replaced copyright mentions + minor comment polishing

SnakeChunks · Jul 3, 2017 · 67de47c · 67de47c
1 parent 4c091ad
commit 67de47c
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diff --git a/scripts/snakefiles/rules/bwa.rules b/scripts/snakefiles/rules/bwa.rules
@@ -61,7 +61,7 @@ rule bwa:
         config["bwa"]["dir"]
         config["bwa"]["threads"]
 
-    Copyright Claire Rioualen
+    Contributors: Claire Rioualen
     """
     input:
         reads = bwa_inputs, 

diff --git a/scripts/snakefiles/rules/bwa_index.rules b/scripts/snakefiles/rules/bwa_index.rules
@@ -27,8 +27,7 @@ rule bwa_index:
 
     Optional parameters:
 
-    Copyright: 
-        Claire Rioualen
+    Contributors: Claire Rioualen
     """
     input: os.path.join(config["dir"]["genome"], config["genome"]["fasta_file"])
     output: os.path.join(bwa_dir, config["genome"]["fasta_file"])

diff --git a/scripts/snakefiles/rules/count_reads.rules b/scripts/snakefiles/rules/count_reads.rules
@@ -1,7 +1,7 @@
 """Rules to count the number of reads in NGS files with different
 formats.
 
-Copyright: Jacques.van-Helden@univ-amu.fr
+Contributors: Jacques van Helden
 
 To do: 
 

diff --git a/scripts/snakefiles/rules/cufflinks.rules b/scripts/snakefiles/rules/cufflinks.rules
@@ -23,9 +23,6 @@ rule cufflinks:
     Assemble transcripts from RNA-seq data and produce a file with
     the location of detected transcripts.
 
-
-    Copyright Jacques van Helden, Claire Rioualen
-
     Required parameters:
         config["qsub"]
         config["dir"]["genome"]
@@ -40,6 +37,7 @@ rule cufflinks:
         assembly_files
         cuffmerge_transcripts
 
+    Contributors: Jacques van Helden, Claire Rioualen
     """
     input:
         bam = "{reads}_sorted_pos.bam", \

diff --git a/scripts/snakefiles/rules/cutadapt.rules b/scripts/snakefiles/rules/cutadapt.rules
@@ -54,8 +54,7 @@ rule cutadapt:
         config["cutadapt"]["qual_threshold"]
         config["metadata"]["strands"]
 
-    Authors:
-        Claire Rioualen, Lucie Khamvongsa
+    Contributors: Claire Rioualen
     """
     input: reads = cutadapt_inputs
     output:

diff --git a/scripts/snakefiles/rules/dot_graph.rules b/scripts/snakefiles/rules/dot_graph.rules
@@ -14,7 +14,10 @@ if not "reports" in config["dir"].keys():
 rule dot_graph:
     """This rule generates dot files for snakemake's DAG and rulegraph. 
 
-    Copyright: Claire Rioualen, Jacques van Helden
+    Required parameter: 
+        config["metadata"]["configfile"]
+
+    Contributors: Claire Rioualen, Jacques van Helden
     """
     output: "{path}{graph,(rulegraph|dag)}.dot"
     params: 

diff --git a/scripts/snakefiles/rules/dot_to_image.rules b/scripts/snakefiles/rules/dot_to_image.rules
@@ -6,7 +6,7 @@ if not "qsub" in config.keys():
 rule dot_to_image:
     """Following rule dot_graph, this rule creates png and pdf outputs for dot graphs from snakemake. 
 
