fix: give conda-forge highest priority to ensure proper semantic unde…

…r strict channel priorities (#508) * Revert "Revert "fix: give conda-forge highest priority to ensure proper semantic under strict channel priorities"" This reverts commit 6a6d28a. * fix indentation * add nodefaults * fixes * add biopython * fixes, add blacklist mechanism * fixes * bump genome config version * add numpy * blacklist * relax numpy constraint * blacklist deepvariant and fix badge in docs
snakemake · Aug 15, 2022 · 6976c9a · 6976c9a
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commit 6976c9a
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diff --git a/bio/adapterremoval/environment.yaml b/bio/adapterremoval/environment.yaml
@@ -1,5 +1,6 @@
 channels:
+  - conda-forge
   - bioconda
-  - defaults
+  - nodefaults
 dependencies:
   - adapterremoval =2.3
diff --git a/bio/arriba/environment.yaml b/bio/arriba/environment.yaml
@@ -1,6 +1,6 @@
 channels:
   - conda-forge
   - bioconda
-  - defaults
+  - nodefaults
 dependencies:
   - arriba ==1.1.0
diff --git a/bio/art/profiler_illumina/environment.yaml b/bio/art/profiler_illumina/environment.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - art ==2016.06.05
diff --git a/bio/assembly-stats/environment.yaml b/bio/assembly-stats/environment.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - assembly-stats=1.0
diff --git a/bio/bamtools/filter/environment.yaml b/bio/bamtools/filter/environment.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - bamtools ==2.5.1
diff --git a/bio/bamtools/filter_json/environment.yaml b/bio/bamtools/filter_json/environment.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - bamtools ==2.5.1
diff --git a/bio/bamtools/split/environment.yaml b/bio/bamtools/split/environment.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - bamtools ==2.5.1
diff --git a/bio/bamtools/stats/environment.yaml b/bio/bamtools/stats/environment.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - bamtools ==2.5.1
diff --git a/bio/bbtools/bbduk/environment.yaml b/bio/bbtools/bbduk/environment.yaml
@@ -1,7 +1,7 @@
 channels:
-  - bioconda
   - conda-forge
-  - defaults
+  - bioconda
+  - nodefaults
 dependencies:
   - bbmap ==38.90
   - snakemake-wrapper-utils ==0.1.3
diff --git a/bio/bcftools/call/environment.yaml b/bio/bcftools/call/environment.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - bcftools =1.11
diff --git a/bio/bcftools/concat/environment.yaml b/bio/bcftools/concat/environment.yaml
@@ -1,6 +1,7 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - bcftools =1.12
   - snakemake-wrapper-utils ==0.2.0
diff --git a/bio/bcftools/filter/environment.yaml b/bio/bcftools/filter/environment.yaml
@@ -1,7 +1,7 @@
 channels:
-  - bioconda
   - conda-forge
-  - defaults
+  - bioconda
+  - nodefaults
 dependencies:
   - bcftools ==1.12
   - snakemake-wrapper-utils ==0.2
diff --git a/bio/bcftools/index/environment.yaml b/bio/bcftools/index/environment.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - bcftools =1.11
diff --git a/bio/bcftools/merge/environment.yaml b/bio/bcftools/merge/environment.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - bcftools =1.11
diff --git a/bio/bcftools/mpileup/environment.yaml b/bio/bcftools/mpileup/environment.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - bcftools =1.11
diff --git a/bio/bcftools/norm/environment.yaml b/bio/bcftools/norm/environment.yaml
@@ -1,6 +1,7 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - bcftools =1.11
