Merge pull request #95 from RBL-NCI/activeDev

Active dev

Author: slsevilla

.editorconfig

@@ -17,7 +17,7 @@ jobs:
     - uses: docker://snakemake/snakemake:v5.24.2
     - name: Dry-run pipeline
       run: |
-        docker run -v $PWD:/tmp/repo snakemake/snakemake:v5.24.2 bash /tmp/repo/run_snakemake.sh test        
+        docker run -v $PWD:/tmp/repo snakemake/snakemake:v5.24.2 bash /tmp/repo/run_snakemake.sh -p git -o /hg38_full/        
     - name: Lint workflow
       continue-on-error: true
       run: |

.gitattributes

@@ -0,0 +1,2 @@
+contrast_1,contrast_2
+Ro_Clip,Control_Clip

.github/workflows/main.yaml

@@ -1,37 +1,45 @@
 # Global configuration file for the pipeline
 #path to snakemake file
-source_dir: ""
+sourceDir: ""
 
 #path to output directory
-output_dir: "hg38_full/"
+outputDir: "hg38_full/"
 
 #path to manifest files
-sample_manifest: ".tests/sample_hg38_full.tsv"
-multiplex_manifest: ".tests/multiplex_hg38_full.tsv"
+sampleManifest: ".tests/sample_hg38_full.tsv"
+multiplexManifest: ".tests/multiplex_hg38_full.tsv"
+contrastManifest: ".test/contrasts_example.tsv"
 
 #path to fastq files
-fastq_dir: ".tests/"
+fastqDir: ".tests/"
 
 #user parameters
-multiplex_flag: "Y" #flag that samples are multiplexed ["Y","N"]
-mismatch_allowance: 1 #number of nt mismatches allowed in barcodes; options [1,2]
-split_value: 10000 #number of sequences in split files [min 3000, default 1000000]
-novoalign_reference: "hg38" #species ["mm10","hg38"]
-splice_aware: 'N' #whether to run spliceaware in pipeline ["Y","N"]
-splice_bp_length: 75 # splice aware bp_length [50,75,150]
-minimum_count: 3 #minimum number of matches to count as a true peak [1,2,3]
-nt_merge: 50 #minimum distance of nucleotides to merge peaks [10,20,30,40,50,60]
-peak_id: "all" #report peaks for unique peaks only or unique and fractional mm ["unique","all"]
-DE_method: "manorm" #choose DE method ["manorm","none"]
-splice_junction: "Y" #include splice junctions in peak calls: "manorm" #choose DE method ["manorm","none"]
+filterlength: 20 #minimum read length to include in analysis [any int >20]
+multiplexflag: "Y" #flag that samples are multiplexed ["Y","N"]
+mismatch: 1 #number of bp mismatches allowed in demultiplexing [1,2,3]
+reference: "hg38" #reference organism ["mm10", "hg38"]
+spliceaware: "N" #whether to run splice_aware part of the pipeline ['y', 'n']
+includerRNA: "N" #include refseq rRNA's in annotations ["Y", "N"]
+spliceBPlength: 75 #length of splice index to use [50, 75, 150]
+splicejunction: "N" #include splice junctions in peak calls: "manorm"
+condenseexon: "N" #whether to collapse exons
+mincount: 3 #minimum number of matches to count as a peak [1,2,3]
+ntmerge: 50 #minimum distance of nucleotides to merge peaks [10,20,30,40,50,60]
+peakid: "ALL" #report peaks for unique peaks only or unique and fractional mm ["unique","all"]
+DEmethod: "none" #choose DE method ["manorm","none"]
+sampleoverlap: 1 #if DEmethod DIFFBIND, minimum number of samples a peak must be found in to be counted [>1]
+pval: 0.005 #if DEmethod, pval cutoff for significance
+fc: 1 #if DEmethod, fold change cut off for significance
 
 #modules, container parameters
-container_dir: "/data/CCBR_Pipeliner/iCLIP/container"
+containerDir: "/data/CCBR_Pipeliner/iCLIP/container"
+fastq_val: "/data/CCBR_Pipeliner/db/PipeDB/bin/fastQValidator"
 bedtools: "bedtools/2.29.2"
 bowtie2: "bowtie/2-2.3.4"
 fastq_screen: "fastq_screen/0.14.0"
 fastqc: "fastqc/0.11.9"
 java: "java/12.0.1"
+manorm: "manorm/1.1.4"
 multiqc: "multiqc/1.9"
 novocraft: "novocraft/4.03.01"
 perl: "perl/5.24.3"