nf-core · edmundmiller · Oct 24, 2023 · Oct 17, 2023 · Oct 17, 2023 · Oct 24, 2023
diff --git a/.github/convert_conda_line_to_env.sh b/.github/convert_conda_line_to_env.sh
@@ -0,0 +1,24 @@
+#!/usr/bin/env bash
+
+# Find all main.nf files in modules
+NF_FILES=$(fd "^main.nf$" modules/)
+
+template=".github/env-template.yml"
+
+for file in $NF_FILES; do
+    # Get the conda line
+    conda_line=$(rg "^    conda" "$file")
+    # Pull out the conda packages
+    conda_packages=$(echo "$conda_line" | sed 's/^.*"\(.*\)".*$/\1/g')
+    # Write the template to the environment.yml
+    cat $template > $(dirname "$file")/environment.yml
+
+    env_yaml=$(dirname "$file")/environment.yml
+    # Put the dependencies in a environment.yaml using yq
+    for package in $conda_packages; do
+        yq -i '.dependencies += ["'"$package"'"]' $env_yaml
+    done
+
+    # Change the conda line to point to the new environment.yml
+    sed -i "s|^    conda.*|    conda '$env_yaml'|g" "$file"
+done
diff --git a/.github/env-template.yml b/.github/env-template.yml
@@ -0,0 +1,4 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
diff --git a/modules/nf-core/abacas/environment.yml b/modules/nf-core/abacas/environment.yml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::abacas=1.3.1
diff --git a/modules/nf-core/abacas/main.nf b/modules/nf-core/abacas/main.nf
@@ -2,7 +2,7 @@ process ABACAS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::abacas=1.3.1"
+    conda 'modules/nf-core/abacas/environment.yml'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/abacas:1.3.1--pl526_0' :
         'biocontainers/abacas:1.3.1--pl526_0' }"

diff --git a/modules/nf-core/abricate/run/environment.yml b/modules/nf-core/abricate/run/environment.yml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::abricate=1.0.1
diff --git a/modules/nf-core/abricate/run/main.nf b/modules/nf-core/abricate/run/main.nf
@@ -2,7 +2,7 @@ process ABRICATE_RUN {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::abricate=1.0.1"
+    conda 'modules/nf-core/abricate/run/environment.yml'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/abricate%3A1.0.1--ha8f3691_1':
         'biocontainers/abricate:1.0.1--ha8f3691_1' }"

diff --git a/modules/nf-core/abricate/summary/environment.yml b/modules/nf-core/abricate/summary/environment.yml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::abricate=1.0.1
diff --git a/modules/nf-core/abricate/summary/main.nf b/modules/nf-core/abricate/summary/main.nf
@@ -2,7 +2,7 @@ process ABRICATE_SUMMARY {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::abricate=1.0.1"
+    conda 'modules/nf-core/abricate/summary/environment.yml'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/abricate%3A1.0.1--ha8f3691_1':
         'biocontainers/abricate:1.0.1--ha8f3691_1' }"

diff --git a/modules/nf-core/abritamr/run/environment.yml b/modules/nf-core/abritamr/run/environment.yml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::abritamr=1.0.14
diff --git a/modules/nf-core/abritamr/run/main.nf b/modules/nf-core/abritamr/run/main.nf
@@ -2,7 +2,7 @@ process ABRITAMR_RUN {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::abritamr=1.0.14"
+    conda 'modules/nf-core/abritamr/run/environment.yml'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/abritamr:1.0.14--pyhdfd78af_0':
         'biocontainers/abritamr:1.0.14--pyhdfd78af_0' }"

diff --git a/modules/nf-core/adapterremoval/environment.yml b/modules/nf-core/adapterremoval/environment.yml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::adapterremoval=2.3.2
diff --git a/modules/nf-core/adapterremoval/main.nf b/modules/nf-core/adapterremoval/main.nf
@@ -2,7 +2,7 @@ process ADAPTERREMOVAL {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::adapterremoval=2.3.2"
+    conda 'modules/nf-core/adapterremoval/environment.yml'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/adapterremoval:2.3.2--hb7ba0dd_0' :
         'biocontainers/adapterremoval:2.3.2--hb7ba0dd_0' }"

diff --git a/modules/nf-core/adapterremovalfixprefix/environment.yml b/modules/nf-core/adapterremovalfixprefix/environment.yml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::adapterremovalfixprefix=0.0.5
diff --git a/modules/nf-core/adapterremovalfixprefix/main.nf b/modules/nf-core/adapterremovalfixprefix/main.nf
@@ -3,7 +3,7 @@ process ADAPTERREMOVALFIXPREFIX {
     label 'process_single'
 