   - snakemake-wrapper-utils =0.2
diff --git a/bio/bcftools/reheader/environment.yaml b/bio/bcftools/reheader/environment.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - bcftools =1.11
diff --git a/bio/bcftools/sort/environment.yaml b/bio/bcftools/sort/environment.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - bcftools ==1.11
diff --git a/bio/bcftools/stats/environment.yaml b/bio/bcftools/stats/environment.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - bcftools ==1.12
diff --git a/bio/bcftools/view/environment.yaml b/bio/bcftools/view/environment.yaml
@@ -1,6 +1,7 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - bcftools ==1.12
   - snakemake-wrapper-utils ==0.2
diff --git a/bio/bedtools/complement/environment.yaml b/bio/bedtools/complement/environment.yaml
@@ -1,6 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
-  - defaults
+  - bioconda
+  - nodefaults
 dependencies:
   - bedtools =2.29
diff --git a/bio/bedtools/coveragebed/environment.yaml b/bio/bedtools/coveragebed/environment.yaml
@@ -1,6 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
-  - defaults
+  - bioconda
+  - nodefaults
 dependencies:
   - bedtools ==2.29.0
diff --git a/bio/bedtools/genomecov/environment.yaml b/bio/bedtools/genomecov/environment.yaml
@@ -1,6 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
-  - defaults
+  - bioconda
+  - nodefaults
 dependencies:
   - bedtools ==2.29.2
diff --git a/bio/bedtools/intersect/environment.yaml b/bio/bedtools/intersect/environment.yaml
@@ -1,6 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
-  - defaults
+  - bioconda
+  - nodefaults
 dependencies:
   - bedtools =2.29.0
diff --git a/bio/bedtools/merge/environment.yaml b/bio/bedtools/merge/environment.yaml
@@ -1,6 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
-  - defaults
+  - bioconda
+  - nodefaults
 dependencies:
   - bedtools =2.29.0
diff --git a/bio/bedtools/slop/environment.yaml b/bio/bedtools/slop/environment.yaml
@@ -1,6 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
-  - defaults
+  - bioconda
+  - nodefaults
 dependencies:
   - bedtools =2.29.0
diff --git a/bio/bedtools/sort/environment.yaml b/bio/bedtools/sort/environment.yaml
@@ -1,6 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
-  - defaults
+  - bioconda
+  - nodefaults
 dependencies:
   - bedtools =2.29
diff --git a/bio/benchmark/chm-eval-kit/environment.yaml b/bio/benchmark/chm-eval-kit/environment.yaml
@@ -1,4 +1,5 @@
 channels:
   - conda-forge
+  - nodefaults
 dependencies:
   - curl
diff --git a/bio/benchmark/chm-eval-sample/environment.yaml b/bio/benchmark/chm-eval-sample/environment.yaml
@@ -1,6 +1,7 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - samtools =1.10
   - curl
diff --git a/bio/benchmark/chm-eval/environment.yaml b/bio/benchmark/chm-eval/environment.yaml
@@ -1,4 +1,5 @@
 channels:
   - conda-forge
+  - nodefaults
 dependencies:
   - perl =5.26
diff --git a/bio/bgzip/environment.yaml b/bio/bgzip/environment.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - htslib ==1.12
diff --git a/bio/biobambam2/bamsormadup/environment.yaml b/bio/biobambam2/bamsormadup/environment.yaml
@@ -1,6 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
-  - defaults
+  - bioconda
+  - nodefaults
 dependencies:
   - biobambam =2.0
diff --git a/bio/bismark/bam2nuc/environment.yaml b/bio/bismark/bam2nuc/environment.yaml
@@ -1,7 +1,7 @@
 channels:
-  - bioconda
   - conda-forge
-  - defaults
+  - bioconda
+  - nodefaults
 dependencies:
   - bowtie2 ==2.4.2
   - bismark ==0.23.0

