Merge pull request #1 from kedhammar/dev

Some additions

Author: Aratz

README.md

@@ -45,7 +45,7 @@ First, prepare a samplesheet with your input data that looks as follows:
 
 ```csv
 sample,fastq_1,fastq_2,rundir,tags
-CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,group1
+CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2
 ```
 
 Each row represents a fastq file (single-end) or a pair of fastq files (paired end).

assets/schema_input.json

@@ -36,8 +36,8 @@
             },
             "tags": {
                 "type": "string",
-                "pattern": "^([A-Za-z0-9_-]+:)*([A-Za-z0-9_-]+)$",
-                "errorMessage": "Tags must consist of numbers, letters, underscores or dashes and must be provided as a column-separated list, e.g. group_01:lane1:pos-CTRL_2.",
+                "pattern": "^([a-z0-9_-]+:)*([a-z0-9_-]+)$",
+                "errorMessage": "Tags must be separated by colons and only consist of lowercase letters, numbers, underscores and hyphens.",
                 "meta": ["tags"]
             }
         },

conf/test.config

@@ -22,7 +22,7 @@ params {
     // Input data
     // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/MiSeq/samplesheet.csv'
+    input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet.csv'
 
     // Genome references
     genome = 'R64-1-1'

docs/usage.md

@@ -44,8 +44,8 @@ sample4 path/to/run_dir/sample4_lane2_group3_r1.fq.gz         path/to/run_dir co
 | `sample`  | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). |
 | `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                                             |
 | `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz" (optional).                                                  |
-| `rundir`  | Path to the runfolder containing extra information about the sequencing run (optional) .                                                                                               |
-| `tags`    | Column-separated list of tags to group samples in special reports.                                                                                                                     |
+| `rundir`  | Path to the runfolder containing extra information about the sequencing run (optional).                                                                                                |
+| `tags`    | Colon-separated list of tags to group samples in special reports.                                                                                                                      |
 
 Another [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
 

modules.json

@@ -12,7 +12,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
+                        "git_sha": "19ca321db5d8bd48923262c2eca6422359633491",
                         "installed_by": ["modules"]
                     }
                 }