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
-    conda "bioconda::adapterremovalfixprefix=0.0.5"
+    conda 'modules/nf-core/adapterremovalfixprefix/environment.yml'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/adapterremovalfixprefix:0.0.5--hdfd78af_2':
         'biocontainers/adapterremovalfixprefix:0.0.5--hdfd78af_2' }"

diff --git a/modules/nf-core/admixture/environment.yml b/modules/nf-core/admixture/environment.yml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::admixture=1.3.0
diff --git a/modules/nf-core/admixture/main.nf b/modules/nf-core/admixture/main.nf
@@ -3,7 +3,7 @@ process ADMIXTURE {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::admixture=1.3.0"
+    conda 'modules/nf-core/admixture/environment.yml'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/admixture:1.3.0--0':
         'biocontainers/admixture:1.3.0--0' }"

diff --git a/modules/nf-core/affy/justrma/environment.yml b/modules/nf-core/affy/justrma/environment.yml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::bioconductor-affy=1.78.0
diff --git a/modules/nf-core/affy/justrma/main.nf b/modules/nf-core/affy/justrma/main.nf
@@ -2,7 +2,7 @@ process AFFY_JUSTRMA {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::bioconductor-affy=1.78.0"
+    conda 'modules/nf-core/affy/justrma/environment.yml'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-affy:1.78.0--r43ha9d7317_1':
         'biocontainers/bioconductor-affy:1.78.0--r43ha9d7317_1' }"

diff --git a/modules/nf-core/agat/convertspgff2gtf/environment.yml b/modules/nf-core/agat/convertspgff2gtf/environment.yml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::agat=1.0.0
diff --git a/modules/nf-core/agat/convertspgff2gtf/main.nf b/modules/nf-core/agat/convertspgff2gtf/main.nf
@@ -2,7 +2,7 @@ process AGAT_CONVERTSPGFF2GTF {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::agat=1.0.0"
+    conda 'modules/nf-core/agat/convertspgff2gtf/environment.yml'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/agat:1.0.0--pl5321hdfd78af_0' :
         'biocontainers/agat:1.0.0--pl5321hdfd78af_0' }"

diff --git a/modules/nf-core/agat/convertspgxf2gxf/environment.yml b/modules/nf-core/agat/convertspgxf2gxf/environment.yml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::agat=1.0.0
diff --git a/modules/nf-core/agat/convertspgxf2gxf/main.nf b/modules/nf-core/agat/convertspgxf2gxf/main.nf
@@ -2,7 +2,7 @@ process AGAT_CONVERTSPGXF2GXF {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::agat=1.0.0"
+    conda 'modules/nf-core/agat/convertspgxf2gxf/environment.yml'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/agat:1.0.0--pl5321hdfd78af_0' :
         'biocontainers/agat:1.0.0--pl5321hdfd78af_0' }"

diff --git a/modules/nf-core/agat/spstatistics/environment.yml b/modules/nf-core/agat/spstatistics/environment.yml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::agat=1.0.0
diff --git a/modules/nf-core/agat/spstatistics/main.nf b/modules/nf-core/agat/spstatistics/main.nf
@@ -2,7 +2,7 @@ process AGAT_SPSTATISTICS {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::agat=1.0.0"
+    conda 'modules/nf-core/agat/spstatistics/environment.yml'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/agat:1.0.0--pl5321hdfd78af_0' :
         'biocontainers/agat:1.0.0--pl5321hdfd78af_0' }"

diff --git a/modules/nf-core/agat/sqstatbasic/environment.yml b/modules/nf-core/agat/sqstatbasic/environment.yml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::agat=1.0.0
diff --git a/modules/nf-core/agat/sqstatbasic/main.nf b/modules/nf-core/agat/sqstatbasic/main.nf
@@ -2,7 +2,7 @@ process AGAT_SQSTATBASIC {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::agat=1.0.0"
+    conda 'modules/nf-core/agat/sqstatbasic/environment.yml'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/agat:1.0.0--pl5321hdfd78af_0' :
         'biocontainers/agat:1.0.0--pl5321hdfd78af_0' }"

diff --git a/modules/nf-core/agrvate/environment.yml b/modules/nf-core/agrvate/environment.yml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::agrvate=1.0.2
diff --git a/modules/nf-core/agrvate/main.nf b/modules/nf-core/agrvate/main.nf
@@ -2,7 +2,7 @@ process AGRVATE {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::agrvate=1.0.2"
+    conda 'modules/nf-core/agrvate/environment.yml'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/agrvate:1.0.2--hdfd78af_0' :
         'biocontainers/agrvate:1.0.2--hdfd78af_0' }"

diff --git a/modules/nf-core/allelecounter/environment.yml b/modules/nf-core/allelecounter/environment.yml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::cancerit-allelecount=4.3.0
diff --git a/modules/nf-core/allelecounter/main.nf b/modules/nf-core/allelecounter/main.nf
@@ -2,7 +2,7 @@ process ALLELECOUNTER {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::cancerit-allelecount=4.3.0"
+    conda 'modules/nf-core/allelecounter/environment.yml'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/cancerit-allelecount:4.3.0--h41abebc_0' :
         'biocontainers/cancerit-allelecount:4.3.0--h41abebc_0' }"

diff --git a/modules/nf-core/ampcombi/environment.yml b/modules/nf-core/ampcombi/environment.yml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::ampcombi=0.1.7
diff --git a/modules/nf-core/ampcombi/main.nf b/modules/nf-core/ampcombi/main.nf
@@ -2,7 +2,7 @@ process AMPCOMBI {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::ampcombi=0.1.7"
+    conda 'modules/nf-core/ampcombi/environment.yml'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ampcombi:0.1.7--pyhdfd78af_0':
         'biocontainers/ampcombi:0.1.7--pyhdfd78af_0' }"

diff --git a/modules/nf-core/ampir/environment.yml b/modules/nf-core/ampir/environment.yml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - conda-forge::r-ampir=1.1.0
diff --git a/modules/nf-core/ampir/main.nf b/modules/nf-core/ampir/main.nf
@@ -2,7 +2,7 @@ process AMPIR {
     tag "$meta.id"
     label 'process_single'
 
