Merge pull request #129 from ggabernet/review-comments

remove fastqc module
nf-core · Dec 21, 2021 · 251afac · 251afac
2 parents 82b508b + fc2ff4d
commit 251afac
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Showing 6 changed files with 1 addition and 123 deletions.
diff --git a/.nf-core.yml b/.nf-core.yml
diff --git a/CITATIONS.md b/CITATIONS.md
@@ -10,7 +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.
 

diff --git a/lib/WorkflowEpitopeprediction.groovy b/lib/WorkflowEpitopeprediction.groovy
@@ -8,12 +8,7 @@ class WorkflowEpitopeprediction {
     // Check and validate parameters
     //
     public static void initialise(params, log) {
-        //genomeExistsError(params, log)
-
-        //if (!params.fasta) {
-        //    log.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file."
-        //    System.exit(1)
-        //}
+        // empty function...
     }
 
     //
@@ -42,18 +37,4 @@ class WorkflowEpitopeprediction {
         yaml_file_text        += "${summary_section}"
         return yaml_file_text
     }
-
-    //
-    // Exit pipeline if incorrect --genome key provided
-    //
-    //private static void genomeExistsError(params, log) {
-    //    if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
-    //        log.error "=============================================================================\n" +
-    //            "  Genome '${params.genome}' not found in any config files provided to the pipeline.\n" +
-    //            "  Currently, the available genome keys are:\n" +
-    //            "  ${params.genomes.keySet().join(", ")}\n" +
-    //            "==================================================================================="
-    //        System.exit(1)
-    //    }
-    //}
 }
diff --git a/modules.json b/modules.json
@@ -6,9 +6,6 @@
             "custom/dumpsoftwareversions": {
                 "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
             },
-            "fastqc": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
-            },
             "multiqc": {
                 "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
             }

diff --git a/modules/nf-core/modules/fastqc/main.nf b/modules/nf-core/modules/fastqc/main.nf
diff --git a/modules/nf-core/modules/fastqc/meta.yml b/modules/nf-core/modules/fastqc/meta.yml
Original file line number	Diff line number	Diff line change
Expand Up		@@ -10,7 +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.

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