-    Copyright Claire Rioualen
+    Contributors: Claire Rioualen
     """
     input: "{graph}.dot"
     output: "{graph}.{ext,(pdf|png|svg)}"

diff --git a/scripts/snakefiles/rules/fastqc.rules b/scripts/snakefiles/rules/fastqc.rules
@@ -23,9 +23,7 @@ rule fastqc:
     Optional parameters:
         config['fastqc']['other_options']
 
-    TODO: execute on BAM files
-
-    Copyright Claire Rioualen, Lucie Khamvongsa, Jacques van Helden
+    Contributors: Claire Rioualen, Lucie Khamvongsa, Jacques van Helden
     """
 #    input: "{reads}.fastq"
     input: "{reads}.{ext,(bam|fastq)}"

diff --git a/scripts/snakefiles/rules/featnb_from_bed.rules b/scripts/snakefiles/rules/featnb_from_bed.rules
@@ -8,7 +8,7 @@ rule featnb_from_bed:
     Required parameters:
         config["qsub"]
 
-    Copyright Jacques van Helden
+    Contributors: Jacques van Helden
     """
     input: "{file}.bed"
     output: "{file}_bed_nb.txt"

diff --git a/scripts/snakefiles/rules/genome_coverage_bedgraph.rules b/scripts/snakefiles/rules/genome_coverage_bedgraph.rules
@@ -27,7 +27,7 @@ rule genome_coverage_bedgraph:
         config["dir"]["genome"]
         config["genome"]["fasta_file"]
 
-    Copyright: Jacques van Helden, Claire Rioualen
+    Contributors: Jacques van Helden, Claire Rioualen
     """
     input: reads = "{reads}_sorted_pos.bam", chrom_size = chrom_size
     output: "{reads}.bedgraph"

diff --git a/scripts/snakefiles/rules/genome_coverage_bedgraph_strands.rules b/scripts/snakefiles/rules/genome_coverage_bedgraph_strands.rules
@@ -14,6 +14,10 @@ rule genome_coverage_bedgraph_strands:
     Required parameters: 
         config["qsub"]
 
+    # TODO
+    Optional parameters:
+        config["metadata"]["strands"]
+
     Copyright Jacques van Helden, Claire Rioualen
     """
     input: reads = "{reads}_sorted_pos.bam"

diff --git a/scripts/snakefiles/rules/genome_coverage_bigwig.rules b/scripts/snakefiles/rules/genome_coverage_bigwig.rules
@@ -11,7 +11,7 @@ rule genome_coverage_bigwig:
     Required parameters:
         config["qsub"]
 
-    Copyright Claire Rioualen
+    Contributors: Claire Rioualen
     """
     input: 
         bam = "{reads}_sorted_pos.bam",

diff --git a/scripts/snakefiles/rules/genome_coverage_bigwig_normalized.rules b/scripts/snakefiles/rules/genome_coverage_bigwig_normalized.rules
@@ -17,7 +17,7 @@ if not "qsub" in config.keys():
 rule genome_coverage_bigwig_normalized:    
     """Uses bamCompare tool from the deepTools suite. 
 
-    Copyright: Claire Rioualen
+    Contributors: Claire Rioualen
     """
     input: 
 

diff --git a/scripts/snakefiles/rules/genome_coverage_dz.rules b/scripts/snakefiles/rules/genome_coverage_dz.rules
@@ -13,7 +13,7 @@ rule genome_coverage_dz:
     Required parameters:
         config["qsub"]
 
-    Copyright Jacques van Helden
+    Contributors: Jacques van Helden
     """
     input: reads="{reads}.bam"
     output: "{reads}_genomecov_dz.txt"

diff --git a/scripts/snakefiles/rules/genome_coverage_wig.rules b/scripts/snakefiles/rules/genome_coverage_wig.rules
@@ -16,7 +16,7 @@ rule genome_coverage_wig:
     reads and produce a wig file, the recommended format to
     upload coverage-type data as UCSC tracks.
 
-    Copyright Jacques van Helden, Claire Rioualen
+    Cntributors: Jacques van Helden, Claire Rioualen
     """
     input: "{reads}.bam"
     output: "{reads}.wig"

diff --git a/scripts/snakefiles/rules/get_chrom_sizes.rules b/scripts/snakefiles/rules/get_chrom_sizes.rules
@@ -7,7 +7,10 @@ rule get_chrom_sizes:
     """This rule generates a file containg the chromosome sizes, with file extension *.genome. 
     This file is required by a number of bedtools utilities.
 
