This problem is focused around generation of tab delimited file/data out of some other computed information. The first example focuses on generating a manifest file based on the input.
Create a manifest tab-delimited file based on the names of files in the folder. Add a column that counts the number of reads in each file.
So the output should look like this for the fastq folder;
Write a tool that will run like this. Optionally have it provided a -o output.tsv to save the results to a file, otherwise just print to the screen.
make_manifest_from_fastq.py -i fastq
SampleID Read_1 Read_2 Read_1_Count Read_2_Count
A Sample_A_S1_R1_L001.fastq.gz Sample_A_S1_R2_L001.fastq.gz 1 1
B Sample_B_S2_R1_L001.fastq.gz Sample_B_S2_R2_L001.fastq.gz 3 3