Merge pull request #153 from nf-core/conda-envs

Conda envs
nf-core · Jun 25, 2024 · 8fce8c2 · 8fce8c2
2 parents 98923dd + aaebb74
commit 8fce8c2
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Showing 13 changed files with 43 additions and 11 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -591,7 +591,7 @@ process {
     }
 
     withName: '.*:ANNOTATION:COMBINE_GTFS' {
-        ext.args = "-k 1,1 -k3,3n -k4,4n -u"
+        ext.args = "-k 1,1 -k4,4n -k5,5n -u"
         ext.suffix = "combined.gtf"
     }
 
@@ -612,7 +612,7 @@ process {
     }
 
     withName: COMBINE_TRANSCRIPTOME_GTFS {
-        ext.args = "-k 1,1 -k3,3n -k4,4n"
+        ext.args = "-k 1,1 -k4,4n -k5,5n"
         ext.suffix = "gtf"
     }
 

diff --git a/modules/local/annotation/environment.yml b/modules/local/annotation/environment.yml
@@ -0,0 +1,5 @@
+name: annotation
+channels:
+  - conda-forge
+dependencies:
+  - pandas=1.5.2
diff --git a/modules/local/annotation/main.nf b/modules/local/annotation/main.nf
@@ -2,7 +2,7 @@ process ANNOTATION {
     tag "$meta.id:$meta.tool"
     label 'process_single'
 
-    conda "bioconda::pandas=1.5.2"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/pandas:1.5.2' :
         'biocontainers/pandas:1.5.2' }"

diff --git a/modules/local/circtest/prepare/main.nf b/modules/local/circtest/prepare/main.nf
@@ -2,9 +2,7 @@ process CIRCTEST_PREPARE {
     label 'process_low'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/biocontainers/r-base:4.2.1' :
-        'biocontainers/r-base:4.2.1' }"
+    container "biocontainers/r-base:4.2.1"
 
     input:
     tuple val(meta), path(circ_counts)

diff --git a/modules/local/count_matrix/merge_samples/environment.yml b/modules/local/count_matrix/merge_samples/environment.yml
@@ -0,0 +1,5 @@
+name: merge_samples
+channels:
+  - conda-forge
+dependencies:
+  - pandas=1.5.2
diff --git a/modules/local/count_matrix/merge_samples/main.nf b/modules/local/count_matrix/merge_samples/main.nf
@@ -1,7 +1,7 @@
 process MERGE_SAMPLES {
     label "process_single"
 
-    conda "bioconda::pandas=1.5.2"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/pandas:1.5.2' :
         'biocontainers/pandas:1.5.2' }"

diff --git a/modules/local/count_matrix/merge_tools/environment.yml b/modules/local/count_matrix/merge_tools/environment.yml
@@ -0,0 +1,5 @@
+name: merge_tools
+channels:
+  - conda-forge
+dependencies:
+  - pandas=1.5.2
diff --git a/modules/local/count_matrix/merge_tools/main.nf b/modules/local/count_matrix/merge_tools/main.nf
@@ -2,7 +2,7 @@ process MERGE_TOOLS {
     tag "$meta.id"
     label "process_single"
 
-    conda "bioconda::pandas=1.5.2"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/pandas:1.5.2' :
         'biocontainers/pandas:1.5.2' }"

diff --git a/modules/local/quantification/merge_experiments/environment.yml b/modules/local/quantification/merge_experiments/environment.yml
@@ -4,6 +4,5 @@ name: "fishpond_swish"
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - "bioconda::bioconductor-rtracklayer==1.62.0--r43ha9d7317_0"
+  - "bioconda::bioconductor-rtracklayer=1.62.0"
diff --git a/modules/local/quantification/merge_experiments/main.nf b/modules/local/quantification/merge_experiments/main.nf
@@ -2,7 +2,7 @@ process MERGE_EXPERIMENTS {
     tag "$meta.id"
     label "process_medium"
 
-    conda "${moduleDir}/environment.yaml"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-rtracklayer:1.62.0--r43ha9d7317_0' :
         'biocontainers/bioconductor-rtracklayer:1.62.0--r43ha9d7317_0' }"

diff --git a/modules/local/quantification/split_types/environment.yml b/modules/local/quantification/split_types/environment.yml
@@ -0,0 +1,6 @@
+name: split_types
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - gawk=5.1.0
diff --git a/modules/local/quantification/transcriptome/environment.yml b/modules/local/quantification/transcriptome/environment.yml
@@ -0,0 +1,6 @@
+name: transcriptome
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - gffread=0.12.1
diff --git a/modules/local/tximeta/tximeta/environment.yml b/modules/local/tximeta/tximeta/environment.yml
@@ -0,0 +1,8 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "tximeta_tximeta"
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::bioconductor-tximeta=1.20.1"