-    Copyright Claire Rioualen
+    Required parameters:
+        config["qsub"]
+
+    Contributors: Claire Rioualen
     """
     input: "{genome}.fa"
     output: "{genome}.genome"

diff --git a/scripts/snakefiles/rules/getfasta.rules b/scripts/snakefiles/rules/getfasta.rules
@@ -14,12 +14,12 @@ fasta_file = os.path.join(config["dir"]["genome"], config["genome"]["fasta_file"
 rule getfasta:
     """Get fasta from bed file using the bedtools suite.
 
-    Parameters:
+    Required parameters:
         config["qsub"]
         config["dir"]["genome"] 
         config["genome"]["fasta_file"]
 
-    Copyright Claire Rioualen
+    Contributors: Claire Rioualen
     """
     input: bed = "{regions}.bed", genome_fasta = fasta_file
     output: "{regions}.fasta"

diff --git a/scripts/snakefiles/rules/gunzip.rules b/scripts/snakefiles/rules/gunzip.rules
@@ -7,7 +7,10 @@ rule gunzip:
     dependencies on.gz extensions, and/or to send compression jobs to
     a queue.
 
-    Copyright Jacques van Helden
+    Required parameters:
+        config["qsub"]
+
+    Contributors: Jacques van Helden
     """
     input: "{file}.gz"
 #    input: "{file}.fastq.gz"

diff --git a/scripts/snakefiles/rules/gzip.rules b/scripts/snakefiles/rules/gzip.rules
@@ -7,7 +7,10 @@ rule gzip:
     dependencies on.gz extensions, and/or to send compression jobs to
     a queue.
 
-    Copyright Jacques van Helden
+    Required parameters:
+        config["qsub"]
+
+    Contributors: Jacques van Helden
     """
     input: "{file}"
     output: "{file}.gz"

diff --git a/scripts/snakefiles/rules/homer.rules b/scripts/snakefiles/rules/homer.rules
@@ -51,6 +51,7 @@ rule homer:
         - a fasta file (see http://homer.salk.edu/homer-fdr{fdr}_peaks/introduction/update.html)          TO be changed
 
     Required parameters:
+        config["qsub"]
         config["dir"]["samples"]
         config["dir"]["peaks"]
         config["genome"]["fasta_file"]
@@ -63,7 +64,7 @@ rule homer:
         config["homer"]["P"]
         config["homer"]["fdr"]
 
-    Copyright Claire Rioualen
+    Contributors: Claire Rioualen
     """
     input:
         treatment = dir_samples + "/{treatment}/{treatment}{preprocess,.*}_sorted_pos.bed",

diff --git a/scripts/snakefiles/rules/index_bam.rules b/scripts/snakefiles/rules/index_bam.rules
@@ -8,7 +8,10 @@ rule index_bam:
     Index a bam file by creating a .bai file with Samtools
     The input bam MUST be sorted by position !
 
-    Copyright Jacques van Helden
+    Required parameters:
+        config["qsub"]
+
+    Contributors: Jacques van Helden
     """
     input: "{reads}_sorted_pos.bam"
     output: "{reads}_sorted_pos.bam.bai"

diff --git a/scripts/snakefiles/rules/index_fasta.rules b/scripts/snakefiles/rules/index_fasta.rules
@@ -7,7 +7,10 @@ rule index_fasta:
     """
     Index a fasta file by creating an .fai file with Samtools
 
-    Copyright Claire Rioualen
+    Required parameters:
+        config["qsub"]
+
+    Contributors: Claire Rioualen
     """
     input: "{genome}"
     output: "{genome}.fai"

diff --git a/scripts/snakefiles/rules/macs14.rules b/scripts/snakefiles/rules/macs14.rules
@@ -51,7 +51,7 @@ rule macs14:
         config["macs14"]["mfold"]
         config["macs14"]["other_options"]
 
