 589c54197..d025c3e14 100644 --- a/snappy_wrappers/wrappers/variant_filtration/filter_denovo_hard/environment.yaml +++ b/snappy_wrappers/wrappers/variant_filtration/filter_denovo_hard/environment.yaml @@ -1,9 +1,9 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- python >=3.6 -- htslib ==1.9 -- bcftools ==1.9 -- pysam >=0.14.0 -- vcfpy >=0.11.0 + - python==3.10.8 + - htslib==1.9 + - bcftools==1.9 + - pysam==0.21.0 + - vcfpy==0.13.8 diff --git a/snappy_wrappers/wrappers/variant_filtration/summarize_counts/environment.yaml b/snappy_wrappers/wrappers/variant_filtration/summarize_counts/environment.yaml index b07bda0f4..46bf5a9fa 100644 --- a/snappy_wrappers/wrappers/variant_filtration/summarize_counts/environment.yaml +++ b/snappy_wrappers/wrappers/variant_filtration/summarize_counts/environment.yaml @@ -1,5 +1,5 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- htslib ==1.5 + - htslib==1.5 diff --git a/snappy_wrappers/wrappers/vcf2maf/vcf2maf/environment.yaml b/snappy_wrappers/wrappers/vcf2maf/vcf2maf/environment.yaml index e6b17c8bc..5b8b253c5 100644 --- a/snappy_wrappers/wrappers/vcf2maf/vcf2maf/environment.yaml +++ b/snappy_wrappers/wrappers/vcf2maf/vcf2maf/environment.yaml @@ -1,9 +1,9 @@ channels: -- bioconda -- conda-forge + - conda-forge + - bioconda dependencies: -- vcf2maf ==1.6.18 -- ensembl-vep =100 -- samtools -- htslib -- bcftools =1.9 + - vcf2maf==1.6.18 + - ensembl-vep==100.4 + - samtools==1.9 + - htslib==1.9 + - bcftools==1.9 diff --git a/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/environment.yaml b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/environment.yaml index 794d134f1..5dcfac91f 100644 --- a/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/environment.yaml +++ b/snappy_wrappers/wrappers/vcf2maf/vcf_to_table/environment.yaml @@ -3,6 +3,6 @@ channels: - bioconda dependencies: - - python >=3.8 - - vcfpy - - ruamel.yaml + - python==3.10.14 + - vcfpy==0.13.8 + - ruamel.yaml==0.18.6 diff --git a/snappy_wrappers/wrappers/vcf_cnv_filter/environment.yaml b/snappy_wrappers/wrappers/vcf_cnv_filter/environment.yaml index d2bdb7726..f873cebcb 100644 --- a/snappy_wrappers/wrappers/vcf_cnv_filter/environment.yaml +++ b/snappy_wrappers/wrappers/vcf_cnv_filter/environment.yaml @@ -1,10 +1,9 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- python =3.6 -- vcfpy ==0.13.3 -- pytabix ==0.0.2 - -- bcftools ==1.9 -- htslib ==1.9 + - python==3.6.15 + - vcfpy==0.13.3 + - pytabix==0.0.2 + - bcftools==1.9 + - htslib==1.9 diff --git a/snappy_wrappers/wrappers/vcf_mei_filter/environment.yaml b/snappy_wrappers/wrappers/vcf_mei_filter/environment.yaml index d5ec345c4..388691e32 100644 --- a/snappy_wrappers/wrappers/vcf_mei_filter/environment.yaml +++ b/snappy_wrappers/wrappers/vcf_mei_filter/environment.yaml @@ -1,10 +1,9 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- python =3.6 -- vcfpy ==0.11.0 -- pytabix ==0.0.2 - -- bcftools =1.8 -- htslib =1.8 + - python==3.6.15 + - vcfpy==0.11.0 + - pytabix==0.0.2 + - bcftools==1.8 + - htslib==1.8 diff --git a/snappy_wrappers/wrappers/vcf_sv_filter/environment.yaml b/snappy_wrappers/wrappers/vcf_sv_filter/environment.yaml index ab03afe79..40fe6f06d 100644 --- a/snappy_wrappers/wrappers/vcf_sv_filter/environment.yaml +++ b/snappy_wrappers/wrappers/vcf_sv_filter/environment.yaml @@ -1,11 +1,11 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- vcfpy ==0.11.1 -- pytabix ==0.0.2 -- intervaltree ==2.1.0 -- parallel -- bcftools ==1.11 -- htslib ==1.11 -- samtools ==1.11 + - vcfpy==0.11.1 + - pytabix==0.0.2 + - intervaltree==2.1.0 + - parallel==20240122 + - bcftools==1.11 + - htslib==1.11 + - samtools==1.11 diff --git a/snappy_wrappers/wrappers/vcfpy/add_bed/environment.yaml