replaced copyright mentions

SnakeChunks · Jul 3, 2017 · ed49799 · ed49799
1 parent 9da6f30
commit ed49799
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Showing 12 changed files with 15 additions and 16 deletions.
diff --git a/scripts/snakefiles/rules/bbduk.rules b/scripts/snakefiles/rules/bbduk.rules
@@ -58,8 +58,7 @@ rule bbduk:
         config["bbduk"]["qual_threshold"]
         config["metadata"]["strands"]
 
-    Authors:
-        Claire Rioualen, Lucie Khamvongsa
+    Contributors: Claire Rioualen
     """
     input: reads = bbduk_inputs
     output:

diff --git a/scripts/snakefiles/rules/bedgraph_to_bigwig.rules b/scripts/snakefiles/rules/bedgraph_to_bigwig.rules
@@ -3,12 +3,12 @@ if not "qsub" in config.keys():
     sys.exit("The parameter qsub must be defined in the config file")
 
 rule bedgraph_to_bigwig:
-    """Convert bedGraph to bigWig format.
+    """Convert bedgraph to bigWig format.
 
     Required parameters:
         config["qsub"]
 
-    Copyright: Claire Rioualen
+    Contributors: Claire Rioualen
     """
     input: chromizes="", bedgraph="{coverage}.bedgraph"
     output: "{coverage}.bw"

diff --git a/scripts/snakefiles/rules/bedgraph_to_tdf.rules b/scripts/snakefiles/rules/bedgraph_to_tdf.rules
@@ -23,7 +23,7 @@ rule bedgraph_to_tdf:
         config["dir"]["genome"]
         config["genome"]["fasta_file"]
 
-    Copyright: Claire Rioualen
+    Contributors: Claire Rioualen
     """
     input: "{coverage}.bedgraph"
     output: "{coverage}.tdf"

diff --git a/scripts/snakefiles/rules/bedtools_closest.rules b/scripts/snakefiles/rules/bedtools_closest.rules
@@ -26,7 +26,7 @@ rule bedtools_closest:
         config["dir"]["genome"]
         config["genome"]["gff3_file"]
 
-    Copyright Claire Rioualen
+    Contributors: Claire Rioualen
     """
 	input: bed = "{regions}.bed", gff3 = gff3_file
 	output: "{regions}_closest_annot.bed"

diff --git a/scripts/snakefiles/rules/bedtools_intersect.rules b/scripts/snakefiles/rules/bedtools_intersect.rules
@@ -25,7 +25,7 @@ rule bedtools_intersect:
         config["dir"]["genome"]
         config["genome"]["gff3_file"]
 
-    Copyright Claire Rioualen
+    Contributors: Claire Rioualen
     """
 	input: bed = "{regions}.bed", gff3 = gff3_file
 	output: "{regions}_intersect_annot.bed"

diff --git a/scripts/snakefiles/rules/bedtools_window.rules b/scripts/snakefiles/rules/bedtools_window.rules
@@ -39,7 +39,7 @@ rule bedtools_window:
     Opional parameters:
         config["bedtools"]["window"]
 
-    Copyright Claire Rioualen
+    Contributors: Claire Rioualen
     """
     input: bed = "{regions}.bed", gff3 = gff3_file
     output: "{regions}_window_annot.bed"

diff --git a/scripts/snakefiles/rules/blast_formatdb.rules b/scripts/snakefiles/rules/blast_formatdb.rules
@@ -13,7 +13,7 @@ rule blast_formatdb:
 
     ## type (formatdb option -p): sequence type: peptidic (-pT) or nucleic (-pF)
 
-    Copyright Jacques van Helden
+    Contributors: Jacques van Helden
     """
     input: fasta_seq="{ref_db}.fa"
     output: "{ref_db}_blastdb_p{type}.{extensions,(phr|psq|psi|psd|pin)}"

diff --git a/scripts/snakefiles/rules/blastall.rules b/scripts/snakefiles/rules/blastall.rules
@@ -33,7 +33,7 @@ rule blastall:
         config["blastall"]["expect"]
         config["blastall"]["view"]
 
-    Copyright Jacques van Helden
+    Contributors: Jacques van Helden
     """
     input: query="{query}.fa", db_index=config["blastall"]["db"] + ".psi"
     output: hits="{query}_{blast_program}_hits.tsv"

diff --git a/scripts/snakefiles/rules/bowtie.rules b/scripts/snakefiles/rules/bowtie.rules
@@ -49,7 +49,7 @@ def bowtie_inputs(wildcards):
 
 # Rule
 rule bowtie:
-    """Read mapping for single end data using bowtie. 
+    """Read mapping using bowtie. 
     Requires the indexing to have previously been done (using the
     rule bowtie_index).
 
@@ -64,7 +64,7 @@ rule bowtie:
         config["bowtie"]["max_mismatches"]
         config["bowtie"]["threads"]
 
-    Copyright Claire Rioualen, Jacques van Helden, Lucie Khamvongsa
+    Contributors: Claire Rioualen, Jacques van Helden, Lucie Khamvongsa
     """
     input:
         reads = bowtie_inputs, 

diff --git a/scripts/snakefiles/rules/bowtie2.rules b/scripts/snakefiles/rules/bowtie2.rules
@@ -49,7 +49,7 @@ def bowtie2_inputs(wildcards):
 
 # Rule
 rule bowtie2:
-    """Read mapping for single end data using Bowtie2. 
+    """Read mapping using Bowtie2. 
     Requires the indexing to have previously been done (using the
     rule bowtie2_index).
 
@@ -64,7 +64,7 @@ rule bowtie2:
         config["bowtie2"]["threads"]
         config["bowtie2"]["max_mismatches"]
 
-    Copyright Claire Rioualen
+    Contributors: Claire Rioualen
     """
     input:
         reads = bowtie2_inputs, 

diff --git a/scripts/snakefiles/rules/bowtie2_index.rules b/scripts/snakefiles/rules/bowtie2_index.rules
@@ -26,7 +26,7 @@ rule bowtie2_index:
 
     Optional parameters:
 
-    Copyright Claire Rioualen
+    Contributors: Claire Rioualen
     """
     input: os.path.join(config["dir"]["genome"], config["genome"]["fasta_file"])
     output: os.path.join(bowtie2_dir, config["genome"]["fasta_file"])

diff --git a/scripts/snakefiles/rules/bowtie_index.rules b/scripts/snakefiles/rules/bowtie_index.rules
@@ -27,7 +27,7 @@ rule bowtie_index:
 
     Optional parameters:
 
-    Copyright Jacques van Helden, Lucie Khamvongsa, Claire Rioualen
+    Contributors: Jacques van Helden, Lucie Khamvongsa, Claire Rioualen
     """
     input: os.path.join(config["dir"]["genome"], config["genome"]["fasta_file"])
     output: os.path.join(bowtie_dir, config["genome"]["fasta_file"])