Merge pull request #65 from nf-core/dev

update master before release
nf-core · Dec 12, 2022 · 18e580e · 18e580e
2 parents ca5a001 + b84d894
commit 18e580e
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Showing 3 changed files with 107 additions and 67 deletions.
diff --git a/assets/email_template.html b/assets/email_template.html
@@ -4,7 +4,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge">
   <meta name="viewport" content="width=device-width, initial-scale=1">
 
-  <meta name="description" content="nf-core/circrna: circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data">
+  <meta name="description" content="nf-core/circrna: Quantification, miRNA target prediction and differential expression analysis of circular RNAs">
   <title>nf-core/circrna Pipeline Report</title>
 </head>
 <body>

diff --git a/nextflow.config b/nextflow.config
@@ -12,6 +12,7 @@ params {
 
     // Input options
     input                      = null
+    outdir                     = './results'
     phenotype                  = null
 
     // workflow options
@@ -21,12 +22,23 @@ params {
     tool_filter                = 0
     duplicates_fun             = 'mean'
     exon_boundary              = 200
+    save_intermediates         = true
+
+    // reference genome options
+    genome                     = null
+    igenomes_base              = 's3://ngi-igenomes/igenomes'
+    igenomes_ignore            = false
+    bowtie                     = null
+    bowtie2                    = null
+    bwa                        = null
+    hisat2                     = null
+    hisat2_build_memory        = '200.GB'
+    segemehl                   = null
+    star                       = null
     gtf                        = null
     mature                     = null
     species                    = null
-    skip_fastqc                = false
     save_reference             = true
-    save_intermediates         = true
 
     // Trimming
     min_trimmed_reads          = 10000
@@ -38,31 +50,28 @@ params {
     save_trimmed               = false
     skip_trimming              = false
 
-    // STAR
+    // Alignment options
+
+    //> STAR
     chimJunctionOverhangMin    = 10
     alignSJDBoverhangMin       = 10
     chimSegmentMin             = 10
     sjdboverhang               = 100
 
-    // MAPSPLICE
+    //> MAPSPLICE
     seglen                     = 25
     min_intron                 = 20
     max_intron                 = 1000000
     min_map_len                = 40
     min_fusion_distance        = 200
 
-    // References
-    genome                     = null
-    igenomes_base              = 's3://ngi-igenomes/igenomes'
-    igenomes_ignore            = false
-    bowtie                     = null
-    bowtie2                    = null
-    bwa                        = null
-    fasta_fai                  = null
-    segemehl                   = null
-    star                       = null
+
+    //> MISC
+    save_unaligned             = false
+    seq_center                 = null
 
     // MultiQC options
+    skip_fastqc                = false
     multiqc_config             = null
     multiqc_title              = null
     multiqc_logo               = null
@@ -237,7 +246,7 @@ manifest {
     name            = 'nf-core/circrna'
     author          = """Barry Digby"""
     homePage        = 'https://github.com/nf-core/circrna'
-    description     = """circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data"""
+    description     = """Quantification, miRNA target prediction and differential expression analysis of circular RNAs"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
     version         = 'dev'