working version 1.0

.github/workflows/nf-test.yml

@@ -118,7 +118,7 @@ jobs:
   confirm-pass:
     needs: [nf-test]
     if: always()
-    runs-on:  # use self-hosted runners
+    runs-on: # use self-hosted runners
       - runs-on=${{ github.run_id }}-confirm-pass
       - runner=2cpu-linux-x64
     steps:

CITATIONS.md

@@ -10,8 +10,6 @@
 
 ## Pipeline tools
 
-
-
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
 > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

assets/schema_input.json

@@ -7,27 +7,30 @@
     "items": {
         "type": "object",
         "properties": {
-            "sample": {
+            "group_id": {
                 "type": "string",
                 "pattern": "^\\S+$",
-                "errorMessage": "Sample name must be provided and cannot contain spaces",
+                "errorMessage": "Group ID must be provided and cannot contain spaces",
                 "meta": ["id"]
             },
-            "fastq_1": {
+            "sample_id": {
                 "type": "string",
-                "format": "file-path",
-                "exists": true,
-                "pattern": "^([\\S\\s]*\\/)?[^\\s\\/]+\\.f(ast)?q\\.gz$",
-                "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
+                "pattern": "^\\S+$",
+                "errorMessage": "Sample ID must be provided and cannot contain spaces"
+            },
+            "sample_type": {
+                "type": "string",
+                "enum": ["case", "control"],
+                "errorMessage": "Sample type must be either 'case' or 'control'"
             },
-            "fastq_2": {
+            "bam_path": {
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
-                "pattern": "^([\\S\\s]*\\/)?[^\\s\\/]+\\.f(ast)?q\\.gz$",
-                "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
+                "pattern": "^([\\S\\s]*\\/)?[^\\s\\/]+\\.bam$",
+                "errorMessage": "BAM file path must be provided, cannot contain spaces and must have extension '.bam'"
             }
         },
-        "required": ["sample", "fastq_1"]
+        "required": ["group_id", "sample_id", "sample_type", "bam_path"]
     }
 }

conf/base.config

@@ -13,10 +13,10 @@ process {
     // TODO nf-core: Check the defaults for all processes
     cpus   = { 1      * task.attempt }
     memory = { 6.GB   * task.attempt }
-    // time   = { 4.h    * task.attempt }
+    time   = { 4.h    * task.attempt }
 
     errorStrategy = { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'finish' }
-    maxRetries    = 1
+    maxRetries    = 2
     maxErrors     = '-1'
 
     // Process-specific resource requirements
@@ -29,22 +29,22 @@ process {
     withLabel:process_single {
         cpus   = { 1                   }
         memory = { 6.GB * task.attempt }
-        time   = { 4.h  * task.attempt }
+        // time   = { 4.h  * task.attempt }
     }
     withLabel:process_low {
         cpus   = { 2     * task.attempt }
         memory = { 12.GB * task.attempt }
-        time   = { 4.h   * task.attempt }
+        // time   = { 4.h   * task.attempt }
     }
     withLabel:process_medium {
         cpus   = { 6     * task.attempt }
         memory = { 36.GB * task.attempt }
-        time   = { 8.h   * task.attempt }
+        // time   = { 8.h   * task.attempt }
     }
     withLabel:process_high {
         cpus   = { 12    * task.attempt }
         memory = { 72.GB * task.attempt }
-        time   = { 16.h  * task.attempt }
+        // time   = { 16.h  * task.attempt }
     }
     withLabel:process_long {
         time   = { 20.h  * task.attempt }