address comments from Christopher

qbic-projects · Jan 21, 2022 · 81874b3 · 81874b3
1 parent d63a6e9
commit 81874b3
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Showing 5 changed files with 21 additions and 10 deletions.
diff --git a/modules/local/jaffal.nf b/modules/local/jaffal.nf
@@ -3,8 +3,11 @@ process JAFFAL {
     echo true
     label 'process_medium'
 
-//    conda     (params.enable_conda ? "bioconda::nanolyse=1.2.0" : null)   //need conda container
+    conda     (params.enable_conda ? "bioconda::jaffa=2.0.0" : null)
     container "docker.io/yuukiiwa/jaffa:2.0"
+    //container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+    //    'https://depot.galaxyproject.org/singularity/jaffa:2.00--hdfd78af_1' :
+    //    'quay.io/biocontainers/jaffa:2.00--hdfd78af_1' }"//tried three biocontainers, all of them got command not found for minimap2 
 
     input:
     tuple val(meta), path(fastq)
@@ -18,6 +21,6 @@ process JAFFAL {
     script:
     """
     bpipe run -p refBase=$jaffal_ref_dir $jaffal_ref_dir/JAFFAL.groovy $fastq
-    echo '2.0' > jaffal_version.txt
+    echo 'jaffa 2.0' > jaffal_version.txt
     """
 }
diff --git a/modules/local/xpore_dataprep.nf b/modules/local/xpore_dataprep.nf
@@ -2,8 +2,10 @@ process XPORE_DATAPREP {
     tag "$meta.id"
     label 'process_medium'
 
-//  conda     (params.enable_conda ? "bioconda::nanopolish==0.13.2" : null) // need to get xpore onto conda
-    container "docker.io/yuukiiwa/xpore:2.1"
+    conda     (params.enable_conda ? "bioconda::xpore=2.1.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/xpore:2.1--pyh5e36f6f_0' :
+        'quay.io/biocontainers/xpore:2.1--pyh5e36f6f_0' }"
 
     input:
     tuple val(meta), path(genome), path(gtf), path(eventalign), path(nanopolish_summary)

diff --git a/modules/local/xpore_diffmod.nf b/modules/local/xpore_diffmod.nf
@@ -1,8 +1,10 @@
 process XPORE_DIFFMOD {
     label 'process_medium'
 
-//  conda     (params.enable_conda ? "bioconda::nanopolish==0.13.2" : null) // need to get xpore onto conda
-    container "docker.io/yuukiiwa/xpore:2.1"
+    conda     (params.enable_conda ? "bioconda::xpore=2.1.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/xpore:2.1--pyh5e36f6f_0' :
+        'quay.io/biocontainers/xpore:2.1--pyh5e36f6f_0' }"
 
     input:
     val dataprep_dirs

diff --git a/subworkflows/local/rna_fusions_jaffal.nf b/subworkflows/local/rna_fusions_jaffal.nf
@@ -1,3 +1,7 @@
+/*
+ * RNA FUSION DETECTION WITH JAFFAL
+ */
+
 include { GET_JAFFAL_REF } from '../../modules/local/get_jaffal_ref'
 include { UNTAR          } from '../../modules/nf-core/modules/untar/main'
 include { JAFFAL         } from '../../modules/local/jaffal'
@@ -27,8 +31,4 @@ workflow RNA_FUSIONS_JAFFAL {
     */
     JAFFAL( ch_jaffal_input, ch_jaffal_ref_dir )
 
-//    emit:
-//    ch_nanopolish_outputs
-//    ch_dataprep_dirs
-//    nanopolish_version
 }
diff --git a/subworkflows/local/rna_modifications_xpore_m6anet.nf b/subworkflows/local/rna_modifications_xpore_m6anet.nf
@@ -1,3 +1,7 @@
+/*
+ * RNA MODIFICATION DETECTION WITH XPORE AND M6ANET
+ */
+
 include { NANOPOLISH_INDEX_EVENTALIGN } from '../../modules/local/nanopolish_index_eventalign'
 include { XPORE_DATAPREP        } from '../../modules/local/xpore_dataprep'
 include { XPORE_DIFFMOD         } from '../../modules/local/xpore_diffmod'