diff --git a/bio/bismark/bismark/environment.yaml b/bio/bismark/bismark/environment.yaml
@@ -1,7 +1,7 @@
 channels:
-  - bioconda
   - conda-forge
-  - defaults
+  - bioconda
+  - nodefaults
 dependencies:
   - bowtie2 ==2.4.2
   - bismark ==0.23.0

diff --git a/bio/bismark/bismark2bedGraph/environment.yaml b/bio/bismark/bismark2bedGraph/environment.yaml
@@ -1,7 +1,7 @@
 channels:
-  - bioconda
   - conda-forge
-  - defaults
+  - bioconda
+  - nodefaults
 dependencies:
   - bowtie2 ==2.4.2
   - bismark ==0.23.0

diff --git a/bio/bismark/bismark2report/environment.yaml b/bio/bismark/bismark2report/environment.yaml
@@ -1,7 +1,7 @@
 channels:
-  - bioconda
   - conda-forge
-  - defaults
+  - bioconda
+  - nodefaults
 dependencies:
   - bowtie2 ==2.4.2
   - bismark ==0.23.0

diff --git a/bio/bismark/bismark2summary/environment.yaml b/bio/bismark/bismark2summary/environment.yaml
@@ -1,7 +1,7 @@
 channels:
-  - bioconda
   - conda-forge
-  - defaults
+  - bioconda
+  - nodefaults
 dependencies:
   - bowtie2 ==2.4.2
   - bismark ==0.23.0

diff --git a/bio/bismark/bismark_genome_preparation/environment.yaml b/bio/bismark/bismark_genome_preparation/environment.yaml
@@ -1,7 +1,7 @@
 channels:
-  - bioconda
   - conda-forge
-  - defaults
+  - bioconda
+  - nodefaults
 dependencies:
   - bowtie2 ==2.4.2
   - bismark ==0.23.0

diff --git a/bio/bismark/bismark_methylation_extractor/environment.yaml b/bio/bismark/bismark_methylation_extractor/environment.yaml
@@ -1,7 +1,7 @@
 channels:
-  - bioconda
   - conda-forge
-  - defaults
+  - bioconda
+  - nodefaults
 dependencies:
   - bowtie2 ==2.4.2
   - bismark ==0.23.0

diff --git a/bio/bismark/bismark_methylation_extractor/meta.yaml b/bio/bismark/bismark_methylation_extractor/meta.yaml
@@ -23,3 +23,4 @@ output:
   - read_base_meth_state_cpg: Per read CpG base methylation info, CpG_context_\*.txt.gz  (if key is provided, the out file will be renamed to this name)
   - read_base_meth_state_chg: Per read CpG base methylation info, CHG_context_\*.txt.gz  (if key is provided, the out file will be renamed to this name)
   - read_base_meth_state_chh: Per read CpG base methylation info, CHH_context_\*.txt.gz  (if key is provided, the out file will be renamed to this name)
+blacklisted: Wrapper fails to move output PNG to the right place.
diff --git a/bio/bismark/deduplicate_bismark/environment.yaml b/bio/bismark/deduplicate_bismark/environment.yaml
@@ -1,7 +1,7 @@
 channels:
-  - bioconda
   - conda-forge
-  - defaults
+  - bioconda
+  - nodefaults
 dependencies:
   - bowtie2 ==2.4.2
   - bismark ==0.23.0

diff --git a/bio/blast/blastn/environment.yaml b/bio/blast/blastn/environment.yaml
@@ -1,6 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
-  - defaults
+  - bioconda
+  - nodefaults
 dependencies:
   - blast ==2.11
diff --git a/bio/blast/makeblastdb/environment.yaml b/bio/blast/makeblastdb/environment.yaml
@@ -1,6 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
-  - defaults
+  - bioconda
+  - nodefaults
 dependencies:
   - blast ==2.11.0
diff --git a/bio/bowtie2/align/environment.yaml b/bio/bowtie2/align/environment.yaml
@@ -1,7 +1,7 @@
 channels:
-  - bioconda
   - conda-forge
-  - defaults
+  - bioconda
+  - nodefaults
 dependencies:
   - bowtie2 =2.4  # Keep consistent with version specified in bowtie2/build
   - samtools =1.14

diff --git a/bio/bowtie2/build/environment.yaml b/bio/bowtie2/build/environment.yaml
@@ -1,6 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
-  - defaults
+  - bioconda
+  - nodefaults
 dependencies:
   - bowtie2 =2.4  # Keep consistent with version specified in bowtie2/align