Merge pull request #152 from nf-core/115-add-bioconda-recipe-for-psirc

Use psirc bioconda package
nf-core · Jun 19, 2024 · 98923dd · 98923dd
2 parents 995775b + 9b57e7f
commit 98923dd
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Showing 4 changed files with 22 additions and 6 deletions.
diff --git a/modules/local/psirc/index/environment.yml b/modules/local/psirc/index/environment.yml
@@ -0,0 +1,6 @@
+name: psirc_index
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::psirc=1.0.0
diff --git a/modules/local/psirc/index/main.nf b/modules/local/psirc/index/main.nf
@@ -2,7 +2,10 @@ process PSIRC_INDEX {
     tag "${meta.id}"
     label 'process_high'
 
-    container "registry.hub.docker.com/bigdatainbiomedicine/psirc"
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/psirc:1.0.0--he1fd2f9_0' :
+        'biocontainers/psirc:1.0.0--he1fd2f9_0' }"
 
     input:
     tuple val(meta), path(fasta)
@@ -12,13 +15,12 @@ process PSIRC_INDEX {
     path "versions.yml",                  emit: versions
 
     script:
-    def VERSION = '1.0'
     """
     psirc-quant index -i psirc.index --make-unique $fasta
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        psirc-quant: $VERSION
+        psirc-quant: \$(psirc-quant version | sed -n 's/^psirc-quant, version \\([0-9.]*\\).*\$/\\1/p')
     END_VERSIONS
     """
 }
diff --git a/modules/local/psirc/quant/environment.yml b/modules/local/psirc/quant/environment.yml
@@ -0,0 +1,6 @@
+name: psirc_quant
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::psirc=1.0.0
diff --git a/modules/local/psirc/quant/main.nf b/modules/local/psirc/quant/main.nf
@@ -2,7 +2,10 @@ process PSIRC_QUANT {
     tag "${meta.id}"
     label 'process_high'
 
-    container "registry.hub.docker.com/bigdatainbiomedicine/psirc"
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/psirc:1.0.0--he1fd2f9_0' :
+        'biocontainers/psirc:1.0.0--he1fd2f9_0' }"
 
     input:
     tuple val(meta), path(reads)
@@ -19,13 +22,12 @@ process PSIRC_QUANT {
     def single_end = meta.single_end ? "--single -l 76 -s 20" : ""
     def genomebam = gtf ? "--genomebam -g $gtf" : ""
     def chromosomes = chrom_sizes ? "-c $chrom_sizes" : ""
-    def VERSION = '1.0'
     """
     psirc-quant quant -t $task.cpus -i $index -o $meta.id $single_end $reads -b $bootstrap_samples $genomebam $chromosomes
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        psirc-quant: $VERSION
+        psirc-quant: \$(psirc-quant version | sed -n 's/^psirc-quant, version \\([0-9.]*\\).*\$/\\1/p')
     END_VERSIONS
     """
 }