-    Copyright Claire Rioualen, Lucie Khamvongsa
+    Contributors: Claire Rioualen, Lucie Khamvongsa
     """
     input:
         treatment = dir_samples + "/{treatment}/{treatment}{preprocess,.*}_sorted_pos.bed",

diff --git a/scripts/snakefiles/rules/macs2.rules b/scripts/snakefiles/rules/macs2.rules
@@ -59,7 +59,7 @@ rule macs2:
         config["macs2"]["other_options"]
         config["macs2"]["type"]
 
-    Copyright Claire Rioualen, Lucie Khamvongsa
+    Contributors: Claire Rioualen, Lucie Khamvongsa
     """
     input:
         treatment = dir_samples + "/{treatment}/{treatment}{preprocess,.*}_sorted_pos.bed",

diff --git a/scripts/snakefiles/rules/matrix_clustering.rules b/scripts/snakefiles/rules/matrix_clustering.rules
@@ -17,7 +17,7 @@ rule matrix_clustering:
     Optional parameters:
         ...
 
-    Copyright Claire Rioualen
+    Contributors: Claire Rioualen
     """
     input: "{caller_dir}/{peaks}.fasta"
     output: "{caller_dir}/peak-motifs/{peaks}_peak-motifs_synthesis.html"

diff --git a/scripts/snakefiles/rules/matrix_quality.rules b/scripts/snakefiles/rules/matrix_quality.rules
@@ -38,7 +38,7 @@ rule matrix_quality
     Optional parameters:
         ...
 
-    Copyright Claire Rioualen, Jacques van Helden
+    Contributors: Claire Rioualen, Jacques van Helden
     """
     input: 
         peakfiles = matrix_quality_inputs,

diff --git a/scripts/snakefiles/rules/md5sum.rules b/scripts/snakefiles/rules/md5sum.rules
@@ -17,6 +17,10 @@ rule md5sum:
            -s gene-regulation/scripts/snakefiles/rules/md5sum.rules \
            --configfile metadata/Glossina_palpalis.yml
 
+    Required parameters:
+        config["qsub"]
+
+    Contributors: Jacques van Helden
     """
     input: "{file}"
     output: "{file}.md5sum"

diff --git a/scripts/snakefiles/rules/merge_lanes.rules b/scripts/snakefiles/rules/merge_lanes.rules
@@ -49,7 +49,7 @@ rule merge_lanes:
     config["metadata"]["lane_merging"] file indicating the source/merged file names
     config["dir"]["fastq"]          base of the directory containing the fastq files
 
-    Copyright Jacques van Helden
+    Contributors: Jacques van Helden
     """
     input: table=config["metadata"]["lane_merging"], \
         source_files=SOURCE_FILES

diff --git a/scripts/snakefiles/rules/mosaics.rules b/scripts/snakefiles/rules/mosaics.rules
@@ -46,7 +46,7 @@ rule mosaics:
         config["mosaics"]["bin_size"]
         config["mosaics"]["type"]
 
-    Author Claire Rioualen, Mishael Sanchez-Perez
+    Contributors: Claire Rioualen, Mishael Sanchez-Perez
     """
     input:
         treatment = dir_samples + "/{treatment}/{treatment}{preprocess,.*}_sorted_pos.bed",

diff --git a/scripts/snakefiles/rules/readnb_from_bam.rules b/scripts/snakefiles/rules/readnb_from_bam.rules
@@ -8,7 +8,7 @@ rule readnb_from_bam:
     Required parameters:
         config["qsub"]
 