b/snappy_wrappers/wrappers/vcfpy/add_bed/environment.yaml index 8d0c6415c..6a9980807 100644 --- a/snappy_wrappers/wrappers/vcfpy/add_bed/environment.yaml +++ b/snappy_wrappers/wrappers/vcfpy/add_bed/environment.yaml @@ -1,8 +1,8 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- bcftools -- vcfpy -- pytabix -- htslib + - bcftools==1.19 + - vcfpy==0.13.8 + - pytabix==0.1 + - htslib==1.19.1 diff --git a/snappy_wrappers/wrappers/vep/environment.yaml b/snappy_wrappers/wrappers/vep/environment.yaml index 01bd4ca32..e47264aa7 100644 --- a/snappy_wrappers/wrappers/vep/environment.yaml +++ b/snappy_wrappers/wrappers/vep/environment.yaml @@ -1,5 +1,5 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- ensembl-vep ==109.3-0 + - ensembl-vep==109.3 diff --git a/snappy_wrappers/wrappers/vep/run/environment.yaml b/snappy_wrappers/wrappers/vep/run/environment.yaml index 711e58eec..a15699e01 100644 --- a/snappy_wrappers/wrappers/vep/run/environment.yaml +++ b/snappy_wrappers/wrappers/vep/run/environment.yaml @@ -1,5 +1,4 @@ channels: - - bioconda + - bioconda dependencies: - - ensembl-vep=102 - + - ensembl-vep==102.0 diff --git a/snappy_wrappers/wrappers/wgs_cnv_filtration/environment.yaml b/snappy_wrappers/wrappers/wgs_cnv_filtration/environment.yaml index 9c953a435..f2e1dcd21 100644 --- a/snappy_wrappers/wrappers/wgs_cnv_filtration/environment.yaml +++ b/snappy_wrappers/wrappers/wgs_cnv_filtration/environment.yaml @@ -1,7 +1,7 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- bcftools =1.8 -- htslib =1.8 -- bedtools ==2.27.0 + - bcftools==1.8 + - htslib==1.8 + - bedtools==2.27.0 diff --git a/snappy_wrappers/wrappers/wgs_cnv_filtration/filter_inheritance/environment.yaml b/snappy_wrappers/wrappers/wgs_cnv_filtration/filter_inheritance/environment.yaml index 9c953a435..f2e1dcd21 100644 --- a/snappy_wrappers/wrappers/wgs_cnv_filtration/filter_inheritance/environment.yaml +++ b/snappy_wrappers/wrappers/wgs_cnv_filtration/filter_inheritance/environment.yaml @@ -1,7 +1,7 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- bcftools =1.8 -- htslib =1.8 -- bedtools ==2.27.0 + - bcftools==1.8 + - htslib==1.8 + - bedtools==2.27.0 diff --git a/snappy_wrappers/wrappers/wgs_cnv_filtration/filter_quality/environment.yaml b/snappy_wrappers/wrappers/wgs_cnv_filtration/filter_quality/environment.yaml index 9c953a435..f2e1dcd21 100644 --- a/snappy_wrappers/wrappers/wgs_cnv_filtration/filter_quality/environment.yaml +++ b/snappy_wrappers/wrappers/wgs_cnv_filtration/filter_quality/environment.yaml @@ -1,7 +1,7 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- bcftools =1.8 -- htslib =1.8 -- bedtools ==2.27.0 + - bcftools==1.8 + - htslib==1.8 + - bedtools==2.27.0 diff --git a/snappy_wrappers/wrappers/wgs_cnv_filtration/filter_regions/environment.yaml b/snappy_wrappers/wrappers/wgs_cnv_filtration/filter_regions/environment.yaml index 9c953a435..f2e1dcd21 100644 --- a/snappy_wrappers/wrappers/wgs_cnv_filtration/filter_regions/environment.yaml +++ b/snappy_wrappers/wrappers/wgs_cnv_filtration/filter_regions/environment.yaml @@ -1,7 +1,7 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- bcftools =1.8 -- htslib =1.8 -- bedtools ==2.27.0 + - bcftools==1.8 + - htslib==1.8 + - bedtools==2.27.0 diff --git a/snappy_wrappers/wrappers/wgs_sv_filtration/environment.yaml b/snappy_wrappers/wrappers/wgs_sv_filtration/environment.yaml index 9c953a435..f2e1dcd21 100644 --- a/snappy_wrappers/wrappers/wgs_sv_filtration/environment.yaml +++ b/snappy_wrappers/wrappers/wgs_sv_filtration/environment.yaml @@ -1,7 +1,7 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- bcftools =1.8 -- htslib =1.8 -- bedtools ==2.27.0 + - bcftools==1.8 + - htslib==1.8 + - bedtools==2.27.0