Verified Commit 75f1069c authored by Aurélien Ginolhac's avatar Aurélien Ginolhac 🚴
Browse files

add one unit for one sample

parent 252e1123
......@@ -4,7 +4,7 @@
samples: "config/samples.tsv"
# The source of fastq files for every sequencing unit of all samples has to be provided in the units.tsv file.
units: "config/units.tsv"
single_end: False
single_end: True
resources:
ref:
......@@ -44,18 +44,18 @@ params:
# when activated the plot profile and heatmap plot are generated, this involves a matrix calculation that requires a lot of working memory.
activate: False
lc_extrap:
activate: True
activate: False
picard_metrics:
activate: True
deseq2:
# set to True to use the vst transformation instead of the rlog transformation for the DESeq2 analysis
vst: False
peak-annotation-analysis:
activate: True
activate: False
peak-qc:
activate: True
consensus-peak-analysis:
activate: True
activate: False
# samtools view parameter suggestions (for full parameters, see: https://www.htslib.org/doc/samtools-view.html):
# if duplicates should be removed in this filtering, add "-F 0x0400" to the params
# if for each read, you only want to retain a single (best) mapping, add "-q 1" to params
......
......@@ -2,5 +2,6 @@ sample unit fq1 fq2 sra_accession platform
A 1 data/single_end_test_data/A-1_chr21.fastq.gz ILLUMINA
B 1 data/single_end_test_data/B-1_chr21.fastq.gz ILLUMINA
C 1 data/single_end_test_data/C-1_chr21.fastq.gz ILLUMINA
C 2 data/single_end_test_data/C-2_chr21.fastq.gz ILLUMINA
D 1 data/single_end_test_data/D-1_chr21.fastq.gz ILLUMINA
E 1 data/single_end_test_data/E-1_chr21.fastq.gz ILLUMINA
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment