add test data and combined genome

stracquadaniolab · Sep 22, 2023 · 1c37459 · 1c37459
1 parent 9f2f474
commit 1c37459
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Showing 33 changed files with 14,242 additions and 272,222 deletions.
diff --git a/.gitignore b/.gitignore
@@ -6,4 +6,7 @@ logs/
 .vscode
 .nextflow*
 bin/test_*
-data/BY4742-archive/
+data/BY4742-archive/
+data/reads
+data/genome/BY4742-genome
+data/genome/syn-yeast-genome
diff --git a/conf/base.config b/conf/base.config
@@ -78,8 +78,25 @@ profiles {
     // profile containing dummy data to test the workflow
     test {
         params {
+
+          // general
           resultsDir = "./results/"
-          inputFile = "testdata/mydata.txt"
+          samplesheet = "testdata/metadata/samplesheet.csv"
+          reads = "testdata/reads"
+
+          // source genome files
+          reference_wt = "data/genome/BY4742-genome/BY4742.fasta"
+          annotation_wt = "data/genome/BY4742-genome/BY4742.gff"
+          reference_syn = "data/genome/syn-yeast-genome/contigs/yeast_chr11_3_39.ref.fasta"
+          annotation_syn = "data/genome/syn-yeast-genome/annotation/yeast_chr11_3_39.ref.gff"
+
+          // combined genome files
+          reference = "data/genome/wt-syn-genome/wt-syn-chr11-ref.fasta"
+          annotation = "data/genome/wt-syn-genome/wt-syn-chr11-ref.gff"
+
+          // TRIM_READS parameters
+          fastp.args = ""
+
         }
     }
 

diff --git a/data/BY4742-genome/annotation/BY4742.chr11.gff b/data/BY4742-genome/annotation/BY4742.chr11.gff
diff --git a/data/BY4742-genome/contigs/BY4742.chr11.fasta b/data/BY4742-genome/contigs/BY4742.chr11.fasta
diff --git a/data/BY4742-genome/BY4742.fasta → ...nome/wt-syn-genome/wt-syn-chr11-ref.fasta b/data/BY4742-genome/BY4742.fasta → ...nome/wt-syn-genome/wt-syn-chr11-ref.fasta
diff --git a/data/BY4742-genome/BY4742.gff → ...genome/wt-syn-genome/wt-syn-chr11-ref.gff b/data/BY4742-genome/BY4742.gff → ...genome/wt-syn-genome/wt-syn-chr11-ref.gff
diff --git a/data/metadata/samplesheet.csv b/data/metadata/samplesheet.csv
@@ -0,0 +1,10 @@
+Sample,Reference,Condition,read1,read2
+x-dCre-Sir2-plus4,syn_BY4742,dCre-sir2_induced,data/reads/x-dCre-Sir2-plus4_R1_001.fastq.gz,data/reads/x-dCre-Sir2-plus4_R2_001.fastq.gz
+x-dCre-Sir2-plus5,syn_BY4742,dCre-sir2_induced,data/reads/x-dCre-Sir2-plus5_R1_001.fastq.gz,data/reads/x-dCre-Sir2-plus5_R2_001.fastq.gz
+x-dCre-Sir2-plus6,syn_BY4742,dCre-sir2_induced,data/reads/x-dCre-Sir2-plus6_R1_001.fastq.gz,data/reads/x-dCre-Sir2-plus6_R2_001.fastq.gz
+x-dCre-Sir2-4,syn_BY4742,uninduced,data/reads/x-dCre-Sir2-4_R1_001.fastq.gz,data/reads/x-dCre-Sir2-4_R2_001.fastq.gz
+x-dCre-Sir2-5,syn_BY4742,uninduced,data/reads/x-dCre-Sir2-5_R1_001.fastq.gz,data/reads/x-dCre-Sir2-5_R2_001.fastq.gz
+x-dCre-Sir2-6,syn_BY4742,uninduced,data/reads/x-dCre-Sir2-6_R1_001.fastq.gz,data/reads/x-dCre-Sir2-6_R2_001.fastq.gz
+x-dCre-plus4,syn_BY4742,dCre_induced,data/reads/x-dCre-plus4_R1_001.fastq.gz,data/reads/x-dCre-plus4_R2_001.fastq.gz
+x-dCre-plus5,syn_BY4742,dCre_induced,data/reads/x-dCre-plus5_R1_001.fastq.gz,data/reads/x-dCre-plus5_R2_001.fastq.gz
+x-dCre-plus6,syn_BY4742,dCre_induced,data/reads/x-dCre-plus6_R1_001.fastq.gz,data/reads/x-dCre-plus6_R2_001.fastq.gz
diff --git a/data/synthetic_yeast/CHECKSUM b/data/synthetic_yeast/CHECKSUM