Merge pull request #102 from zifornd/patch-run-drimseq-filter

patch run drimseq filter
nf-core · Nov 15, 2023 · 6ec7798 · 6ec7798
2 parents 616ded7 + 02f8650
commit 6ec7798
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Showing 5 changed files with 13 additions and 11 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,7 +3,9 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v1.0.0dev - 2023-10-10
+## v1.0.1 - 2023-11-15
+
+Patch for run_drimseq_filter.R to cast command line arguments to numeric. See issue #98 on nf-core/rnasplice.
 
 ## v1.0.0 - 2023-05-22
 

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="/~https://github.com/nf-core/rnasplice/releases/tag/dev" target="_blank">nf-core/rnasplice</a>
+  This report has been generated by the <a href="/~https://github.com/nf-core/rnasplice/releases/tag/1.0.1" target="_blank">nf-core/rnasplice</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/rnasplice/dev/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/rnasplice/1.0.1/docs/output" target="_blank">documentation</a>.
 
 report_section_order:
   "nf-core-rnasplice-methods-description":

diff --git a/bin/run_drimseq_filter.R b/bin/run_drimseq_filter.R
@@ -24,12 +24,12 @@ tximport_tx2gene <- args[2] # tx2gene information
 samplesheet      <- args[3] # samplesheet
 
 # Filter params
-min_samps_gene_expr    <- args[4]
-min_samps_feature_expr <- args[5]
-min_samps_feature_prop <- args[6]
-min_feature_expr       <- args[7]
-min_feature_prop       <- args[8]
-min_gene_expr          <- args[9]
+min_samps_gene_expr    <- as.numeric(args[4])
+min_samps_feature_expr <- as.numeric(args[5])
+min_samps_feature_prop <- as.numeric(args[6])
+min_feature_expr       <- as.numeric(args[7])
+min_feature_prop       <- as.numeric(args[8])
+min_gene_expr          <- as.numeric(args[9])
 
 ######################################
 ########## Process tx2gene ###########

diff --git a/bin/run_edger_exon.R b/bin/run_edger_exon.R
@@ -18,7 +18,7 @@ samplesheet <- argv[2]
 
 contrastsheet <- argv[3]
 
-ntop  <- argv[4]
+ntop  <- as.integer(argv[4])
 
 
 # Load required packages

diff --git a/nextflow.config b/nextflow.config
@@ -352,7 +352,7 @@ manifest {
     description     = """Alternative splicing analysis using RNA-seq."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '1.1.0dev'
+    version = '1.0.1'
     doi             = ''
 }