Config file setup example for paired end and replicates
Issue #76
new
Is there an example config.yaml file I can look at which tells me how to correctly setup my paired end files and deal with replicates please? I can't understand what format is required from the tutorial pages. Here's what I'm currently trying:
# ATTENTION: You should and only should choose one type of input file between "samples" and "counts".
# Configuration of samples (Cannot set "counts" as valid at the same time!)
samples:
# The following sample information was inferred from the given FASTQ files.
# Adjust it according to your needs (e.g. providing descriptive sample names and grouping replicates together).
A.day0:
- /reads/Sample_1_1.fastq.gz
- /reads/Sample_1_2.fastq.gz
A.day7_1:
- /reads/Sample_3_1.fastq.gz
- /reads/Sample_3_2.fastq.gz
A.day7_2:
- /reads/Sample_4_1.fastq.gz
- /reads/Sample_4_2.fastq.gz
A.day14_1:
- /reads/Sample_7_1.fastq.gz
- /reads/Sample_7_2.fastq.gz
A.day14_2:
- /reads/Sample_8_1.fastq.gz
- /reads/Sample_8_2.fastq.gz
# Provide paired fastq files if pair-end sequencing data is available.
# paired:
# # provide a label and a paths to the paired fastq files for each sample
# A: path/to/A_R2.fastq
# B: path/to/B_R2.fastq
# C:
# - path/to/C.1_R2.fastq
# - path/to/C.2_R2.fastq
Same issue. Is MAGeCK-VISPR being actively maintained? I see a few issues like this unresolved.