fix: fix channel order under strict priorities

snakemake-workflows · Aug 25, 2022 · bdbfb10 · bdbfb10
1 parent f8f3648
commit bdbfb10
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Showing 15 changed files with 19 additions and 9 deletions.
diff --git a/workflow/envs/cpat.yaml b/workflow/envs/cpat.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - cpat =2.0.0
diff --git a/workflow/envs/curl.yaml b/workflow/envs/curl.yaml
@@ -1,7 +1,6 @@
 channels:
   - conda-forge
-  - bioconda
-  - defaults
+  - nodefaults
 dependencies:
   - curl=7.65.3
 
diff --git a/workflow/envs/ens_gene_to_go.yaml b/workflow/envs/ens_gene_to_go.yaml
@@ -1,7 +1,7 @@
 channels:
   - conda-forge
   - bioconda
-  - defaults
+  - nodefaults
 dependencies:
   - r-base=4.1
   - r-tidyverse=1.3
diff --git a/workflow/envs/fgsea.yaml b/workflow/envs/fgsea.yaml
@@ -1,6 +1,7 @@
 channels:
   - conda-forge
   - bioconda
+  - nodefaults
 dependencies:
   - r-base =4.1
   - r-tidyverse =1.3

diff --git a/workflow/envs/goatools.yaml b/workflow/envs/goatools.yaml
@@ -1,8 +1,7 @@
-name: goatools
 channels:
   - conda-forge
   - bioconda
-  - defaults
+  - nodefaults
 dependencies:
   - goatools =0.9.7
   - python =3.7

diff --git a/workflow/envs/hmmer.yaml b/workflow/envs/hmmer.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - hmmer =3.3
diff --git a/workflow/envs/ihw.yaml b/workflow/envs/ihw.yaml
@@ -1,6 +1,7 @@
 channels:
   - conda-forge
   - bioconda
+  - nodefaults
 dependencies:
   - r-base =4.1
   - bioconductor-ihw =1.20.0

diff --git a/workflow/envs/isoform-switch-analyzer.yaml b/workflow/envs/isoform-switch-analyzer.yaml
@@ -1,6 +1,7 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - bioconductor-isoformswitchanalyzer =1.14
   - bioconductor-rhdf5 =2.36

diff --git a/workflow/envs/kallisto.yaml b/workflow/envs/kallisto.yaml
@@ -1,5 +1,6 @@
 channels:
   - conda-forge
   - bioconda
+  - nodefaults
 dependencies:
   - kallisto =0.46
diff --git a/workflow/envs/pfam.yaml b/workflow/envs/pfam.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - pfam_scan =1.6
diff --git a/workflow/envs/sleuth.yaml b/workflow/envs/sleuth.yaml
@@ -1,6 +1,7 @@
 channels:
   - conda-forge
   - bioconda
+  - nodefaults
 dependencies:
   - r-sleuth =0.30
   - bioconductor-rhdf5lib =1.12

diff --git a/workflow/envs/spia.yaml b/workflow/envs/spia.yaml
@@ -1,6 +1,7 @@
 channels:
   - conda-forge
   - bioconda
+  - nodefaults
 dependencies:
   - r-base =4.1
   - bioconductor-spia =2.44

diff --git a/workflow/envs/vega.yaml b/workflow/envs/vega.yaml
@@ -1,5 +1,6 @@
 channels:
   - conda-forge
+  - nodefaults
 dependencies:
   - vega-lite-cli =4.17
   - python >=3.9,<4

diff --git a/workflow/rules/enrichment.smk b/workflow/rules/enrichment.smk
@@ -17,6 +17,7 @@ rule download_bioconductor_species_database:
 # topology- and interaction-aware pathway enrichment analysis
 
 
+# TODO consider cellphonedb for receptor ligand interaction (Sarah Teichmann, Nature Methods?)
 rule spia:
     input:
         samples="results/sleuth/samples.tsv",

diff --git a/workflow/rules/ref.smk b/workflow/rules/ref.smk
@@ -1,3 +1,4 @@
+# TODO add ability to use gencode (more complete)
 rule get_transcriptome:
     output:
         "resources/transcriptome.{type}.fasta",