-    Copyright Jacques van Helden
+    Contributors: Jacques van Helden
     """
     input: "{file}.bam"
     output: "{file}_bam_readnb.txt"

diff --git a/scripts/snakefiles/rules/readnb_from_fastq.rules b/scripts/snakefiles/rules/readnb_from_fastq.rules
@@ -8,7 +8,7 @@ rule readnb_from_fastq:
     Required parameters:
         config["qsub"]
 
-    Copyright Jacques van Helden
+    Contributors: Jacques van Helden
     """
     input: "{file}.fastq"
     output: "{file}_fastq_readnb.txt"

diff --git a/scripts/snakefiles/rules/readnb_from_sam.rules b/scripts/snakefiles/rules/readnb_from_sam.rules
@@ -8,7 +8,7 @@ rule readnb_from_sam:
     Required parameters:
         config["qsub"]
 
-    Copyright Jacques van Helden
+    Contributors: Jacques van Helden
     """
     input: "{file}.sam"
     output: "{file}_sam_readnb.txt"

diff --git a/scripts/snakefiles/rules/sam_to_bam.rules b/scripts/snakefiles/rules/sam_to_bam.rules
@@ -8,7 +8,10 @@ rule sam_to_bam:
     Convert reads from SAM (sequence alignment map) to BAM (binary
     alignment map) format.
 
-    Copyright Claire Rioualen
+    Required parameters:
+        config["qsub"]
+
+    Contributors: Claire Rioualen
     """
     input: sam="{reads}.sam"
     output: bam="{reads}.bam"

diff --git a/scripts/snakefiles/rules/sartools_DESeq2.rules b/scripts/snakefiles/rules/sartools_DESeq2.rules
@@ -49,7 +49,8 @@ if not "locfunc" in config["DESeq2"].keys():
 
 # Rule
 rule sartools_DESeq2:
-    """This rule is designed to perform differential expression analysis of RNA-seq data
+    """
+    This rule is designed to perform differential expression analysis of RNA-seq data
     with DESeq2, using the R package SARTools (https://github.com/PF2-pasteur-fr/SARTools/). 
 
     It requires replicated data to run properly.
@@ -73,8 +74,7 @@ rule sartools_DESeq2:
         config["DESeq2"]["typeTrans"]
         config["DESeq2"]["locfunc"]
 
-    Copyright: 
-        Claire Rioualen (claire.rioualen@inserm.fr)
+    Contributors: Claire Rioualen
     """
     input: 
         targetFile = "{diffexpr_dir}/{test}_vs_{ref}/{preprocess,.*}SARTools_targetfile.txt"

diff --git a/scripts/snakefiles/rules/sartools_edgeR.rules b/scripts/snakefiles/rules/sartools_edgeR.rules
@@ -43,7 +43,8 @@ if not "normalizationMethod" in config["edgeR"].keys():
 
 # Rule
 rule sartools_edgeR:
-    """This rule is designed to perform differential expression analysis of RNA-seq data
+    """
+    This rule is designed to perform differential expression analysis of RNA-seq data
     with edgeR, using the R package SARTools (https://github.com/PF2-pasteur-fr/SARTools/). 
 
     It requires replicated data to run properly.
@@ -66,7 +67,7 @@ rule sartools_edgeR:
         config["edgeR"]["gene_selection"]
         config["edgeR"]["normalizationMethod"]
 
-    Copyright: Claire Rioualen
+    Contributors: Claire Rioualen
     """
     input: 
         targetFile = "{diffexpr_dir}/{test}_vs_{ref}/{preprocess,.*}SARTools_targetfile.txt"

diff --git a/scripts/snakefiles/rules/sartools_targetfile.rules b/scripts/snakefiles/rules/sartools_targetfile.rules
@@ -37,7 +37,7 @@ rule sartools_targetfile:
         config["dir"]["samples"]
         config["dir"]["diffexpr"]
 
-    Copyright Claire Rioualen
+    Contributors: Claire Rioualen
     """
     input: 
         count_files = targetfiles_inputs