-    conda "conda-forge::r-ampir=1.1.0"
+    conda 'modules/nf-core/ampir/environment.yml'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/r-ampir:1.1.0':
         'biocontainers/r-ampir:1.1.0' }"

diff --git a/modules/nf-core/amplify/predict/environment.yml b/modules/nf-core/amplify/predict/environment.yml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::amplify=1.1.0
diff --git a/modules/nf-core/amplify/predict/main.nf b/modules/nf-core/amplify/predict/main.nf
@@ -3,7 +3,7 @@ process AMPLIFY_PREDICT {
     label 'process_single'
 
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
-    conda "bioconda::amplify=1.1.0"
+    conda 'modules/nf-core/amplify/predict/environment.yml'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/amplify:1.1.0--hdfd78af_0':
         'biocontainers/amplify:1.1.0--hdfd78af_0' }"

diff --git a/modules/nf-core/amps/environment.yml b/modules/nf-core/amps/environment.yml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::hops=0.35
diff --git a/modules/nf-core/amps/main.nf b/modules/nf-core/amps/main.nf
@@ -1,7 +1,7 @@
 process AMPS {
     label 'process_low'
 
-    conda "bioconda::hops=0.35"
+    conda 'modules/nf-core/amps/environment.yml'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/hops:0.35--hdfd78af_1' :
         'biocontainers/hops:0.35--hdfd78af_1' }"

diff --git a/modules/nf-core/amrfinderplus/run/environment.yml b/modules/nf-core/amrfinderplus/run/environment.yml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::ncbi-amrfinderplus=3.11.18
diff --git a/modules/nf-core/amrfinderplus/run/main.nf b/modules/nf-core/amrfinderplus/run/main.nf
@@ -2,7 +2,7 @@ process AMRFINDERPLUS_RUN {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::ncbi-amrfinderplus=3.11.18"
+    conda 'modules/nf-core/amrfinderplus/run/environment.yml'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.11.18--h283d18e_0':
         'biocontainers/ncbi-amrfinderplus:3.11.18--h283d18e_0' }"

diff --git a/modules/nf-core/amrfinderplus/update/environment.yml b/modules/nf-core/amrfinderplus/update/environment.yml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::ncbi-amrfinderplus=3.11.18
diff --git a/modules/nf-core/amrfinderplus/update/main.nf b/modules/nf-core/amrfinderplus/update/main.nf
@@ -2,7 +2,7 @@ process AMRFINDERPLUS_UPDATE {
     tag "update"
     label 'process_single'
 
-    conda "bioconda::ncbi-amrfinderplus=3.11.18"
+    conda 'modules/nf-core/amrfinderplus/update/environment.yml'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.11.18--h283d18e_0':
         'biocontainers/ncbi-amrfinderplus:3.11.18--h283d18e_0' }"

diff --git a/modules/nf-core/angsd/contamination/environment.yml b/modules/nf-core/angsd/contamination/environment.yml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::angsd=0.940
diff --git a/modules/nf-core/angsd/contamination/main.nf b/modules/nf-core/angsd/contamination/main.nf
@@ -2,7 +2,7 @@ process ANGSD_CONTAMINATION {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::angsd=0.940"
+    conda 'modules/nf-core/angsd/contamination/environment.yml'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/angsd:0.939--h468462d_0':
         'biocontainers/angsd:0.939--h468462d_0' }"

diff --git a/modules/nf-core/angsd/docounts/environment.yml b/modules/nf-core/angsd/docounts/environment.yml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::angsd=0.939
diff --git a/modules/nf-core/angsd/docounts/main.nf b/modules/nf-core/angsd/docounts/main.nf
@@ -2,7 +2,7 @@ process ANGSD_DOCOUNTS {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::angsd=0.939"
+    conda 'modules/nf-core/angsd/docounts/environment.yml'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/angsd:0.939--h468462d_0':
         'biocontainers/angsd:0.939--h468462d_0' }"

diff --git a/modules/nf-core/annotsv/annotsv/environment.yml b/modules/nf-core/annotsv/annotsv/environment.yml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::annotsv=3.3.6
diff --git a/modules/nf-core/annotsv/annotsv/main.nf b/modules/nf-core/annotsv/annotsv/main.nf
@@ -2,7 +2,7 @@ process ANNOTSV_ANNOTSV {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::annotsv=3.3.6"
+    conda 'modules/nf-core/annotsv/annotsv/environment.yml'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/annotsv:3.3.6--py311hdfd78af_0' :
         'biocontainers/annotsv:3.3.6--py311hdfd78af_0' }"